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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Zadelenie študentov do skupín:  
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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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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 }} '''Čítajú Herencsár, B.Ivan, Šuníková, F.Marek, Gergeľ, Gibaštíková, Mizerák'''
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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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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}} '''Čítajú  Račko, Repka, Racik, Šušuková, Lacko, Štibraný, Hlavenková'''
 
  
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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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'''Groups:'''
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patterns. | journal=Proc Natl Acad Sci U S A | year= 1998 | volume= 95 | issue= 25 | pages= 14863-8 | pmid=9843981 }} '''Čítajú Sternmüller, Pukancová, Kotrlová, Chripko, Jusko, Filipčík, Bohunský'''
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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 }} '''Čítajú  Rapčík, Miniariková, Bielik, Byrtus, Fečík, Baláž, Zamba'''
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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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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 }} '''Čítajú  '''
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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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==Nevybrané články==
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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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1. {{cite journal| author=Zerbino DR, Birney E| title=Velvet: algorithms for de novo short read assembly using de Bruijn graphs. | journal=Genome Res | year= 2008 | volume= 18 | issue= 5 | pages= 821-0 | pmid=18349386 | doi=10.1101/gr.074492.107 }}
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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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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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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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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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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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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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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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'''Unused papers:'''
  
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9. {{cite journal |author=Bystroff C, Thorsson V, Baker D |title=HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins |journal=J. Mol. Biol. |volume=301 |issue=1 |pages=173–90 |year=2000 |month=August |pmid=10926500 |doi=10.1006/jmbi.2000.3837 |url=http://www.bioinfo.rpi.edu/bystrc/pdf/JMB301p173_2000.pdf}}
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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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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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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

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