http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&feed=atom&action=history
Journal club papers - História úprav
2024-03-28T14:00:50Z
História úprav pre túto stránku na wiki
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http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&diff=2958&oldid=prev
Brona na 08:17, 19. október 2023
2023-10-19T08:17:43Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 08:17, 19. október 2023</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''<del class="diffchange diffchange-inline">List of papers</del>:'''</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''<ins class="diffchange diffchange-inline">Groups</ins>:'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>3. Bradley, P., Den Bakker, H.C., Rocha, E.P., McVean, G. and Iqbal, Z., 2019. Ultrafast search of all deposited bacterial and viral genomic data. Nature biotechnology, 37(2), pp.152-159. https://doi.org/10.1038/s41587-018-0010-1 '''Man, Király, Pidlypska, Bisták, Pizarroso Troncoso, Mayoz Aranda, Alonso Jirout'''</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>3. Bradley, P., Den Bakker, H.C., Rocha, E.P., McVean, G. and Iqbal, Z., 2019. Ultrafast search of all deposited bacterial and viral genomic data. Nature biotechnology, 37(2), pp.152-159. https://doi.org/10.1038/s41587-018-0010-1 '''Man, Király, Pidlypska, Bisták, Pizarroso Troncoso, Mayoz Aranda, Alonso Jirout'''</div></td></tr>
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Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&diff=2956&oldid=prev
Brona na 07:09, 19. október 2023
2023-10-19T07:09:40Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 07:09, 19. október 2023</td>
</tr><tr><td colspan="2" class="diff-lineno">Riadok 1:</td>
<td colspan="2" class="diff-lineno">Riadok 1:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>A detailed description of the journal club activity is included in the [[Rules#Journal club|course rules]].</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>A detailed description of the journal club activity is included in the [[Rules#Journal club|course rules]].</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* All links to papers should work in our University network (e.g. Eduroam or [https://uniba.sk/index.php?id=6828 proxy])</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><!--</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Please submit your preferences regarding these papers using '''[https://forms.gle/K7BZJD5fA3wRmmXk8 this form]''' until Wednesday  '''Oct. 18, 2023, 22:00'''. In the form, include '''numbers of three papers from this list''' in the order of preference.  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Please submit your preferences regarding these papers using '''[https://forms.gle/K7BZJD5fA3wRmmXk8 this form]''' until Wednesday  '''Oct. 18, 2023, 22:00'''. In the form, include '''numbers of three papers from this list''' in the order of preference.  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Students from the same study program will typically not be in the same group.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Students from the same study program will typically not be in the same group.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">* All links to papers should work in our University network (e.g. Eduroam or [https://uniba.sk/index.php?id=6828 proxy])</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Also please indicate if you are willing to work in a group with English-speaking students (this means group discussions and final report in English)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Also please indicate if you are willing to work in a group with English-speaking students (this means group discussions and final report in English)</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">--></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>'''List of papers:'''</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>'''List of papers:'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">1</del>. <del class="diffchange diffchange-inline">Curry</del>, <del class="diffchange diffchange-inline">K.D</del>., <del class="diffchange diffchange-inline">Wang</del>, <del class="diffchange diffchange-inline">Q</del>.<del class="diffchange diffchange-inline">, Nute, M.G</del>., <del class="diffchange diffchange-inline">Tyshaieva, A., Reeves</del>, E.<del class="diffchange diffchange-inline">, Soriano, S., Wu, Q., Graeber, E., Finzer, </del>P., <del class="diffchange diffchange-inline">Mendling</del>, <del class="diffchange diffchange-inline">W</del>. and <del class="diffchange diffchange-inline">Savidge</del>, <del class="diffchange diffchange-inline">T</del>., <del class="diffchange diffchange-inline">2022</del>. <del class="diffchange diffchange-inline">Emu: species-level microbial community profiling </del>of <del class="diffchange diffchange-inline">full-length 16S rRNA Oxford Nanopore sequencing </del>data. Nature <del class="diffchange diffchange-inline">methods</del>, <del class="diffchange diffchange-inline">19</del>(<del class="diffchange diffchange-inline">7</del>), pp.<del class="diffchange diffchange-inline">845</del>-<del class="diffchange diffchange-inline">853</del>. https://doi.org/10.1038/<del class="diffchange diffchange-inline">s41592</del>-<del class="diffchange diffchange-inline">022</del>-<del class="diffchange diffchange-inline">01520</del>-<del class="diffchange diffchange-inline">4</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">3</ins>. <ins class="diffchange diffchange-inline">Bradley</ins>, <ins class="diffchange diffchange-inline">P</ins>., <ins class="diffchange diffchange-inline">Den Bakker</ins>, <ins class="diffchange diffchange-inline">H</ins>.<ins class="diffchange diffchange-inline">C</ins>., <ins class="diffchange diffchange-inline">Rocha</ins>, E.P., <ins class="diffchange diffchange-inline">McVean</ins>, <ins class="diffchange diffchange-inline">G</ins>. and <ins class="diffchange diffchange-inline">Iqbal</ins>, <ins class="diffchange diffchange-inline">Z</ins>., <ins class="diffchange diffchange-inline">2019</ins>. <ins class="diffchange diffchange-inline">Ultrafast search </ins>of <ins class="diffchange diffchange-inline">all deposited bacterial and viral genomic </ins>data. Nature <ins class="diffchange diffchange-inline">biotechnology</ins>, <ins class="diffchange diffchange-inline">37</ins>(<ins class="diffchange diffchange-inline">2</ins>), pp.<ins class="diffchange diffchange-inline">152</ins>-<ins class="diffchange diffchange-inline">159</ins>. https://doi.org/10.1038/<ins class="diffchange diffchange-inline">s41587</ins>-<ins class="diffchange diffchange-inline">018</ins>-<ins class="diffchange diffchange-inline">0010</ins>-<ins class="diffchange diffchange-inline">1 '''Man, Király, Pidlypska, Bisták, Pizarroso Troncoso, Mayoz Aranda, Alonso Jirout'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">2</del>. <del class="diffchange diffchange-inline">Edgar, R.C., Taylor, J., Lin, V., Altman, T., Barbera, P., Meleshko, D., Lohr, D., Novakovsky, </del>G.<del class="diffchange diffchange-inline">, Buchfink, B., Al</del>-<del class="diffchange diffchange-inline">Shayeb, B. </del>and <del class="diffchange diffchange-inline">Banfield, J</del>.<del class="diffchange diffchange-inline">F</del>.<del class="diffchange diffchange-inline">, 2022. Petabase-scale sequence alignment catalyses viral discovery. Nature, 602</del>(<del class="diffchange diffchange-inline">7895</del>)<del class="diffchange diffchange-inline">, pp.142</del>-<del class="diffchange diffchange-inline">147</del>.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">4</ins>. <ins class="diffchange diffchange-inline">Lunter </ins>G <ins class="diffchange diffchange-inline">(2007)</ins>. <ins class="diffchange diffchange-inline">"Probabilistic whole</ins>-<ins class="diffchange diffchange-inline">genome alignments reveal high indel rates in the human </ins>and <ins class="diffchange diffchange-inline">mouse genomes</ins>.<ins class="diffchange diffchange-inline">"</ins>. <ins class="diffchange diffchange-inline">Bioinformatics 23 </ins>(<ins class="diffchange diffchange-inline">13</ins>)<ins class="diffchange diffchange-inline">: i289</ins>-<ins class="diffchange diffchange-inline">96</ins>. https://doi.org/10.<ins class="diffchange diffchange-inline">1093</ins>/<ins class="diffchange diffchange-inline">bioinformatics/btm185 '''Jurčák, Pásztor, Lichmanová, Hašan, Uhrin, Horváthová'''</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>https://doi.org/10.<del class="diffchange diffchange-inline">1038</del>/<del class="diffchange diffchange-inline">s41586-021-04332-2</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">3</del>. <del class="diffchange diffchange-inline">Bradley</del>, <del class="diffchange diffchange-inline">P.</del>, <del class="diffchange diffchange-inline">Den Bakker</del>, <del class="diffchange diffchange-inline">H.C., Rocha, E.P., McVean, G</del>. and <del class="diffchange diffchange-inline">Iqbal, Z., 2019. Ultrafast search </del>of <del class="diffchange diffchange-inline">all deposited bacterial and viral genomic data</del>. Nature <del class="diffchange diffchange-inline">biotechnology, 37</del>(<del class="diffchange diffchange-inline">2</del>)<del class="diffchange diffchange-inline">, pp.152</del>-<del class="diffchange diffchange-inline">159</del>. <del class="diffchange diffchange-inline">https</del>://<del class="diffchange diffchange-inline">doi</del>.<del class="diffchange diffchange-inline">org</del>/<del class="diffchange diffchange-inline">10</del>.<del class="diffchange diffchange-inline">1038/s41587-018-0010-1</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">5</ins>. <ins class="diffchange diffchange-inline">Wapinski I</ins>, <ins class="diffchange diffchange-inline">Pfeffer A</ins>, <ins class="diffchange diffchange-inline">Friedman N</ins>, <ins class="diffchange diffchange-inline">Regev A (2007)</ins>. <ins class="diffchange diffchange-inline">"Natural history </ins>and <ins class="diffchange diffchange-inline">evolutionary principles </ins>of <ins class="diffchange diffchange-inline">gene duplication in fungi"</ins>. Nature <ins class="diffchange diffchange-inline">449 </ins>(<ins class="diffchange diffchange-inline">7158</ins>)<ins class="diffchange diffchange-inline">: 54</ins>-<ins class="diffchange diffchange-inline">61</ins>. <ins class="diffchange diffchange-inline">[http</ins>://<ins class="diffchange diffchange-inline">llama</ins>.<ins class="diffchange diffchange-inline">mshri.on.ca/courses/Biophysics205</ins>/<ins class="diffchange diffchange-inline">Papers/Wapinski_2007</ins>.<ins class="diffchange diffchange-inline">pdf pdf] '''Skrypnyk, Ondrejová, Kostrian, Murin, Vicianová, Revúcky'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">4</del>. <del class="diffchange diffchange-inline">Lunter G </del>(2007). "<del class="diffchange diffchange-inline">Probabilistic whole</del>-<del class="diffchange diffchange-inline">genome alignments reveal high indel rates </del>in the human <del class="diffchange diffchange-inline">and mouse genomes</del>.". <del class="diffchange diffchange-inline">Bioinformatics 23 </del>(<del class="diffchange diffchange-inline">13</del>): <del class="diffchange diffchange-inline">i289</del>-<del class="diffchange diffchange-inline">96</del>. https://doi.org/10.<del class="diffchange diffchange-inline">1093</del>/<del class="diffchange diffchange-inline">bioinformatics/btm185</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">6. Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF et al</ins>. (2007). "<ins class="diffchange diffchange-inline">Distinguishing protein</ins>-<ins class="diffchange diffchange-inline">coding and noncoding genes </ins>in the human <ins class="diffchange diffchange-inline">genome</ins>.". <ins class="diffchange diffchange-inline">Proc Natl Acad Sci U S A 104 </ins>(<ins class="diffchange diffchange-inline">49</ins>): <ins class="diffchange diffchange-inline">19428</ins>-<ins class="diffchange diffchange-inline">33</ins>. https://doi.org/10.<ins class="diffchange diffchange-inline">1073</ins>/<ins class="diffchange diffchange-inline">pnas.0709013104 '''Samporová, Švec, Jurkovičová, Vnenčáková, Zhukova, Obšivanová, Burianová'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">5</del>. <del class="diffchange diffchange-inline">Wapinski I</del>, <del class="diffchange diffchange-inline">Pfeffer A</del>, <del class="diffchange diffchange-inline">Friedman N</del>, <del class="diffchange diffchange-inline">Regev A </del>(<del class="diffchange diffchange-inline">2007</del>). "<del class="diffchange diffchange-inline">Natural history and evolutionary principles </del>of <del class="diffchange diffchange-inline">gene duplication in fungi</del>". Nature <del class="diffchange diffchange-inline">449 </del>(<del class="diffchange diffchange-inline">7158</del>): <del class="diffchange diffchange-inline">54</del>-<del class="diffchange diffchange-inline">61</del>. <del class="diffchange diffchange-inline">[http</del>://<del class="diffchange diffchange-inline">llama</del>.<del class="diffchange diffchange-inline">mshri</del>.<del class="diffchange diffchange-inline">on</del>.<del class="diffchange diffchange-inline">ca</del>/<del class="diffchange diffchange-inline">courses</del>/<del class="diffchange diffchange-inline">Biophysics205</del>/<del class="diffchange diffchange-inline">Papers</del>/<del class="diffchange diffchange-inline">Wapinski_2007.pdf pdf]</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">7</ins>. <ins class="diffchange diffchange-inline">Harbison CT</ins>, <ins class="diffchange diffchange-inline">Gordon DB</ins>, <ins class="diffchange diffchange-inline">Lee TI</ins>, <ins class="diffchange diffchange-inline">Rinaldi NJ, Macisaac KD, Danford TW et al. </ins>(<ins class="diffchange diffchange-inline">2004</ins>). "<ins class="diffchange diffchange-inline">Transcriptional regulatory code </ins>of <ins class="diffchange diffchange-inline">a eukaryotic genome.</ins>". Nature <ins class="diffchange diffchange-inline">431 </ins>(<ins class="diffchange diffchange-inline">7004</ins>): <ins class="diffchange diffchange-inline">99</ins>-<ins class="diffchange diffchange-inline">104</ins>. <ins class="diffchange diffchange-inline"> https</ins>://<ins class="diffchange diffchange-inline">www</ins>.<ins class="diffchange diffchange-inline">ncbi</ins>.<ins class="diffchange diffchange-inline">nlm</ins>.<ins class="diffchange diffchange-inline">nih.gov</ins>/<ins class="diffchange diffchange-inline">pmc</ins>/<ins class="diffchange diffchange-inline">articles</ins>/<ins class="diffchange diffchange-inline">PMC3006441</ins>/ <ins class="diffchange diffchange-inline">'''Drobná, Čerňanský, Kravec, Hamidová, Martyrosian, Jakubovský, Holenda'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">6</del>. <del class="diffchange diffchange-inline">Clamp M</del>, <del class="diffchange diffchange-inline">Fry </del>B, <del class="diffchange diffchange-inline">Kamal </del>M, <del class="diffchange diffchange-inline">Xie X</del>, <del class="diffchange diffchange-inline">Cuff </del>J, <del class="diffchange diffchange-inline">Lin MF et al</del>. <del class="diffchange diffchange-inline">(2007). "Distinguishing protein-coding </del>and <del class="diffchange diffchange-inline">noncoding genes </del>in <del class="diffchange diffchange-inline">the human genome</del>.<del class="diffchange diffchange-inline">". Proc Natl Acad Sci U S A 104 </del>(<del class="diffchange diffchange-inline">49</del>)<del class="diffchange diffchange-inline">: 19428-33</del>. https://doi.org/10.<del class="diffchange diffchange-inline">1073</del>/<del class="diffchange diffchange-inline">pnas.0709013104</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">8</ins>. <ins class="diffchange diffchange-inline">Huang</ins>, <ins class="diffchange diffchange-inline">K.L., Scott, A.D., Zhou, D.C., Wang, L.</ins>B<ins class="diffchange diffchange-inline">., Weerasinghe, A., Elmas, A., Liu, R., Wu, Y., Wendl</ins>, M<ins class="diffchange diffchange-inline">.C.</ins>, <ins class="diffchange diffchange-inline">Wyczalkowski, M.A. and Baral</ins>, J<ins class="diffchange diffchange-inline">.</ins>, <ins class="diffchange diffchange-inline">2021</ins>. <ins class="diffchange diffchange-inline">Spatially interacting phosphorylation sites </ins>and <ins class="diffchange diffchange-inline">mutations </ins>in <ins class="diffchange diffchange-inline">cancer</ins>. <ins class="diffchange diffchange-inline">Nature communications, 12</ins>(<ins class="diffchange diffchange-inline">1</ins>)<ins class="diffchange diffchange-inline">, p.2313</ins>. https://doi.org/10.<ins class="diffchange diffchange-inline">1038</ins>/<ins class="diffchange diffchange-inline">s41467-021-22481-w '''Lebed, Korbeľová, Šoošová, Al-Shafe´i, Paluch, Mok'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">7. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW et al. (2004). "Transcriptional regulatory code of a eukaryotic genome.". Nature 431 (7004): 99-104.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006441/</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">8</del>. <del class="diffchange diffchange-inline">Huang</del>, K.<del class="diffchange diffchange-inline">L</del>., <del class="diffchange diffchange-inline">Scott</del>, A.<del class="diffchange diffchange-inline">D</del>., <del class="diffchange diffchange-inline">Zhou</del>, <del class="diffchange diffchange-inline">D</del>.<del class="diffchange diffchange-inline">C</del>., <del class="diffchange diffchange-inline">Wang</del>, <del class="diffchange diffchange-inline">L</del>.<del class="diffchange diffchange-inline">B</del>., <del class="diffchange diffchange-inline">Weerasinghe</del>, <del class="diffchange diffchange-inline">A</del>., <del class="diffchange diffchange-inline">Elmas</del>, <del class="diffchange diffchange-inline">A</del>., <del class="diffchange diffchange-inline">Liu</del>, R., <del class="diffchange diffchange-inline">Wu</del>, <del class="diffchange diffchange-inline">Y</del>., <del class="diffchange diffchange-inline">Wendl</del>, <del class="diffchange diffchange-inline">M</del>.<del class="diffchange diffchange-inline">C</del>., <del class="diffchange diffchange-inline">Wyczalkowski</del>, <del class="diffchange diffchange-inline">M</del>.<del class="diffchange diffchange-inline">A</del>. and <del class="diffchange diffchange-inline">Baral</del>, J., <del class="diffchange diffchange-inline">2021</del>. <del class="diffchange diffchange-inline">Spatially interacting phosphorylation sites and mutations in cancer</del>. Nature <del class="diffchange diffchange-inline">communications</del>, <del class="diffchange diffchange-inline">12</del>(<del class="diffchange diffchange-inline">1</del>), <del class="diffchange diffchange-inline">p</del>.<del class="diffchange diffchange-inline">2313</del>. https://doi.org/10.1038/<del class="diffchange diffchange-inline">s41467</del>-021-<del class="diffchange diffchange-inline">22481</del>-<del class="diffchange diffchange-inline">w</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">'''Unused papers:'''</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">1</ins>. <ins class="diffchange diffchange-inline">Curry</ins>, K.<ins class="diffchange diffchange-inline">D., Wang, Q., Nute, M.G</ins>., <ins class="diffchange diffchange-inline">Tyshaieva</ins>, A.<ins class="diffchange diffchange-inline">, Reeves, E</ins>., <ins class="diffchange diffchange-inline">Soriano</ins>, <ins class="diffchange diffchange-inline">S</ins>.<ins class="diffchange diffchange-inline">, Wu, Q</ins>., <ins class="diffchange diffchange-inline">Graeber</ins>, <ins class="diffchange diffchange-inline">E</ins>.<ins class="diffchange diffchange-inline">, Finzer, P</ins>., <ins class="diffchange diffchange-inline">Mendling</ins>, <ins class="diffchange diffchange-inline">W</ins>. <ins class="diffchange diffchange-inline">and Savidge</ins>, <ins class="diffchange diffchange-inline">T.</ins>, <ins class="diffchange diffchange-inline">2022</ins>. <ins class="diffchange diffchange-inline">Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nature methods</ins>, <ins class="diffchange diffchange-inline">19(7), pp.845-853. https://doi.org/10.1038/s41592-022-01520-4</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">2. Edgar</ins>, R<ins class="diffchange diffchange-inline">.C</ins>., <ins class="diffchange diffchange-inline">Taylor</ins>, <ins class="diffchange diffchange-inline">J</ins>., <ins class="diffchange diffchange-inline">Lin</ins>, <ins class="diffchange diffchange-inline">V</ins>.<ins class="diffchange diffchange-inline">, Altman, T</ins>., <ins class="diffchange diffchange-inline">Barbera</ins>, <ins class="diffchange diffchange-inline">P</ins>.<ins class="diffchange diffchange-inline">, Meleshko, D., Lohr, D., Novakovsky, G., Buchfink, B., Al-Shayeb, B</ins>. and <ins class="diffchange diffchange-inline">Banfield</ins>, J<ins class="diffchange diffchange-inline">.F</ins>., <ins class="diffchange diffchange-inline">2022</ins>. <ins class="diffchange diffchange-inline">Petabase-scale sequence alignment catalyses viral discovery</ins>. Nature, <ins class="diffchange diffchange-inline">602</ins>(<ins class="diffchange diffchange-inline">7895</ins>), <ins class="diffchange diffchange-inline">pp</ins>.<ins class="diffchange diffchange-inline">142-147</ins>.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>https://doi.org/10.1038/<ins class="diffchange diffchange-inline">s41586</ins>-021-<ins class="diffchange diffchange-inline">04332</ins>-<ins class="diffchange diffchange-inline">2</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>9. Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). https://doi.org/10.1126/science.abe9403</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>9. Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). https://doi.org/10.1126/science.abe9403</div></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&diff=2951&oldid=prev
Brona na 13:10, 12. október 2023
2023-10-12T13:10:30Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 13:10, 12. október 2023</td>
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<td colspan="2" class="diff-lineno">Riadok 7:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Also please indicate if you are willing to work in a group with English-speaking students (this means group discussions and final report in English)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Also please indicate if you are willing to work in a group with English-speaking students (this means group discussions and final report in English)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>List of papers:</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">'''</ins>List of papers:<ins class="diffchange diffchange-inline">'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>1. Curry, K.D., Wang, Q., Nute, M.G., Tyshaieva, A., Reeves, E., Soriano, S., Wu, Q., Graeber, E., Finzer, P., Mendling, W. and Savidge, T., 2022. Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nature methods, 19(7), pp.845-853. https://doi.org/10.1038/s41592-022-01520-4</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>1. Curry, K.D., Wang, Q., Nute, M.G., Tyshaieva, A., Reeves, E., Soriano, S., Wu, Q., Graeber, E., Finzer, P., Mendling, W. and Savidge, T., 2022. Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nature methods, 19(7), pp.845-853. https://doi.org/10.1038/s41592-022-01520-4</div></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&diff=2950&oldid=prev
Brona na 13:10, 12. október 2023
2023-10-12T13:10:08Z
<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 13:10, 12. október 2023</td>
</tr><tr><td colspan="2" class="diff-lineno">Riadok 1:</td>
<td colspan="2" class="diff-lineno">Riadok 1:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>A detailed description of the journal club activity is included in the [[Rules#Journal club|course rules]].</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>A detailed description of the journal club activity is included in the [[Rules#Journal club|course rules]].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Please submit your preferences regarding these papers using '''[https://forms.gle/K7BZJD5fA3wRmmXk8 this form]''' until Wednesday  '''18<del class="diffchange diffchange-inline">.10.</del>2023, 22:00'''. In the form, include '''numbers of three papers from this list''' in the order of preference.  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Please submit your preferences regarding these papers using '''[https://forms.gle/K7BZJD5fA3wRmmXk8 this form]''' until Wednesday  '''<ins class="diffchange diffchange-inline">Oct. </ins>18<ins class="diffchange diffchange-inline">, </ins>2023, 22:00'''. In the form, include '''numbers of three papers from this list''' in the order of preference.  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Students from the same study program will typically not be in the same group.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Students from the same study program will typically not be in the same group.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&diff=2949&oldid=prev
Brona na 13:09, 12. október 2023
2023-10-12T13:09:43Z
<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 13:09, 12. október 2023</td>
</tr><tr><td colspan="2" class="diff-lineno">Riadok 4:</td>
<td colspan="2" class="diff-lineno">Riadok 4:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Students from the same study program will typically not be in the same group.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Students from the same study program will typically not be in the same group.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* All links to papers should work in our University network (e.g. Eduroam or [https://uniba.sk/<del class="diffchange diffchange-inline">o-univerzite/fakulty-a-dalsie-sucasti/cit/citps/sietove-sluzby/proxy/ </del>proxy])</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* All links to papers should work in our University network (e.g. Eduroam or [https://uniba.sk/<ins class="diffchange diffchange-inline">index.php?id=6828 </ins>proxy])</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Also please indicate if you are willing to work in a group with English-speaking students (this means group discussions and final report in English)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Also please indicate if you are willing to work in a group with English-speaking students (this means group discussions and final report in English)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&diff=2936&oldid=prev
Brona na 08:11, 11. október 2023
2023-10-11T08:11:51Z
<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 08:11, 11. október 2023</td>
</tr><tr><td colspan="2" class="diff-lineno">Riadok 5:</td>
<td colspan="2" class="diff-lineno">Riadok 5:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* All links to papers should work in our University network (e.g. Eduroam or [https://uniba.sk/o-univerzite/fakulty-a-dalsie-sucasti/cit/citps/sietove-sluzby/proxy/ proxy])</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* All links to papers should work in our University network (e.g. Eduroam or [https://uniba.sk/o-univerzite/fakulty-a-dalsie-sucasti/cit/citps/sietove-sluzby/proxy/ proxy])</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* Also please indicate if you are willing to work in a group with English-speaking students (this means group discussions and final report in English)</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>List of papers:</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>List of papers:</div></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&diff=2935&oldid=prev
Brona na 08:09, 11. október 2023
2023-10-11T08:09:44Z
<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 08:09, 11. október 2023</td>
</tr><tr><td colspan="2" class="diff-lineno">Riadok 4:</td>
<td colspan="2" class="diff-lineno">Riadok 4:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Students from the same study program will typically not be in the same group.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Students from the same study program will typically not be in the same group.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">* All links to papers should work in our University network (e.g. Eduroam or [https://uniba.sk/o-univerzite/fakulty-a-dalsie-sucasti/cit/citps/sietove-sluzby/proxy/ proxy])</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>List of papers:</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>List of papers:</div></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&diff=2934&oldid=prev
Brona na 08:08, 11. október 2023
2023-10-11T08:08:22Z
<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 08:08, 11. október 2023</td>
</tr><tr><td colspan="2" class="diff-lineno">Riadok 5:</td>
<td colspan="2" class="diff-lineno">Riadok 5:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">1. Curry, K.D., Wang, Q., Nute, M.G., Tyshaieva, A., Reeves, E., Soriano, S., Wu, Q., Graeber, E., Finzer, P., Mendling, W. and Savidge, T., 2022. Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nature methods, 19(7), pp.845-853. https://doi.org/10.1038/s41592-022-01520-4</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">List of papers:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">1. Curry, K.D., Wang, Q., Nute, M.G., Tyshaieva, A., Reeves, E., Soriano, S., Wu, Q., Graeber, E., Finzer, P., Mendling, W. and Savidge, T., 2022. Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nature methods, 19(7), pp.845-853. https://doi.org/10.1038/s41592-022-01520-4</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>2. Edgar, R.C., Taylor, J., Lin, V., Altman, T., Barbera, P., Meleshko, D., Lohr, D., Novakovsky, G., Buchfink, B., Al-Shayeb, B. and Banfield, J.F., 2022. Petabase-scale sequence alignment catalyses viral discovery. Nature, 602(7895), pp.142-147.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>2. Edgar, R.C., Taylor, J., Lin, V., Altman, T., Barbera, P., Meleshko, D., Lohr, D., Novakovsky, G., Buchfink, B., Al-Shayeb, B. and Banfield, J.F., 2022. Petabase-scale sequence alignment catalyses viral discovery. Nature, 602(7895), pp.142-147.</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Riadok 15:</td>
<td colspan="2" class="diff-lineno">Riadok 17:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>4. Lunter G (2007). "Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.". Bioinformatics 23 (13): i289-96. https://doi.org/10.1093/bioinformatics/btm185</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>4. Lunter G (2007). "Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.". Bioinformatics 23 (13): i289-96. https://doi.org/10.1093/bioinformatics/btm185</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>5. Wapinski I, Pfeffer A, Friedman N, Regev A (2007). "Natural history and evolutionary principles of gene duplication in fungi". Nature 449 (7158): 54-61. <del class="diffchange diffchange-inline">https://doi.org/10.1038/nature06107  (check also the </del>[http://<del class="diffchange diffchange-inline">www</del>.<del class="diffchange diffchange-inline">nature</del>.<del class="diffchange diffchange-inline">com/nature/journal</del>/<del class="diffchange diffchange-inline">v449</del>/<del class="diffchange diffchange-inline">n7158</del>/<del class="diffchange diffchange-inline">suppinfo</del>/<del class="diffchange diffchange-inline">nature06107</del>.<del class="diffchange diffchange-inline">html Online supplement</del>]<del class="diffchange diffchange-inline">)</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>5. Wapinski I, Pfeffer A, Friedman N, Regev A (2007). "Natural history and evolutionary principles of gene duplication in fungi". Nature 449 (7158): 54-61. [http://<ins class="diffchange diffchange-inline">llama</ins>.<ins class="diffchange diffchange-inline">mshri</ins>.<ins class="diffchange diffchange-inline">on.ca</ins>/<ins class="diffchange diffchange-inline">courses</ins>/<ins class="diffchange diffchange-inline">Biophysics205</ins>/<ins class="diffchange diffchange-inline">Papers</ins>/<ins class="diffchange diffchange-inline">Wapinski_2007</ins>.<ins class="diffchange diffchange-inline">pdf pdf</ins>]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>6. Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF et al. (2007). "Distinguishing protein-coding and noncoding genes in the human genome.". Proc Natl Acad Sci U S A 104 (49): 19428-33. https://doi.org/10.1073/pnas.0709013104</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>6. Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF et al. (2007). "Distinguishing protein-coding and noncoding genes in the human genome.". Proc Natl Acad Sci U S A 104 (49): 19428-33. https://doi.org/10.1073/pnas.0709013104</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>7. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW et al. (2004). "Transcriptional regulatory code of a eukaryotic genome.". Nature 431 (7004): 99-104.  https://<del class="diffchange diffchange-inline">doi</del>.<del class="diffchange diffchange-inline">org/10</del>.<del class="diffchange diffchange-inline">1038</del>/<del class="diffchange diffchange-inline">nature02800</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>7. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW et al. (2004). "Transcriptional regulatory code of a eukaryotic genome.". Nature 431 (7004): 99-104.  https://<ins class="diffchange diffchange-inline">www</ins>.<ins class="diffchange diffchange-inline">ncbi</ins>.<ins class="diffchange diffchange-inline">nlm.nih.gov/pmc/articles/PMC3006441</ins>/</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>8. Huang, K.L., Scott, A.D., Zhou, D.C., Wang, L.B., Weerasinghe, A., Elmas, A., Liu, R., Wu, Y., Wendl, M.C., Wyczalkowski, M.A. and Baral, J., 2021. Spatially interacting phosphorylation sites and mutations in cancer. Nature communications, 12(1), p.2313. https://doi.org/10.1038/s41467-021-22481-w</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>8. Huang, K.L., Scott, A.D., Zhou, D.C., Wang, L.B., Weerasinghe, A., Elmas, A., Liu, R., Wu, Y., Wendl, M.C., Wyczalkowski, M.A. and Baral, J., 2021. Spatially interacting phosphorylation sites and mutations in cancer. Nature communications, 12(1), p.2313. https://doi.org/10.1038/s41467-021-22481-w</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>9. Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). https://doi.org/10.1126/science.abe9403</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>9. Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). https://doi.org/10.1126/science.abe9403</div></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&diff=2933&oldid=prev
Brona na 07:54, 11. október 2023
2023-10-11T07:54:51Z
<p></p>
<table class='diff diff-contentalign-left'>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 07:54, 11. október 2023</td>
</tr><tr><td colspan="2" class="diff-lineno">Riadok 1:</td>
<td colspan="2" class="diff-lineno">Riadok 1:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>A detailed description of the journal club activity is included in the [[Rules#Journal club|course rules]].</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>A detailed description of the journal club activity is included in the [[Rules#Journal club|course rules]].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"><!--</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Please submit your preferences regarding these papers using '''[https://forms.gle/K7BZJD5fA3wRmmXk8 this form]''' until Wednesday  '''<ins class="diffchange diffchange-inline">18</ins>.10.<ins class="diffchange diffchange-inline">2023</ins>, 22:00'''. In the form, include '''numbers of three papers from this list''' in the order of preference.  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Please submit your preferences regarding these papers using '''[https://forms.gle/K7BZJD5fA3wRmmXk8 this form]''' until Wednesday  '''<del class="diffchange diffchange-inline">19</del>.10.<del class="diffchange diffchange-inline">2022</del>, 22:00'''. In the form, include '''numbers of three papers from this list''' in the order of preference.  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Students from the same study program will typically not be in the same group.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Students from the same study program will typically not be in the same group.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Preferences submitted earlier will be considered with higher preference.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">--></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* 3 Wahba L, Jain N, Fire AZ, Shoura MJ, Artiles KL, McCoy MJ, Jeong DE</del>. <del class="diffchange diffchange-inline">An extensive meta-metagenomic search identifies SARS-CoV-2-homologous sequences in pangolin lung viromes. MSphere. 2020 May 6;5(3):e00160-20. [https://journals.asm.org/doi/full/10.1128/mSphere.00160-20]</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">1</ins>. <ins class="diffchange diffchange-inline">Curry</ins>, K.<ins class="diffchange diffchange-inline">D</ins>., <ins class="diffchange diffchange-inline">Wang</ins>, <ins class="diffchange diffchange-inline">Q</ins>., <ins class="diffchange diffchange-inline">Nute</ins>, M.<ins class="diffchange diffchange-inline">G</ins>., <ins class="diffchange diffchange-inline">Tyshaieva</ins>, <ins class="diffchange diffchange-inline">A</ins>., <ins class="diffchange diffchange-inline">Reeves</ins>, <ins class="diffchange diffchange-inline">E</ins>., <ins class="diffchange diffchange-inline">Soriano</ins>, <ins class="diffchange diffchange-inline">S</ins>., <ins class="diffchange diffchange-inline">Wu</ins>, <ins class="diffchange diffchange-inline">Q</ins>., <ins class="diffchange diffchange-inline">Graeber</ins>, E., <ins class="diffchange diffchange-inline">Finzer</ins>, <ins class="diffchange diffchange-inline">P</ins>., <ins class="diffchange diffchange-inline">Mendling</ins>, <ins class="diffchange diffchange-inline">W</ins>. and <ins class="diffchange diffchange-inline">Savidge</ins>, <ins class="diffchange diffchange-inline">T</ins>., <ins class="diffchange diffchange-inline">2022</ins>. <ins class="diffchange diffchange-inline">Emu: species</ins>-<ins class="diffchange diffchange-inline">level microbial community profiling </ins>of <ins class="diffchange diffchange-inline">full</ins>-<ins class="diffchange diffchange-inline">length 16S rRNA Oxford Nanopore sequencing data. Nature methods, </ins>19<ins class="diffchange diffchange-inline">(7), pp</ins>.<ins class="diffchange diffchange-inline">845-853</ins>. https://<ins class="diffchange diffchange-inline">doi</ins>.<ins class="diffchange diffchange-inline">org</ins>/<ins class="diffchange diffchange-inline">10</ins>.<ins class="diffchange diffchange-inline">1038</ins>/<ins class="diffchange diffchange-inline">s41592-022-01520-4</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">** Čítajú Macko</del>, <del class="diffchange diffchange-inline">Kajan, Daniš, Petrová</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* 4 Zhang S, Amahong </del>K<del class="diffchange diffchange-inline">, Zhang C, Li F, Gao J, Qiu Y, Zhu F</del>. <del class="diffchange diffchange-inline">RNA–RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection</del>. <del class="diffchange diffchange-inline">Briefings in Bioinformatics. 2021 Sep 28. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8500159/] </del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">** Čítajú Sojka, Kreutzová, Šoucová</del>, <del class="diffchange diffchange-inline">Piatrová</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* 5 Korber</del>, <del class="diffchange diffchange-inline">B</del>., <del class="diffchange diffchange-inline">Fischer</del>, <del class="diffchange diffchange-inline">W.</del>M.<del class="diffchange diffchange-inline">, Gnanakaran, S</del>., <del class="diffchange diffchange-inline">Yoon</del>, <del class="diffchange diffchange-inline">H</del>., <del class="diffchange diffchange-inline">Theiler</del>, <del class="diffchange diffchange-inline">J</del>., <del class="diffchange diffchange-inline">Abfalterer</del>, <del class="diffchange diffchange-inline">W</del>., <del class="diffchange diffchange-inline">Hengartner</del>, <del class="diffchange diffchange-inline">N</del>., <del class="diffchange diffchange-inline">Giorgi</del>, <del class="diffchange diffchange-inline">E.</del>E., <del class="diffchange diffchange-inline">Bhattacharya</del>, <del class="diffchange diffchange-inline">T</del>., <del class="diffchange diffchange-inline">Foley</del>, <del class="diffchange diffchange-inline">B</del>. and <del class="diffchange diffchange-inline">Hastie</del>, <del class="diffchange diffchange-inline">K.M</del>., <del class="diffchange diffchange-inline">2020</del>. <del class="diffchange diffchange-inline">Tracking changes in SARS</del>-<del class="diffchange diffchange-inline">CoV-2 Spike: evidence that D614G increases infectivity </del>of <del class="diffchange diffchange-inline">the COVID</del>-19 <del class="diffchange diffchange-inline">virus</del>. <del class="diffchange diffchange-inline">Cell</del>. <del class="diffchange diffchange-inline">[</del>https://<del class="diffchange diffchange-inline">www</del>.<del class="diffchange diffchange-inline">sciencedirect.com</del>/<del class="diffchange diffchange-inline">science/article/pii/S0092867420308205] (comment on the paper from different authors  [https://www</del>.<del class="diffchange diffchange-inline">sciencedirect.com</del>/<del class="diffchange diffchange-inline">science/article/pii/S0092867420308175]) </del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">** Čítajú Švorc, Jankechová, Zivák, Čačaná</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">==Unused papers==</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* 1 Lemey P</del>, <del class="diffchange diffchange-inline">Hong SL</del>, <del class="diffchange diffchange-inline">Hill V</del>, <del class="diffchange diffchange-inline">Baele G</del>, <del class="diffchange diffchange-inline">Poletto C</del>, <del class="diffchange diffchange-inline">Colizza </del>V, <del class="diffchange diffchange-inline">O’toole Á</del>, <del class="diffchange diffchange-inline">McCrone JT</del>, <del class="diffchange diffchange-inline">Andersen KG</del>, <del class="diffchange diffchange-inline">Worobey M</del>, <del class="diffchange diffchange-inline">Nelson MI</del>. <del class="diffchange diffchange-inline">Accommodating individual travel history </del>and <del class="diffchange diffchange-inline">unsampled diversity in Bayesian phylogeographic inference of SARS</del>-<del class="diffchange diffchange-inline">CoV-2</del>. Nature <del class="diffchange diffchange-inline">communications. 2020 Oct 9;11</del>(<del class="diffchange diffchange-inline">1</del>)<del class="diffchange diffchange-inline">:1</del>-<del class="diffchange diffchange-inline">4</del>. <del class="diffchange diffchange-inline">[</del>https://<del class="diffchange diffchange-inline">www</del>.<del class="diffchange diffchange-inline">nature</del>.<del class="diffchange diffchange-inline">com</del>/<del class="diffchange diffchange-inline">articles/s41467</del>-<del class="diffchange diffchange-inline">020</del>-<del class="diffchange diffchange-inline">18877</del>-<del class="diffchange diffchange-inline">9]</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">2. Edgar</ins>, <ins class="diffchange diffchange-inline">R.C.</ins>, <ins class="diffchange diffchange-inline">Taylor</ins>, <ins class="diffchange diffchange-inline">J.</ins>, <ins class="diffchange diffchange-inline">Lin</ins>, V<ins class="diffchange diffchange-inline">.</ins>, <ins class="diffchange diffchange-inline">Altman</ins>, <ins class="diffchange diffchange-inline">T.</ins>, <ins class="diffchange diffchange-inline">Barbera</ins>, <ins class="diffchange diffchange-inline">P.</ins>, <ins class="diffchange diffchange-inline">Meleshko, D., Lohr, D., Novakovsky, G., Buchfink, B., Al-Shayeb, B</ins>. and <ins class="diffchange diffchange-inline">Banfield, J.F., 2022. Petabase</ins>-<ins class="diffchange diffchange-inline">scale sequence alignment catalyses viral discovery</ins>. Nature<ins class="diffchange diffchange-inline">, 602</ins>(<ins class="diffchange diffchange-inline">7895</ins>)<ins class="diffchange diffchange-inline">, pp.142</ins>-<ins class="diffchange diffchange-inline">147</ins>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* </del>2 <del class="diffchange diffchange-inline">Quick J</del>, <del class="diffchange diffchange-inline">Grubaugh ND</del>, <del class="diffchange diffchange-inline">Pullan ST</del>, <del class="diffchange diffchange-inline">Claro IM</del>, <del class="diffchange diffchange-inline">Smith AD</del>, <del class="diffchange diffchange-inline">Gangavarapu K</del>, <del class="diffchange diffchange-inline">Oliveira </del>G, <del class="diffchange diffchange-inline">Robles-Sikisaka R</del>, <del class="diffchange diffchange-inline">Rogers TF</del>, <del class="diffchange diffchange-inline">Beutler NA</del>, <del class="diffchange diffchange-inline">Burton DR</del>. <del class="diffchange diffchange-inline">Multiplex PCR method for MinION and Illumina sequencing of Zika </del>and <del class="diffchange diffchange-inline">other virus </del>genomes <del class="diffchange diffchange-inline">directly from clinical samples</del>. <del class="diffchange diffchange-inline">Nature protocols</del>. <del class="diffchange diffchange-inline">2017 Jun;12</del>(<del class="diffchange diffchange-inline">6</del>):<del class="diffchange diffchange-inline">1261</del>. <del class="diffchange diffchange-inline">[</del>https://<del class="diffchange diffchange-inline">www</del>.<del class="diffchange diffchange-inline">nature</del>.<del class="diffchange diffchange-inline">com</del>/<del class="diffchange diffchange-inline">articles</del>/<del class="diffchange diffchange-inline">nprot</del>.<del class="diffchange diffchange-inline">2017</del>.<del class="diffchange diffchange-inline">066] or [</del>https://<del class="diffchange diffchange-inline">www</del>.<del class="diffchange diffchange-inline">ncbi</del>.<del class="diffchange diffchange-inline">nlm</del>.<del class="diffchange diffchange-inline">nih</del>.<del class="diffchange diffchange-inline">gov</del>/<del class="diffchange diffchange-inline">pmc</del>/<del class="diffchange diffchange-inline">articles</del>/<del class="diffchange diffchange-inline">PMC5902022</del>/] (<del class="diffchange diffchange-inline">application to SARS</del>-<del class="diffchange diffchange-inline">CoV</del>-<del class="diffchange diffchange-inline">2 [</del>https://<del class="diffchange diffchange-inline">artic</del>.<del class="diffchange diffchange-inline">network</del>/<del class="diffchange diffchange-inline">ncov</del>-<del class="diffchange diffchange-inline">2019]</del>)  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>https://<ins class="diffchange diffchange-inline">doi</ins>.<ins class="diffchange diffchange-inline">org/10</ins>.<ins class="diffchange diffchange-inline">1038</ins>/<ins class="diffchange diffchange-inline">s41586</ins>-<ins class="diffchange diffchange-inline">021</ins>-<ins class="diffchange diffchange-inline">04332</ins>-2</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* 6 </del>Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). <del class="diffchange diffchange-inline">[</del>https://<del class="diffchange diffchange-inline">science.sciencemag</del>.org/<del class="diffchange diffchange-inline">content</del>/<del class="diffchange diffchange-inline">370/6521/eabe9403</del>.<del class="diffchange diffchange-inline">abstract]</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">3. Bradley</ins>, <ins class="diffchange diffchange-inline">P.</ins>, <ins class="diffchange diffchange-inline">Den Bakker</ins>, <ins class="diffchange diffchange-inline">H.C.</ins>, <ins class="diffchange diffchange-inline">Rocha</ins>, <ins class="diffchange diffchange-inline">E.P., McVean</ins>, G<ins class="diffchange diffchange-inline">. and Iqbal</ins>, <ins class="diffchange diffchange-inline">Z.</ins>, <ins class="diffchange diffchange-inline">2019. Ultrafast search of all deposited bacterial and viral genomic data. Nature biotechnology</ins>, <ins class="diffchange diffchange-inline">37(2)</ins>, <ins class="diffchange diffchange-inline">pp</ins>.<ins class="diffchange diffchange-inline">152-159. https://doi.org/10.1038/s41587-018-0010-1</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">4. Lunter G (2007). "Probabilistic whole-genome alignments reveal high indel rates in the human </ins>and <ins class="diffchange diffchange-inline">mouse </ins>genomes.<ins class="diffchange diffchange-inline">"</ins>. <ins class="diffchange diffchange-inline">Bioinformatics 23 </ins>(<ins class="diffchange diffchange-inline">13</ins>): <ins class="diffchange diffchange-inline">i289-96</ins>. https://<ins class="diffchange diffchange-inline">doi</ins>.<ins class="diffchange diffchange-inline">org/10</ins>.<ins class="diffchange diffchange-inline">1093</ins>/<ins class="diffchange diffchange-inline">bioinformatics</ins>/<ins class="diffchange diffchange-inline">btm185</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">5</ins>. <ins class="diffchange diffchange-inline">Wapinski I, Pfeffer A, Friedman N, Regev A (2007). "Natural history and evolutionary principles of gene duplication in fungi". Nature 449 (7158): 54-61</ins>. https://<ins class="diffchange diffchange-inline">doi</ins>.<ins class="diffchange diffchange-inline">org/10</ins>.<ins class="diffchange diffchange-inline">1038/nature06107  (check also the [http://www</ins>.<ins class="diffchange diffchange-inline">nature</ins>.<ins class="diffchange diffchange-inline">com</ins>/<ins class="diffchange diffchange-inline">nature</ins>/<ins class="diffchange diffchange-inline">journal</ins>/<ins class="diffchange diffchange-inline">v449</ins>/<ins class="diffchange diffchange-inline">n7158/suppinfo/nature06107.html Online supplement</ins>]<ins class="diffchange diffchange-inline">)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">6. Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF et al. </ins>(<ins class="diffchange diffchange-inline">2007). "Distinguishing protein</ins>-<ins class="diffchange diffchange-inline">coding and noncoding genes in the human genome.". Proc Natl Acad Sci U S A 104 (49): 19428</ins>-<ins class="diffchange diffchange-inline">33. </ins>https://<ins class="diffchange diffchange-inline">doi</ins>.<ins class="diffchange diffchange-inline">org</ins>/<ins class="diffchange diffchange-inline">10.1073/pnas.0709013104</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">7. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW et al. (2004). "Transcriptional regulatory code of a eukaryotic genome.". Nature 431 (7004): 99</ins>-<ins class="diffchange diffchange-inline">104.  https://doi.org/10.1038/nature02800</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">8. Huang, K.L., Scott, A.D., Zhou, D.C., Wang, L.B., Weerasinghe, A., Elmas, A., Liu, R., Wu, Y., Wendl, M.C., Wyczalkowski, M.A. and Baral, J., 2021. Spatially interacting phosphorylation sites and mutations in cancer. Nature communications, 12(1</ins>)<ins class="diffchange diffchange-inline">, p.2313. https://doi.org/10.1038/s41467-021-22481-w</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">9. </ins>Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). https://<ins class="diffchange diffchange-inline">doi</ins>.org/<ins class="diffchange diffchange-inline">10.1126</ins>/<ins class="diffchange diffchange-inline">science</ins>.<ins class="diffchange diffchange-inline">abe9403</ins></div></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&diff=2844&oldid=prev
Brona na 06:57, 27. október 2022
2022-10-27T06:57:56Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 06:57, 27. október 2022</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* 3 Wahba L, Jain N, Fire AZ, Shoura MJ, Artiles KL, McCoy MJ, Jeong DE. An extensive meta-metagenomic search identifies SARS-CoV-2-homologous sequences in pangolin lung viromes. MSphere. 2020 May 6;5(3):e00160-20. [https://journals.asm.org/doi/full/10.1128/mSphere.00160-20]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* 3 Wahba L, Jain N, Fire AZ, Shoura MJ, Artiles KL, McCoy MJ, Jeong DE. An extensive meta-metagenomic search identifies SARS-CoV-2-homologous sequences in pangolin lung viromes. MSphere. 2020 May 6;5(3):e00160-20. [https://journals.asm.org/doi/full/10.1128/mSphere.00160-20]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>** Čítajú Macko, Kajan, Daniš, Petrová</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>** Čítajú Macko, Kajan, Daniš, Petrová</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* 4 Zhang S, Amahong K, Zhang C, Li F, Gao J, Qiu Y, Zhu F. RNA–RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection. Briefings in Bioinformatics. 2021 Sep 28. [https://<del class="diffchange diffchange-inline">academic</del>.<del class="diffchange diffchange-inline">oup</del>.<del class="diffchange diffchange-inline">com</del>/<del class="diffchange diffchange-inline">bib/advance-article/doi/10.1093</del>/<del class="diffchange diffchange-inline">bib</del>/<del class="diffchange diffchange-inline">bbab397</del>/<del class="diffchange diffchange-inline">6377518</del>]  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* 4 Zhang S, Amahong K, Zhang C, Li F, Gao J, Qiu Y, Zhu F. RNA–RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection. Briefings in Bioinformatics. 2021 Sep 28. [https://<ins class="diffchange diffchange-inline">www</ins>.<ins class="diffchange diffchange-inline">ncbi</ins>.<ins class="diffchange diffchange-inline">nlm.nih.gov</ins>/<ins class="diffchange diffchange-inline">pmc</ins>/<ins class="diffchange diffchange-inline">articles</ins>/<ins class="diffchange diffchange-inline">PMC8500159</ins>/]  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>** Čítajú Sojka, Kreutzová, Šoucová, Piatrová</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>** Čítajú Sojka, Kreutzová, Šoucová, Piatrová</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* 5 Korber, B., Fischer, W.M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E.E., Bhattacharya, T., Foley, B. and Hastie, K.M., 2020. Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell. [https://www.sciencedirect.com/science/article/pii/S0092867420308205] (comment on the paper from different authors  [https://www.sciencedirect.com/science/article/pii/S0092867420308175])  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* 5 Korber, B., Fischer, W.M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E.E., Bhattacharya, T., Foley, B. and Hastie, K.M., 2020. Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell. [https://www.sciencedirect.com/science/article/pii/S0092867420308205] (comment on the paper from different authors  [https://www.sciencedirect.com/science/article/pii/S0092867420308175])  </div></td></tr>
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