1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2023/24

Introduction · Rules · Tasks and dates · Materials · Moodle
Quizzes can be found in Moodle.
Homework assignments and journal club papers can be found in Tasks and dates.
Exam rules, example questions and syllabus
Groups for journal club have each their own group in Moodle.


Journal club papers: Rozdiel medzi revíziami

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Podľa vašich preferencií sme Vás zadelili ku článkom (v prípade, že o vaše vybrané články bol velký záujem, snažili sme sa dať prednosť študentom, ktorí svoje preferencie odvzdali skôr).
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A detailed description of the journal club activity is included in the [[Rules#Journal club|course rules]].
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* All links to papers should work in our University network (e.g. Eduroam or [https://uniba.sk/index.php?id=6828 proxy])
  
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1. {{cite journal| author=Do CB, Mahabhashyam MS, Brudno M, Batzoglou S| title=ProbCons: Probabilistic consistency-based multiple sequence alignment. | journal=Genome Res | year= 2005 | volume= 15 | issue= 2 | pages= 330-40 | pmid=15687296 }}
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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.
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* Students from the same study program will typically not be in the same group.
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* Preferences submitted earlier will be considered with higher preference.
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* 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)
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2. {{cite journal| author=Lunter G| title=Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes. | journal=Bioinformatics | year= 2007 | volume= 23 | issue= 13 | pages= i289-96 | pmid=17646308 | doi=10.1093/bioinformatics/btm185 }}
 
  
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3. {{cite journal| author=Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D| title=Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. | journal=Proc Natl Acad Sci U S A | year= 2003 | volume= 100 | issue= 20 | pages= 11484-9 | pmid=14500911 | doi=10.1073/pnas.1932072100 }}
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'''Groups:'''
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::: '''Čítajú''' Michal Burger, Peter Galiovský, Peter Jurčo, Marcel Kucharík, Bianka Mateášiková
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4. {{cite journal| author=Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K et al.| title=Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes | journal=Genome Res | year= 2005 | volume= 15 | issue= 8 | pages= 1034-50 | pmid=16024819 | doi=10.1101/gr.3715005}}
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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'''
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::: '''Čítajú''' Tomáš Eichler, Martin Gallus, Martin Sárközi, Martina Višňovská, Matej Vitko
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5. {{cite journal| author=Wapinski I, Pfeffer A, Friedman N, Regev A| title=Natural history and evolutionary principles of gene duplication in fungi | journal=Nature | year= 2007 | volume= 449 | issue= 7158 | pages= 54-61 | pmid=17805289 | doi=10.1038/nature06107 | url=http://www.eecs.ucf.edu/~shzhang/CAP6938/p7_nature06107_aviv_duplication.pdf}}
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::: '''Čítajú''' Barbora Candráková, Jakub Kováč, Michal Kožuch, Ján Kriška, Milan Uherčík
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6. {{cite journal| author=Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF et al.| title=Distinguishing protein-coding and noncoding genes in the human genome. | journal=Proc Natl Acad Sci U S A | year= 2007 | volume= 104 | issue= 49 | pages= 19428-33 | pmid=18040051 | doi=10.1073/pnas.0709013104}}
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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 '''Jurčák, Pásztor, Lichmanová, Hašan, Uhrin, Horváthová'''
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::: '''Čítajú''' Michal Antonič, Matej Darebník, Juraj Mešťánek, Pavol Panák, Tomáš Paulenda
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7. {{cite journal| author=Eisen MB, Spellman PT, Brown PO, Botstein D| title=Cluster analysis and display of genome-wide expression
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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://llama.mshri.on.ca/courses/Biophysics205/Papers/Wapinski_2007.pdf pdf] '''Skrypnyk, Ondrejová, Kostrian, Murin, Vicianová, Revúcky'''
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patterns. | journal=Proc Natl Acad Sci U S A | year= 1998 | volume= 95 | issue= 25 | pages= 14863-8 | pmid=9843981 }}
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8. {{cite journal| author=Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW et al.| title=Transcriptional regulatory code of a eukaryotic genome. | journal=Nature | year= 2004 | volume= 431 | issue= 7004 | pages= 99-104 | pmid=15343339  | doi=10.1038/nature02800 | url=http://www.psrg.csail.mit.edu/pubs/nature-2004.pdf }}
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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 '''Samporová, Švec, Jurkovičová, Vnenčáková, Zhukova, Obšivanová, Burianová'''
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::: '''Čítajú''' Ladislav Benc, Maroš Gálik, Jana Konkoľová, Martin Kravec, Michaela Libiaková
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9. {{cite journal| author=Bystroff C, Baker D| title=Prediction of local structure in proteins using a library of sequence-structure motifs. | journal=J Mol Biol | year= 1998 | volume= 281 | issue= 3 | pages= 565-77 | pmid=9698570 | doi=10.1006/jmbi.1998.1943 | url=http://depts.washington.edu/bakerpg/papers/Bystroff-JMB-v281-p565.pdf}}
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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/ '''Drobná, Čerňanský, Kravec, Hamidová, Martyrosian, Jakubovský, Holenda'''
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::: '''Čítajú''' Matúš Fedák, Jana Hlavačiková, Adam Ješko, Lenka Kyjacová, Michal Nánási
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10. {{cite journal| author=Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P et al.| title=Conserved patterns of protein interaction in multiple species. | journal=Proc Natl Acad Sci U S A | year= 2005 | volume= 102 | issue= 6 | pages= 1974-9 | pmid=15687504 | doi=10.1073/pnas.0409522102 }}
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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 '''Lebed, Korbeľová, Šoošová, Al-Shafe´i, Paluch, Mok'''
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::: '''Čítajú''' Stanislav Hreha, Martin Králik, Martin Macko, Miroslav Nadhajský, Martina Petrušová
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11. {{cite journal| author=Andronescu M, Fejes AP, Hutter F, Hoos HH, Condon A| title=A new algorithm for RNA secondary structure design. | journal=J Mol Biol | year= 2004 | volume= 336 | issue= 3 | pages= 607-24 | pmid=15095976 | doi=10.1016/j.jmb.2003.12.041 | url=http://people.cs.ubc.ca/~hutter/papers/jmb04-rna-ssd.pdf }}
 
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::: '''Čítajú''' Peter Herman, Jakub Kollár, Peter Kováč, Peter Perešíni, Ladislav Rampášek, Jozef Vavro
 
  
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12. {{cite journal| author=Hernandez RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J et al.| title=Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. | journal=Science | year= 2007 | volume= 316 | issue= 5822 | pages= 240-3 | pmid=17431170 | url=http://www.sciencemag.org/cgi/content/full/316/5822/240 |  doi=10.1126/science.1140462 }}
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'''Unused papers:'''
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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
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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.
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https://doi.org/10.1038/s41586-021-04332-2
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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

Aktuálna revízia z 10:17, 19. október 2023

A detailed description of the journal club activity is included in the course rules.

  • All links to papers should work in our University network (e.g. Eduroam or proxy)


Groups:

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

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 Jurčák, Pásztor, Lichmanová, Hašan, Uhrin, Horváthová

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. pdf Skrypnyk, Ondrejová, Kostrian, Murin, Vicianová, Revúcky

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 Samporová, Švec, Jurkovičová, Vnenčáková, Zhukova, Obšivanová, Burianová

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/ Drobná, Čerňanský, Kravec, Hamidová, Martyrosian, Jakubovský, Holenda

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 Lebed, Korbeľová, Šoošová, Al-Shafe´i, Paluch, Mok


Unused papers:

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

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. https://doi.org/10.1038/s41586-021-04332-2


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

Zdroj: „http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Journal_club_papers&oldid=2958“