97 Publications (Page 2 of 4)
2014
Identification of Diversity-Generating Retroelements in Human MicrobiomesYe, YuzhenInternational Journal of Molecular Sciences, vol. 15, (no. 8), pp. 14234-14246, 2014.
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POSA: a user-driven, interactive multiple protein structure alignment server.Li, Zhanwen⋅Li, Zhanwen⋅Natarajan, Padmaja⋅Natarajan, Padmaja⋅Ye, Yuzhen⋅Ye, Yuzhen⋅Hrabe, Thomas⋅Hrabe, Thomas⋅Godzik, Adam and Godzik, AdamNucleic acids research, vol. 42, (no. Web Server issue), pp. W240-5, 2014/Jul.
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2013
Allosteric inhibition of a zinc-sensing transcriptional repressor: insights into the arsenic repressor (ArsR) family.Campanello, Gregory C⋅Ma, Zhen⋅Grossoehme, Nicholas E⋅Guerra, Alfredo J⋅Ward, Brian P⋅Di Marchi, Richard D⋅Ye, Yuzhen⋅Dann Iii, Charles E and Giedroc, David PJournal of molecular biology, vol. 425, (no. 7), pp. 1143-57, 2013/Apr/12.
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Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.Jiao, Dazhi⋅Ye, Yuzhen and Tang, HaixuPLoS computational biology, vol. 9, (no. 3), pp. e1002981, 2013.
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Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences. e1002981Jiao, Dazhi⋅Ye, Yuzhen and Tang, HaixuPLoS Computational Biology, vol. 9, (no. 3), 2013.
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The gain and loss of chromosomal integron systems in the Treponema species.Wu, Yu-Wei⋅Doak, Thomas and Ye, YuzhenBMC evolutionary biology, vol. 13, pp. 16, 2013.
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2012
A core human microbiome as viewed through 16S rRNA sequence clusters.Huse, Susan⋅Huse, Susan M⋅Ye, Yuzhen⋅Ye, Yuzhen⋅Zhou, Yanjiao⋅Zhou, Yanjiao⋅Fodor, Anthony A and Fodor, Anthony APloS one, vol. 7, (no. 6), pp. e34242, 2012.
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A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community.Wang, Mingjie⋅Wang, Mingjie⋅Ye, Yuzhen⋅Ye, Yuzhen⋅Tang, Haixu and Tang, HaixuJournal of computational biology : a journal of computational molecular cell biology, vol. 19, (no. 6), pp. 814-25, 2012/Jun.
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Artificial functional difference between microbial communities caused by length difference of sequencing reads.Zhang, Quan⋅Doak, Thomas and Ye, YuzhenPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 259-70, 2012.
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Diverse CRISPRs evolving in human microbiomes.Rho, Mina⋅Guttman, David S⋅Rho, Mina⋅Wu, Yu-Wei⋅Wu, Yu-Wei⋅Tang, Haixu⋅Tang, Haixu⋅Doak, Thomas⋅Doak, Thomas G⋅Ye, Yuzhen and Ye, YuzhenPLoS genetics, vol. 8, (no. 6), pp. e1002441, 2012.
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Oral Spirochetes Implicated in Dental Diseases Are Widespread in Normal Human Subjects and Carry Extremely Diverse Integron Gene CassettesWu, Yu-Wei⋅Rho, Mina⋅Doak, Thomas and Ye, YuzhenApplied and Environmental Microbiology, vol. 78, (no. 15), Aug 2012.
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RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data.Zhao, Yongan⋅Tang, Haixu and Ye, YuzhenBioinformatics (Oxford, England), vol. 28, (no. 1), pp. 125-6, 2012/Jan/1.
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Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery.Lee, Chul W⋅Chakravorty, Dhruva K⋅Chang, Feng-Ming J⋅Reyes-Caballero, Hermes⋅Ye, Yuzhen⋅Merz, Kenneth M and Giedroc, David PBiochemistry, vol. 51, (no. 12), pp. 2619-29, 2012/Mar/27.
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Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomicsWu, Yu-Wei⋅Rho, Mina⋅Doak, Thomas and Ye, YuzhenBioinformatics, vol. 28, (no. 18), pp. i363-i369, 2012.
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The "most wanted" taxa from the human microbiome for whole genome sequencing.Fodor, Anthony A⋅Desantis, Todd Z⋅Wylie, Kristine M⋅Badger, Jonathan H⋅Ye, Yuzhen⋅Hepburn, Theresa⋅Hu, Ping⋅Sodergren, Erica⋅Liolios, Konstantinos⋅Huot-Creasy, Heather⋅Birren, Bruce W and Earl, Ashlee MPloS one, vol. 7, (no. 7), pp. e41294, 2012.
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2011
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using I-tuplesWu, Y-W and Ye, YuzhenJournal of Computational Biology, vol. 18, (no. 3), pp. 523-534, 2011.
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A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.Wu, Yu-Wei and Ye, YuzhenJournal of computational biology : a journal of computational molecular cell biology, vol. 18, (no. 3), pp. 523-34, 2011/Mar.
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Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics.Shah, Neethu⋅Tang, Haixu⋅Doak, Thomas and Ye, YuzhenPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 165-76, 2011.
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Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment.Ye, YuzhenProceedings. IEEE International Conference on Bioinformatics and Biomedicine, vol. 2010, pp. 153-157, February 4, 2011.
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RAPSearch: a fast protein similarity search tool for short reads.Ye, Yuzhen⋅Choi, Jeong-Hyeon and Tang, HaixuBMC bioinformatics, vol. 12, (no. 1), pp. 159, 2011.
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The ecoresponsive genome of Daphnia pulex.Colbourne, John K⋅Colbourne, John K⋅Pfrender, Michael E⋅Pfrender, Michael E⋅Gilbert, Donald G⋅Gilbert, Donald⋅Thomas, William Kelley⋅Thomas, W Kelley⋅Tucker, Abraham⋅Tucker, Abraham⋅Oakley, Todd H⋅Oakley, Todd⋅Tokishita, Shinichi⋅Tokishita, Shinichi⋅Aerts, Andrea⋅Aerts, Andrea⋅Arnold, Georg J⋅Arnold, Georg J⋅Basu, Malay Kumar⋅Basu, Malay K⋅Bauer, Darren J⋅Bauer, Darren J⋅Cáceres, Carla E⋅Caceres, Carla⋅Cáceres, Carla E⋅Carmel, Liran⋅Carmel, Liran⋅Casola, Claudio⋅Casola, Claudio⋅Choi, Jeong-Hyeon⋅Choi, Jeong-Hyeon⋅Detter, John C⋅Detter, John C⋅Dong, Qunfeng⋅Dong, Qunfeng⋅Dusheyko, Serge⋅Dusheyko, Serge⋅Eads, Brian D⋅Eads, Brian⋅Fröhlich, Thomas⋅Fröhlich, Thomas⋅Geiler-Samerotte, Kerry A⋅Geiler-Samerotte, Kerry A⋅Gerlach, Daniel⋅Gerlach, Daniel⋅Hatcher, Phil⋅Hatcher, Phil⋅Jogdeo, Sanjuro⋅Jogdeo, Sanjuro⋅Krijgsveld, Jeroen⋅Krijgsveld, Jeroen⋅Kriventseva, Evgenia V⋅Kriventseva, Evgenia V⋅Kultz, Dietmar⋅Kültz, Dietmar⋅Kültz, Dietmar⋅Laforsch, Christian⋅Laforsch, Christian⋅Lindquist, Erika⋅Lindquist, Erika⋅Lopez, Jacqueline⋅Lopez, Jacqueline⋅Manak, J Robert⋅Manak, J R⋅Muller, Jean⋅Muller, Jean⋅Pangilinan, Jasmyn⋅Pangilinan, Jasmyn⋅Patwardhan, Rupali P⋅Patwardhan, Rupali P⋅Pitluck, Samuel⋅Pitluck, Samuel⋅Pritham, Ellen J⋅Pritham, Ellen J⋅Rechtsteiner, Andreas⋅Rechtsteiner, Andreas⋅Rho, Mina⋅Rho, Mina⋅Rogozin, Igor B⋅Rogozin, Igor B⋅Sakarya, Onur⋅Sakarya, Onur⋅Salamov, Asaf⋅Salamov, Asaf⋅Schaack, Sarah⋅Schaack, Sarah⋅Shapiro, Harris⋅Shapiro, Harris⋅Shiga, Yasuhiro⋅Shiga, Yasuhiro⋅Skalitzky, Courtney⋅Skalitzky, Courtney⋅Smith, Zachary⋅Smith, Zachary⋅Souvorov, Alexander⋅Souvorov, Alexander⋅Sung, Way⋅Sung, Way⋅Tang, Zuojian⋅Tang, Zuojian⋅Tsuchiya, Dai⋅Tsuchiya, Dai⋅Tu, Hank⋅Tu, Hank⋅Vos, Harmjan⋅Vos, Harmjan⋅Wang, Mei⋅Wang, Mei⋅Wolf, Yuri I⋅Wolf, Yuri I⋅Yamagata, Hideo⋅Yamagata, Hideo⋅Yamada, Takuji⋅Yamada, Takuji⋅Ye, Yuzhen⋅Ye, Yuzhen⋅Shaw, Joseph R⋅Shaw, Joseph⋅Andrews, Justen⋅Andrews, Justen⋅Crease, Teresa J⋅Crease, Teresa J⋅Tang, Haixu⋅Tang, Haixu⋅Lucas, Susan M⋅Lucas, Susan M⋅Robertson, Hugh M⋅Robertson, Hugh M⋅Bork, Peer⋅Bork, Peer⋅Koonin, Eugene V⋅Koonin, Eugene V⋅Zdobnov, Evgeny⋅Zdobnov, Evgeny M⋅Grigoriev, Igor⋅Grigoriev, Igor V⋅Lynch, Michael⋅Lynch, Michael⋅Boore, Jeffrey L and Boore, Jeffrey LScience (New York, N.Y.), vol. 331, (no. 6017), pp. 555-61, 2011/Feb/4.
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2010
FragGeneScan: predicting genes in short and error-prone reads.Rho, Mina⋅Tang, Haixu and Ye, YuzhenNucleic acids research, vol. 38, (no. 20), pp. e191, 2010/Nov.
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Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignmentYe, Yuzhen2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), vol. 2010, pp. 157, 2010-Dec..
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Metagenomics: Facts and Artifacts, and Computational ChallengesWooley, John C and Ye, YuzhenJournal of Computer Science and Technology, vol. 25, (no. 1), pp. 71-81, 2010.
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