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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<!-- Svoje preferencie ohľadom článkov na journal club odovzdajte pomocou '''[https://docs.google.com/forms/d/e/1FAIpQLSc_smiqzJVw0h0Gwgb1wIgEXF07CIR9Fu4s4VLNIwC96HZAxw/viewform tohto formulára]''' najneskôr do stredy '''24.10.2017, 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])
  
Detaily ohľadom požiadavok na journal club nájdete v [[Pravidlá#Journal club|pravidlách predmetu]].
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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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1. {{cite journal| author=David M, Dursi LJ, Yao D, Boutros PC, Simpson JT | title=Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data| journal = Bioinformatics | year = 2016 | url=http://bioinformatics.oxfordjournals.org/content/early/2016/09/07/bioinformatics.btw569.abstract}} '''Čítajú''' Baláž Bérešová Kováč Psota Smoľak Szelleová
 
  
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 | url = http://bioinformatics.oxfordjournals.org/content/23/13/i289 }} '''Čítajú''' Fabianová Forbak Husár Mišíková Šomodi Szendy
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'''Groups:'''
  
3. {{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 | doi=10.1038/nature06107 | url=http://llama.mshri.on.ca/courses/Biophysics205/Papers/Wapinski_2007.pdf}} (pozrite aj [http://www.nature.com/nature/journal/v449/n7158/suppinfo/nature06107.html Online supplement]) '''Čítajú''' Bakoš Bilisics Heinz Kačír Kolková Kotrlová Százová
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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'''
  
4. {{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 | url= http://www.pnas.org/content/104/49/19428}}  '''Čítajú''' Jamrichová Koza Mašlej Ondriašová Trubač Zeman
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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'''
  
5. {{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 |  doi=10.1038/nature02800 | url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006441/ }} '''Čítajú''' Borbová Brojo Bujna Búran Hadžega Hoľa Kellner
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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'''
  
7. {{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 | doi=10.1016/j.jmb.2003.12.041 | url=http://people.cs.ubc.ca/~hutter/papers/jmb04-rna-ssd.pdf }}  '''Čítajú''' Adamec Harmanová Ištok Krajčiová Kvačkay Mayerová Mudroch
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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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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'''
  
==Nepoužité články==
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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'''
  
6. {{cite journal| author=Heger, Andreas, and Liisa Holm | title=Exhaustive enumeration of protein domain families | journal= Journal of molecular biology | year=2003 | volume=328 | issue=3 | pages=749-67 | url= https://www.researchgate.net/profile/Liisa_Holm/publication/10794155_Exhaustive_Enumeration_of_Protein_Domain_Families/links/55d35f0608ae0b8f3ef92c1b.pdf }}
 
  
8. {{cite journal| author=Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, Lin ZY, Breitkreutz BJ, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, Qin ZS, Pawson T, Gingras AC, Nesvizhskii AI, Tyers M.| title=A global protein kinase and phosphatase interaction network in yeast | journal=Science | year= 2010 | volume= 328 | issue=5981 | pages= 1043-6 | doi=10.1126/science.1176495 | url=https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20489023/ }}  (pozrite aj [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983991/bin/NIHMS345024-supplement.pdf Online supplement])
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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