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6,497 results
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Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.
Jiao D, Ye Y, Tang H. Jiao D, et al. Among authors: ye y. PLoS Comput Biol. 2013;9(3):e1002981. doi: 10.1371/journal.pcbi.1002981. Epub 2013 Mar 21. PLoS Comput Biol. 2013. PMID: 23555216 Free PMC article.
An ORFome assembly approach to metagenomics sequences analysis.
Ye Y, Tang H. Ye Y, et al. J Bioinform Comput Biol. 2009 Jun;7(3):455-71. doi: 10.1142/s0219720009004151. J Bioinform Comput Biol. 2009. PMID: 19507285 Free PMC article.
An ORFome assembly approach to metagenomics sequences analysis.
Ye Y, Tang H. Ye Y, et al. Comput Syst Bioinformatics Conf. 2008;7:3-13. Comput Syst Bioinformatics Conf. 2008. PMID: 19642264
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.
Ye Y, Doak TG. Ye Y, et al. PLoS Comput Biol. 2009 Aug;5(8):e1000465. doi: 10.1371/journal.pcbi.1000465. Epub 2009 Aug 14. PLoS Comput Biol. 2009. PMID: 19680427 Free PMC article.
Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics.
Shah N, Tang H, Doak TG, Ye Y. Shah N, et al. Among authors: ye y. Pac Symp Biocomput. 2011:165-76. doi: 10.1142/9789814335058_0018. Pac Symp Biocomput. 2011. PMID: 21121044
The ecoresponsive genome of Daphnia pulex.
Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL. Colbourne JK, et al. Among authors: ye y. Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761. Science. 2011. PMID: 21292972 Free PMC article.
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.
Wu YW, Ye Y. Wu YW, et al. Among authors: ye y. J Comput Biol. 2011 Mar;18(3):523-34. doi: 10.1089/cmb.2010.0245. J Comput Biol. 2011. PMID: 21385052 Free PMC article.
RAPSearch: a fast protein similarity search tool for short reads.
Ye Y, Choi JH, Tang H. Ye Y, et al. BMC Bioinformatics. 2011 May 15;12:159. doi: 10.1186/1471-2105-12-159. BMC Bioinformatics. 2011. PMID: 21575167 Free PMC article.
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data.
Zhao Y, Tang H, Ye Y. Zhao Y, et al. Among authors: ye y. Bioinformatics. 2012 Jan 1;28(1):125-6. doi: 10.1093/bioinformatics/btr595. Epub 2011 Oct 28. Bioinformatics. 2012. PMID: 22039206 Free PMC article.
Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment.
Ye Y. Ye Y. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2011 Feb 4;2010:153-157. doi: 10.1109/BIBM.2010.5706555. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2011. PMID: 22102981 Free PMC article.
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