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  CSE 428,  Sp '18:  Approximate Schedule
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Schedule details will evolve as we go.

    Due Lecture Topic Reading
Week 1
3/26-3/30		 Tu   Introduction & Overview Papers Below
Th
Week 2
4/2-4/6		 Tu  
Th
Week 3
4/9-4/13		 Tu   Work !  
Th
Week 4
4/16-4/20		 Tu   Work !!
Th
Week 5
4/23-4/27		 Tu   Work !!!
Th
Week 6
4/30-5/4		 Tu   Work !!!!
Th
Week 7
5/7-5/11		 Tu   Work !!!!!
Th
Week 8
5/14-5/18		 Tu   Work !!!!!!
Th
Week 9
5/21-5/25		 Tu   Work !!!!!!!
Th
Week 10
5/28-6/1		 Tu   Demos?
Th

References:  Here is a sampling of relevant literature. If you find other interesting articles, please share them.

Most links below take you to PubMed, the NIH bibliographic database. Usually, but counterintuitively, from a PubMed abstract you click the icon of the publisher (or sometimes the icon saying "UW article online") to get to the actual article.

padlock   Journal access: Some of the journals and articles cited below are completely open access, or are freely available via PubMed Central (look for the "Free in PMC" icon).  Electronic access to other cited articles is generally free from on-campus IP addresses.  For off-campus access, follow the "[offcampus]" links or look at the UW library "proxy server" instructions.  Let me know if none of these work for you. padlock

References -- Introduction & Overview: Some background:

  1. WS Noble, "A quick guide to organizing computational biology projects." PLoS Comput. Biol., 5, #7 (2009) e1000424.
  2. Wetterstrand KA. DNA Sequencing Costs: Data from the NHGRI Large-Scale Genome Sequencing Program. Available at: http://www.genome.gov/sequencingcosts/ Accessed 30 Mar 2012.
  3. V Makinen, D Belazzougui, F Cunial, AI Tomescu, Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing, Cambridge, 2015. (Amazon)

References -- SeqBias: Technical Biases in RNASeq

  1. DC Jones, WL Ruzzo, X Peng, MG Katze, "A new approach to bias correction in RNA-Seq." Bioinformatics, 28, #7 (2012) 921-8. [offcampus]

References -- ASE: Allele-Specific Expression

  1. JC Knight, "Allele-specific gene expression uncovered." Trends Genet., 20, #3 (2004) 113-6. [offcampus]
  2. CG Bell, S Beck, "Advances in the identification and analysis of allele-specific expression." Genome Med, 1, #5 (2009) 56. [offcampus]
  3. J Rozowsky, A Abyzov, J Wang, P Alves, D Raha, A Harmanci, J Leng, R Bjornson, Y Kong, N Kitabayashi, et 4 al., "AlleleSeq: analysis of allele-specific expression and binding in a network framework." Mol. Syst. Biol., 7, (2011) 522. [offcampus]
  4. Z Liu, J Yang, H Xu, C Li, Z Wang, Y Li, X Dong, Y Li, "Comparing computational methods for identification of allele-specific expression based on next generation sequencing data." Genet. Epidemiol., 38, #7 (2014) 591-8. [offcampus]
  5. DL Wood, K Nones, A Steptoe, A Christ, I Harliwong, F Newell, TJ Bruxner, D Miller, N Cloonan, SM Grimmond, "Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data." PLoS ONE, 10, #5 (2015) e0126911.
  6. A Conesa, P Madrigal, S Tarazona, D Gomez-Cabrero, A Cervera, A McPherson, MW Szcześniak, DJ Gaffney, LL Elo, X Zhang, et 1 al., "A survey of best practices for RNA-seq data analysis." Genome Biol., 17, (2016) 13. [offcampus]

References -- Phasing: Which Variants Lie on the Same Chromosome?

  1. https://en.wikipedia.org/wiki/Haplotype_estimation
  2. http://www.chromosomechronicles.com/2009/09/08/phasing-determining-which-snps-are-inherited-together/ [offcampus]

References -- Reviews: Some Review articles on genome assembly:

  1. K Paszkiewicz, DJ Studholme, "De novo assembly of short sequence reads." Brief. Bioinformatics, 11, #5 (2010) 457-72. [offcampus]
  2. SD Jackman, I Birol, "Assembling genomes using short-read sequencing technology." Genome Biol., 11, #1 (2010) 202. [offcampus]
  3. J Henson, G Tischler, Z Ning, "Next-generation sequencing and large genome assemblies." Pharmacogenomics, 13, #8 (2012) 901-15. [offcampus]
  4. JR Miller, S Koren, G Sutton, "Assembly algorithms for next-generation sequencing data." Genomics, 95, #6 (2010) 315-27. [offcampus]
  5. JT Simpson, M Pop, "The Theory and Practice of Genome Sequence Assembly." Annu Rev Genomics Hum Genet, 16, (2015) 153-72. [offcampus]

References -- DeBruijn: DeBruijn Graphs and Euler Tours:

  1. PA Pevzner, H Tang, MS Waterman, "An Eulerian path approach to DNA fragment assembly." Proc. Natl. Acad. Sci. U.S.A., 98, #17 (2001) 9748-53. [offcampus]
  2. DR Zerbino, E Birney, "Velvet: algorithms for de novo short read assembly using de Bruijn graphs." Genome Res., 18, #5 (2008) 821-9. [offcampus]
  3. MJ Chaisson, D Brinza, PA Pevzner, "De novo fragment assembly with short mate-paired reads: Does the read length matter?" Genome Res., 19, #2 (2009) 336-46. [offcampus]
  4. PE Compeau, PA Pevzner, G Tesler, "How to apply de Bruijn graphs to genome assembly." Nat. Biotechnol., 29, #11 (2011) 987-91. [offcampus]
  5. JT Simpson, K Wong, SD Jackman, JE Schein, SJ Jones, I Birol, "ABySS: a parallel assembler for short read sequence data." Genome Res., 19, #6 (2009) 1117-23. [offcampus]
  6. R Luo, B Liu, Y Xie, Z Li, W Huang, J Yuan, G He, Y Chen, Q Pan, Y Liu, et 20 al., "SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler." Gigascience, 1, #1 (2012) 18. [offcampus] (Erratum: Gigascience. 2015 Jul 8;4:30. doi: 10.1186/s13742-015-0069-2. eCollection 2015, PMID: 26161257)
  7. Y Safonova, A Bankevich, PA Pevzner, "dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes." J. Comput. Biol., 22, #6 (2015) 528-45. [offcampus]

References -- String Graphs: Fragment assembly via string graphs:

  1. EW Myers, "The fragment assembly string graph." Bioinformatics, 21 Suppl 2, (2005) ii79-85. [offcampus]
  2. JT Simpson, R Durbin, "Efficient construction of an assembly string graph using the FM-index." Bioinformatics, 26, #12 (2010) i367-73. [offcampus]
  3. JT Simpson, R Durbin, "Efficient de novo assembly of large genomes using compressed data structures." Genome Res., 22, #3 (2012) 549-56. [offcampus]
  4. I Ben-Bassat, B Chor, "String graph construction using incremental hashing." Bioinformatics, 30, #24 (2014) 3515-23. [offcampus]

References -- String Indices: Suffix Arrays, BWT, FM-index, etc.:

  1. U Manber, E Myers (1990). Suffix arrays: a new method for on-line string searches. First Annual ACM-SIAM Symposium on Discrete Algorithms. pp. 319-327.
  2. U Manber, E Myers (1991), Suffix arrays: A new method for on-line string searches. http://webglimpse.net/pubs/suffix.pdf [offcampus]
  3. https://discuss.codechef.com/questions/21385/a-tutorial-on-suffix-arrays [offcampus]
  4. https://en.wikipedia.org/wiki/Suffix_array
  5. Ben Langmead's BWT/FM-index tutorial: http://www.cs.jhu.edu/~langmea/resources/bwt_fm.pdf

References -- Evaluation: How good is your assembly?:

  1. D Earl, K Bradnam, J St John, A Darling, D Lin, J Fass, HO Yu, V Buffalo, DR Zerbino, M Diekhans, et 61 al., "Assemblathon 1: a competitive assessment of de novo short read assembly methods." Genome Res., 21, #12 (2011) 2224-41. [offcampus]
  2. KR Bradnam, JN Fass, A Alexandrov, P Baranay, M Bechner, I Birol, S Boisvert, JA Chapman, G Chapuis, R Chikhi, et 81 al., "Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species." Gigascience, 2, #1 (2013) 10. [offcampus]
  3. G Narzisi, B Mishra, "Comparing de novo genome assembly: the long and short of it." PLoS ONE, 6, #4 (2011) e19175.
  4. W Zhang, J Chen, Y Yang, Y Tang, J Shang, B Shen, "A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies." PLoS ONE, 6, #3 (2011) e17915.
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