1-BIN-301, 2-AIN-501 Methods in Bioinformatics

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Journal club papers: Rozdiel medzi revíziami

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Svoje preferencie ohľadom článkov na journal club odovzdajte pomocou [https://docs.google.com/spreadsheet/viewform?formkey=dHJzUkhOM0FfdWdXbTFGejQ3WmtpS3c6MA&ifq tejto linky] najneskôr do stredy '''22.10.2014, 22:00'''. Vo formulári uveďte čísla '''troch článkov z tohto zoznamu''' v poradí podľa preferencie.
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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=Valouev, A., Schwartz, D. C., Zhou, S., & Waterman, M. S|title=An algorithm for assembly of ordered restriction maps from single DNA molecules | journal = Proceedings of the National Academy of Sciences| volume= 03 | issue=43 (2006) | pages= 15770-15775| url=http://www.pnas.org/content/103/43/15770.full}}
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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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-->
  
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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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4. {{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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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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5. {{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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6. {{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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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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7. {{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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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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8. {{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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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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9. {{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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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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'''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 09:17, 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

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