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

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Journal club papers: Rozdiel medzi revíziami

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Riadok 5: Riadok 5:
 
* Preferences submitted earlier will be considered with higher preference.
 
* Preferences submitted earlier will be considered with higher preference.
  
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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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List of 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
  
 
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.
 
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.
Riadok 15: Riadok 17:
 
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
 
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
  
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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. https://doi.org/10.1038/nature06107  (check also the [http://www.nature.com/nature/journal/v449/n7158/suppinfo/nature06107.html Online supplement])
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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]
  
 
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
 
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
  
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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://doi.org/10.1038/nature02800
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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/
  
 
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
 
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
  
 
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
 
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

Verzia zo dňa a času 09:08, 11. október 2023

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

Please submit your preferences regarding these papers using this form until Wednesday 18.10.2023, 22:00. In the form, include numbers of three papers from this list in the order of preference.

  • Students from the same study program will typically not be in the same group.
  • Preferences submitted earlier will be considered with higher preference.


List of 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

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

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

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

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

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/

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

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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