BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. - Wenming Zhao; Jing Wang 003; Ximiao He; Xiaobing Huang; Yongzhi Jiao; Mingtao Dai; Shulin Wei; Jian Fu; Ye Chen; Xiaoyu Ren; Yong Zhang 036; Peixiang Ni; et al. (Nucleic Acids Res., 2004)

ChickVD: a sequence variation database for the chicken genome. - Jing Wang 003; Ximiao He; Jue Ruan; Mingtao Dai; Jie Chen; Yong Zhang 036; Yafeng Hu; Chen Ye; Shengting Li; Lijuan Cong; Lin Fang; Bin Liu; et al. (Nucleic Acids Res., 2005)

SilkDB: a knowledgebase for silkworm biology and genomics. - Jing Wang 003; Qingyou Xia; Ximiao He; Mingtao Dai; Jue Ruan; Jie Chen; Guo Yu; Haifeng Yuan; Yafeng Hu; Ruiqiang Li; Tao Feng; Chen Ye; et al. (Nucleic Acids Res., 2005)

ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun. - Ruiqiang Li; Jia Ye; Songgang Li; Jing Wang 003; Yujun Han; Chen Ye; Jian Wang 065; Huanming Yang; Jun Yu 004; Gane Ka-Shu Wong; Jun Wang 004 (PLoS Comput. Biol., 2005)

KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging. - Zhang Zhang 002; Jun Li 051; Xiao-Qian Zhao; Jun Wang 004; Gane Ka-Shu Wong; Jun Yu 004 (Genom. Proteom. Bioinform., 2006)

TreeFam: a curated database of phylogenetic trees of animal gene families. - Heng Li 002; Avril Coghlan; Jue Ruan; Lachlan James M. Coin; Jean-Karim Hériché; Lara Osmotherly; Ruiqiang Li; Tao Liu; Zhang Zhang 002; Lars Bolund; Gane Ka-Shu Wong; Wei-Mou Zheng; et al. (Nucleic Acids Res., 2006)

WEGO: a web tool for plotting GO annotations. - Jia Ye; Lin Fang; Hongkun Zheng; Yong Zhang 036; Jie Chen; Zengjin Zhang; Jing Wang 003; Shengting Li; Ruiqiang Li; Lars Bolund; Jun Wang 004 (Nucleic Acids Res., 2006)

A cross-species alignment tool (CAT). - Heng Li 002; Liang Guan; Tao Liu; Yiran Guo; Wei-Mou Zheng; Gane Ka-Shu Wong; Jun Wang 004 (BMC Bioinform., 2007)

Snap: an integrated SNP annotation platform. - Shengting Li; Lijia Ma; Heng Li 002; Søren Vang; Yafeng Hu; Lars Bolund; Jun Wang 004 (Nucleic Acids Res., 2007)

PigGIS: Pig Genomic Informatics System. - Jue Ruan; Yiran Guo; Heng Li 002; Yafeng Hu; Fei Song; Xin Huang; Karsten Kristiansen; Lars Bolund; Jun Wang 004 (Nucleic Acids Res., 2007)

FGF: A web tool for Fishing Gene Family in a whole genome database. - Hongkun Zheng; Junjie Shi; Xiaodong Fang; Yuan Li; Søren Vang; Wei Fan; Junyi Wang; Zhang Zhang 002; Wen Wang; Karsten Kristiansen; Jun Wang 004 (Nucleic Acids Res., 2007)

SOAP: short oligonucleotide alignment program. - Ruiqiang Li; Yingrui Li; Karsten Kristiansen; Jun Wang 004 (Bioinform., 2008)

TreeFam: 2008 Update. - Jue Ruan; Heng Li 002; Zhongzhong Chen; Avril Coghlan; Lachlan James M. Coin; Yiran Guo; Jean-Karim Hériché; Yafeng Hu; Karsten Kristiansen; Ruiqiang Li; Tao Liu; Alan Moses; et al. (Nucleic Acids Res., 2008)

SOAP2: an improved ultrafast tool for short read alignment. - Ruiqiang Li; Chang Yu; Yingrui Li; Tak Wah Lam; Siu-Ming Yiu; Karsten Kristiansen; Jun Wang 004 (Bioinform., 2009)

The YH database: the first Asian diploid genome database. - Guoqing Li; Lijia Ma; Chao Song; Zhentao Yang; Xiulan Wang; Hui Huang; Yingrui Li; Ruiqiang Li; Xiuqing Zhang; Huanming Yang; Jian Wang 065; Jun Wang 004 (Nucleic Acids Res., 2009)

Evolutionary Transients in the Rice Transcriptome. - Jun Wang 004; Jianguo Zhang; Ruiqiang Li; Hongkun Zheng; Jun Li 051; Yong Zhang 036; Heng Li 002; Peixiang Ni; Songgang Li; Shengting Li; Jingqiang Wang; Dongyuan Liu; et al. (Genom. Proteom. Bioinform., 2010)

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology. - Jun Duan; Ruiqiang Li; Daojun Cheng; Wei Fan; Xingfu Zha; Tingcai Cheng; Yuqian Wu; Jun Wang 004; Kazuei Mita; Zhonghuai Xiang; Qingyou Xia (Nucleic Acids Res., 2010)

Estimation of allele frequency and association mapping using next-generation sequencing data. - Su Yeon Kim; Kirk E. Lohmueller; Anders Albrechtsen; Yingrui Li; Thorfinn Korneliussen; Geng Tian; Niels Grarup; Tao Jiang; Gitte Andersen; Daniel Witte; Torben Jørgensen; Torben Hansen; et al. (BMC Bioinform., 2011)

An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis. - Lachlan James M. Coin; Dandan Cao; Jingjing Ren; Xianbo Zuo; Liangdan Sun; Sen Yang; Xuejun Zhang; Yong Cui; Yingrui Li; Xin Jin; Jun Wang 004 (Bioinform., 2012)

SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads. - Jikun Wu; Wenqian Zhang; Songbo Huang; Zengquan He; Yanbing Cheng; Jun Wang 004; Tak Wah Lam; Zhiyu Peng; Siu-Ming Yiu (Bioinform., 2013)

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments. - Bo Wen; Shaohang Xu; Gloria M. Sheynkman; Qiang Feng; Liang Lin; Quanhui Wang; Xun Xu; Jun Wang 004; Siqi Liu (Bioinform., 2014)

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. - Yinlong Xie; Gengxiong Wu; Jingbo Tang; Ruibang Luo; Jordan Patterson; Shanlin Liu; Weihua Huang; Guangzhu He; Shengchang Gu; Shengkang Li; Xin Zhou; Tak Wah Lam; et al. (Bioinform., 2014)

Addendum: Enterotypes of the human gut microbiome. - Manimozhiyan Arumugam; Jeroen Raes; Eric Pelletier; Denis Le Paslier; Takuji Yamada; Daniel R. Mende; Gabriel R. Fernandes; Julien Tap; Thomas Brüls; Jean-Michel Batto; Marcelo Bertalan; Natalia Borruel; et al. (Nat., 2014)

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC). - Ruibang Luo; Jeanno Cheung; Edward Wu; Heng Wang; Sze-Hang Chan; Wai-Chun Law; Guangzhu He; Chang Yu; Chi-Man Liu; Dazong Zhou; Yingrui Li; Ruiqiang Li; et al. (BMC Bioinform., 2015)

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. - Kristoffer Forslund; Falk Hildebrand; Trine Nielsen; Gwen Falony; Emmanuelle Le Chatelier; Shinichi Sunagawa; Edi Prifti; Sara Vieira-Silva; Valborg Gudmundsdottir; Helle Krogh Pedersen; Manimozhiyan Arumugam; Karsten Kristiansen; et al. (Nat., 2015)

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. - Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; Jette Bork-Jensen; et al. (Nat., 2017)

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. - Maria Luisa Matey-Hernandez; Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; et al. (BMC Bioinform., 2018)

Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios. - Mengyang Xu; Lidong Guo; Xiao Du; Lei Li; Brock A. Peters; Li Deng; Ou Wang; Fang Chen; Jun Wang 004; Zhesheng Jiang; Jinglin Han; Ming Ni; et al. (Bioinform., 2021)