97 Publications (Page 3 of 4)
2009
An ORFome assembly approach to metagenomics sequences analysis.
Ye, Yuzhen and Tang, Haixu
Journal of bioinformatics and computational biology, vol. 7, (no. 3), pp. 455-71, 2009/Jun. | Journal Article
 
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes
Ye, Yuzhen⋅Doak, Thomas and Ouzounis, Christos A
PLoS Computational Biology, vol. 5, (no. 8), pp. e1000465, 2009. | Journal Article
 
Genetic Stability of Progeny from an Artificial Allotetraploid Carp Using Sperm from Five Fish Species
Ye, Yuzhen⋅Wang, Zhongwei⋅Zhou, Jianfeng and Wu, Qingjiang
Biochemical genetics, vol. 47, (no. 7-8), pp. 539, 2009-Aug. | Journal Article
 
Metagenomics: Facts and Artifacts, and Computational Challenges*
Wooley, John C and Ye, Yuzhen
Journal of computer science and technology, vol. 25, (no. 1), pp. 71-81, January 2009. | Journal Article
2008
An ORFome assembly approach to metagenomics sequences analysis.
Ye, Yuzhen and Tang, Haixu
Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference, vol. 7, pp. 3-13, 2008. | Journal Article
 
Novel genes dramatically alter regulatory network topology in amphioxus.
Zhang, Qing⋅Zmasek, Christian M⋅Dishaw, Larry J⋅Mueller, M. G⋅Ye, Yuzhen⋅Litman, Gary W and Godzik, Adam
Genome Biology [NLM - MEDLINE], vol. 9, (no. 8), pp. R123, 2008. | Journal Article
 
The amphioxus genome illuminates vertebrate origins and cephalochordate biology.
Holland, Linda Z⋅Albalat, Ricard⋅Azumi, Kaoru⋅Benito-Gutiérrez, Elia⋅Blow, Matthew J⋅Bronner-Fraser, Marianne⋅Brunet, Frederic⋅Butts, Thomas⋅Candiani, Simona⋅Dishaw, Larry J⋅Ferrier, David⋅Garcia-Fernàndez, Jordi⋅Gibson Brown, Jeremy J⋅Gissi, Carmela⋅Godzik, Adam⋅Hallböök, Finn⋅Hirose, Dan⋅Hosomichi, Kazuyoshi⋅Ikuta, Tetsuro⋅Inoko, Hidetoshi⋅Kasahara, Masanori⋅Kasamatsu, Jun⋅Kawashima, Takeshi⋅Kimura, Ayuko⋅Kobayashi, Masaaki⋅Kozmik, Zbyněk⋅Kubokawa, Kaoru⋅Laudet, Vincent⋅Litman, Gary W⋅Mc Hardy, Alice⋅Meulemans, Daniel⋅Nonaka, Masaru⋅Olinski, Robert P⋅Pancer, Zeev⋅Pennacchio, Len A⋅Pestarino, Mario⋅Rast, Jonathan⋅Rigoutsos, Isidore⋅Robinson-Rechavi, Marc⋅Roch, Graeme⋅Saiga, Hidetoshi⋅Sasakura, Yasunori⋅Satake, Masanobu⋅Satou, Yutaka⋅Schubert, Michael⋅Sherwood, Nancy⋅Shiina, Takashi⋅Takatori, Naohito⋅Tello, Javier⋅Vopalensky, Pavel⋅Wada, Shuichi⋅Xu, Anlong⋅Ye, Yuzhen⋅Yoshida, Keita⋅Yoshizaki, Fumiko⋅Yu, Jr Kai⋅Zhang, Qing⋅Zmasek, Christian M⋅de Jong, Pieter J⋅Osoegawa, Kazutoyo⋅Putnam, Nicholas H⋅Rokhsar, Dan⋅Satoh, Noriyuki and Holland, Peter
Genome research, vol. 18, (no. 7), pp. 1100-11, 2008/Jul. | Journal Article
 
TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model.
Veeramalai, Mallika⋅Ye, Yuzhen and Godzik, Adam
BMC bioinformatics, vol. 9, pp. 358, 2008. | Journal Article
 
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model
Veeramalai, Mallika⋅Veeramalai, Mallika⋅Ye, Yuzhen⋅Ye, Yuzhen⋅Godzik, Adam and Godzik, Adam
BMC Bioinformatics, vol. 9, pp. 358-358, 2008. | Journal Article
2007
Subunit-Specific Roles of Glycine-Binding Domains in Activation of NR1/NR3 N-Methyl-d-aspartate Receptors
Awobuluyi, Marc⋅Yang, Jin⋅Ye, Yuzhen⋅Chatterton, Jon⋅Godzik, Adam⋅Lipton, Stuart and Zhang, Dongxian
Molecular Pharmacology, vol. 71, (no. 1), pp. 122, 20070101. | Journal Article
 
Surprising complexity of the ancestral apoptosis network.
Zmasek, Christian M⋅Zhang, Qing⋅Ye, Yuzhen and Godzik, Adam
Genome Biology [NLM - MEDLINE], vol. 8, (no. 10), pp. R226, 2007. | Journal Article
2006
Flexible Structural Neighborhood--a database of protein structural similarities and alignments
Li, Zhanwen⋅Ye, Yuzhen and Godzik, Adam
Nucleic Acids Research, vol. 34, (no. S1), pp. D277, 2006. | Journal Article
 
Flexible Structural Neighborhood--a database of protein structural similarities and alignments
Li, Zhanwen⋅Ye, Yuzhen and Godzik, Adam
Nucleic Acids Research, vol. 34, (no. S1), pp. D277-80, Jan 2006. | Journal Article
 
Flexible Structural Neighborhood--a database of protein structural similarities and alignments.
Li, Zhanwen⋅Ye, Yuzhen and Godzik, Adam
Nucleic acids research, vol. 34, (no. Database issue), pp. D277-80, 2006/Jan/1. | Journal Article
 
Flexible Structural Neighborhood--a database of protein structural similarities and alignments.
Li, Zhanwen⋅Ye, Yuzhen and Godzik, Adam
Nucleic acids research., vol. 34, pp. D277-D280, 2006. | Journal Article
 
Flexible Structural Neighborhood-a database of protein structural similarities and alignments
Li, Zhanwen⋅Ye, Yuzhen and Godzik, Adam
Nucleic Acids Research, vol. 34, pp. D277-D280, 2006. | Journal Article
 
Genetic Structure and Low-genetic Diversity Suggesting the Necessity for Conservation of the Chinese Longsnout Catfish, Leiocassis longirostris (Pisces: Bagriidae)
Wang, Zhongwei⋅Zhou, Jianfeng⋅Ye, Yuzhen⋅Wei, Qiwei and Wu, Qingjiang
Environmental Biology of Fishes, vol. 75, (no. 4), pp. 463, 20060400. | Journal Article
 
Modeling and analyzing three-dimensional structures of human disease proteins.
Ye, Yuzhen⋅Li, Zhanwen and Godzik, Adam
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 439-50, 2006. | Journal Article
2005
Automatic detection of subsystem/pathway variants in genome analysis
Ye, Yuzhen⋅Osterman, Andrei⋅Overbeek, Ross and Godzik, Adam
Bioinformatics, vol. 21, pp. i478-i486, 2005. | Journal Article
 
Automatic detection of subsystem/pathway variants in genome analysis
Ye, Yuzhen⋅Osterman, Andrei⋅Overbeek, Ross and Godzik, Adam
Bioinformatics, vol. 21, (no. S1), pp. i478, 2005. | Journal Article
 
Automatic detection of subsystem/pathway variants in genome analysis
Ye, Yuzhen⋅Osterman, Andrei⋅Overbeek, Ross and Godzik, Adam
Bioinformatics, vol. 21, (no. S1), pp. i478-86, Jun 2005. | Journal Article
 
Automatic detection of subsystem/pathway variants in genome analysis.
Ye, Yuzhen⋅Osterman, Andrei⋅Overbeek, Ross and Godzik, Adam
Bioinformatics (Oxford, England), vol. 21 Suppl 1, pp. i478-86, 2005/Jun. | Journal Article
 
Multiple flexible structure alignment using partial order graphs
Ye, Yuzhen and Godzik, Adam
Bioinformatics, vol. 21, (no. 10), pp. 2362-9, May 15, 2005. | Journal Article
 
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Overbeek, Ross⋅Begley, Tadhg P⋅Butler, Ralph M⋅Choudhuri, Jomuna V⋅Chuang, Han-Yu⋅Cohoon, Matthew⋅De Crécy Lagard, Valérie⋅Diaz, Naryttza⋅Disz, Terry⋅Edwards, Robert⋅Fonstein, Michael⋅Frank, Ed D⋅Gerdes, Svetlana⋅Glass, Elizabeth M⋅Goesmann, Alexander⋅Hanson, Andrew D⋅Iwata Reuyl, Dirk⋅Jensen, Roy⋅Jamshidi, Neema⋅Krause, Lutz⋅Kubal, Michael⋅Larsen, Niels⋅Linke, Burkhard⋅Mc Hardy, Alice⋅Meyer, Folker⋅Neuweger, Heiko⋅Olsen, Gary⋅Olson, Robert⋅Osterman, Andrei⋅Portnoy, Vasiliy⋅Pusch, Gordon D⋅Rodionov, Dmitry A⋅Rückert, Christian⋅Steiner, Jason⋅Stevens, Rick⋅Thiele, Ines⋅Vassieva, Olga⋅Ye, Yuzhen⋅Zagnitko, Olga and Vonstein, Veronika
Nucleic acids research, vol. 33, (no. 17), pp. 5691-702, 2005. | Journal Article
2004
Comparative analysis of protein domain organization.
Ye, Yuzhen and Godzik, Adam
Genome research, vol. 14, (no. 3), pp. 343-353, March 2004. | Journal Article