Research paper presentations

• Tuesday March 22, 2016:

  Elizabeth Trippe
  Christian M. Zmasek, and Sean R. Eddy A simple algorithm to infer gene duplication and speciation events on a gene tree, Bioinformatics (2001) 17 (9): 821-828

  Shelton Griffith
  Liu L, Li Y, Li S, Hu N, He Y, et al. (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012: 251364.

• Thursday March 24, 2016

  Tito Peña-Montenegro
  Yu Peng, Henry C. M. Leung, S. M. Yiu and Francis Y. L. Chin. (2011) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420–1428

• Monday March 28, 2016

  Yecheng Huang
  Can Alkan, Saba Sajjadian & Evan E Eichler, Limitations of next-generation genome sequence assembly Nature Methods,8,61–65(2011), doi:10.1038/nmeth.1527

• Tuesday March 29, 2016

  Josh Watson
  Yong Lin, Jian Li, Hui Shen, Lei Zhang, Christopher J Papasian, Hong-Wen Deng, Comparative Studies of de novo Assembly Tools for Next-generation Sequencing Technologies, Bioinformatics, Advance Access published June 2, 2011

  Shelton Griffith
  Additional biology behind the sequencing technologies in
  Liu L, Li Y, Li S, Hu N, He Y, et al. (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012: 251364.

• Thursday March 31, 2016

  Brigitte Hofmeister
  Ilie L, Fazayeli F, Ilie S (2011) HiTEC: accurate error correction in high-throughput sequencing data. Bioinformatics 27: 295–302.

• Tuesday April 7, 2016

  Hongye Zhou
  Eugene M. McCarthy ∗ and John F. McDonald LTR STRUC: a novel search and identification program for LTR retrotransposons, Bioinformatics, Vol. 19 no. 3 2003, pages 362–367.

• Tuesday April 7, 2016

  Shan Gao
  Erwin L. van Dijk, Hélène Auger, Yan Jaszczyszyn, Claude Thermes, Ten years of next-generation sequencing technology, Trends in Genetics September 2014, Vol. 30, No. 9.

• Monday April 11, 2016

  Shubham Basu
  Berlin et al, Assembling large genomes with single-molecule, sequencing and locality-sensitive hashing, Nature Biotechnology 33, 623-630, 2015.

• Tuesday April 12, 2016

  Norman Hassell
  Chaisson MJ, Pevzner PA (2008) Short read fragment assembly of bacterial genomes. Genome Res 18: 324–330. doi: 10.1101/gr.7088808 http://genome.cshlp.org/content/18/2/324.full.pdf+html

• Thursday April 14, 2016

  Rahil Taujale
  Grabherr et al, (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, Vol 29, 644-652.

  Tao Sheng
  Chengxi Ye, Zhanshan Sam Ma, Charles H Cannon, Mihai Pop, and Douglas W Yu, Exploiting sparseness in de novo genome assembly, BMC Bioinformatics201213(Suppl 6):S1 DOI: 10.1186/1471-2105-13-S6-S1

• Monday April 25, 2016

  Di Chang (The graph construction and simplification stages in)
  Sara El-Metwally, Taher Hamza, Magdi Zakaria, and Mohamed Helmy, Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges, PLoS Computational Biology, 2013 DOI: 10.1371/journal.pcbi.1003345

• Tuesday April 26, 2016

  Swarnali Louha
  Butler et al., ALLPATHS: De novo assembly of whole-genome shotgun microreads, Genome Res. 2008. 18: 810-820.

  Liang-Chin Huang
  Diego Calzolari et al., Search Algorithms as a Framework for the Optimization of Drug Combinations, PLoS Computational Biology, Dec 26, 2008.

• Thursday April 28, 2016

  Jin Wang
  Teo SM, Pawitan Y, Ku CS, Chia KS, Salim A. Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics. 2012 Nov 1;28(21):2711-8. doi: 10.1093/bioinformatics/bts535. Epub 2012 Aug 31.