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Alterations in subgingival microbiota during full-fixed appliance orthodontic treatment-A prospective study.
Chen, Isaac; Chung, Jennifer; Vella, Raven; Weinstock, George M; Zhou, Yanjiao; Jheon, Andrew H Orthodontics & craniofacial research 2021 Sep;
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Introduction to mammalian genome special issue: the microbiome in human health and disease.
Pavlovic, Guillaume; Seong, Je Kyung; Weinstock, George M Mammalian genome : official journal of the International Mammalian Genome Society 2021 Jun;
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Circadian rhythms and the gut microbiome synchronize the host's metabolic response to diet.
Gutierrez Lopez, Diana E; Lashinger, Laura M; Weinstock, George M; Bray, Molly S Cell metabolism 2021 May;33(5):873-887
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Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice.
Lee, Se-Hoon; Cho, Sung-Yup; Yoon, Youngmin; Park, Changho; Sohn, Jinyoung; Jeong, Jin-Ju; Jeon, Bu-Nam; Jang, Mongjoo; An, Choa; Lee, Suro; Kim, Yun Yeon; Kim, Gihyeon; Kim, Sujeong; Kim, Yunjae; Lee, Gwang Bin; Lee, Eun Ju; Kim, Sang Gyun; Kim, Hong Sook; Kim, Yeongmin; Kim, Hyun; Yang, Hyun-Suk; Kim, Sarang; Kim, Seonggon; Chung, Hayung; Moon, Myeong Hee; Nam, Myung Hee; Kwon, Jee Young; Won, Sungho; Park, Joon-Suk; Weinstock, George M; Lee, Charles; Yoon, Kyoung Wan; Park, Hansoo Nature microbiology 2021 Mar;6(3):277-288
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Supraglottic Lung Microbiome Taxa Are Associated with Pulmonary Abnormalities in an HIV Longitudinal Cohort.
Zhou, Jin J; Zhai, Jing; Zhou, Hua; Chen, Yin; Guerra, Stefano; Robey, Ian; Weinstock, George M; Weinstock, Erica; Dong, Qunfeng; Knox, Kenneth S; Twigg, Homer L American journal of respiratory and critical care medicine 2020 Dec;202(12):1727-1731
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Deciphering functional redundancy in the human microbiome.
Tian, Liang; Wang, Xu-Wen; Wu, Ang-Kun; Fan, Yuhang; Friedman, Jonathan; Dahlin, Amber; Waldor, Matthew K; Weinstock, George M; Weiss, Scott T; Liu, Yang-Yu Nature communications 2020 Dec;11(1):6217
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Genetic Basis of Aerobically Supported Voluntary Exercise: Results from a Selection Experiment with House Mice.
Hillis, David A; Yadgary, Liran; Weinstock, George M; Pardo-Manuel de Villena, Fernando; Pomp, Daniel; Fowler, Alexandra S; Xu, Shizhong; Chan, Frank; Garland, Theodore Genetics 2020 Nov;216(3):781-804
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Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients.
Spakowicz, Daniel; Lou, Shaoke; Barron, Brian; Gomez, Jose L; Li, Tianxiao; Liu, Qing; Grant, Nicole; Yan, Xiting; Hoyd, Rebecca; Weinstock, George; Chupp, Geoffrey L; Gerstein, Mark Genome biology 2020 Jun;21(1):150
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Longitudinal Analysis of Serum Cytokine Levels and Gut Microbial Abundance Links IL-17/IL-22 with Clostridia and Insulin Sensitivity in Humans.
Zhou, Xin; Johnson, Jethro S; Spakowicz, Daniel; Zhou, Wenyu; Zhou, Yanjiao; Sodergren, Erica; Snyder, Michael; Weinstock, George M Diabetes 2020 May;
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Improving Characterization of Understudied Human Microbiomes Using Targeted Phylogenetics.
Rosa, Bruce A; Mihindukulasuriya, Kathie; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Martin, John; Snowden, Caroline; Dunne, William Michael; Weinstock, George M; Burnham, C A; Mitreva, Makedonka mSystems 2020 Feb;5(1):
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Differences in Gut Microbiome in Hospitalized Immunocompetent vs. Immunocompromised Children, Including Those With Sickle Cell Disease.
Mohandas, Sindhu; Soma, Vijaya L; Tran, Thi Dong Binh; Sodergren, Erica; Ambooken, Tresa; Goldman, David L; Weinstock, George; Herold, Betsy C Frontiers in pediatrics 2020 Jan;8583446
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The upper-airway microbiota and loss of asthma control among asthmatic children.
Zhou, Yanjiao; Jackson, Daniel; Bacharier, Leonard B; Mauger, David; Boushey, Homer; Castro, Mario; Durack, Juliana; Huang, Yvonne; Lemanske, Robert F; Storch, Gregory A; Weinstock, George M; Wylie, Kristine; Covar, Ronina; Fitzpatrick, Anne M; Phipatanakul, Wanda; Robison, Rachel G; Beigelman, Avraham Nature communications 2019 Dec;10(1):5714
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Colon Cancer Prevention with Walnuts: A Longitudinal Study in Mice from the Perspective of a Gut Enterotype-like Cluster.
Chen, Yanfei; Nakanishi, Masako; Bautista, Eddy J; Qendro, Veneta; Sodergren, Erica; Rosenberg, Daniel W; Weinstock, George M Cancer prevention research (Philadelphia, Pa.) 2019 Dec;
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Characterization of Mucosal Dysbiosis of Early Colonic Neoplasia.
Hong, Bo-Young; Ideta, Takayasu; Lemos, Bruno S; Igarashi, Yuichi; Tan, Yuliana; DiSiena, Michael; Mo, Allen; Birk, John W; Forouhar, Faripour; Devers, Thomas J; Weinstock, George M; Rosenberg, Daniel W NPJ Precision Oncology 2019 Nov;310
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Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis.
Johnson, Jethro S; Spakowicz, Daniel J; Hong, Bo-Young; Petersen, Lauren M; Demkowicz, Patrick; Chen, Lei; Leopold, Shana R; Hanson, Blake M; Agresta, Hanako O; Gerstein, Mark; Sodergren, Erica; Weinstock, George M Nature communications 2019 Nov;10(1):5029
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Microbiome Signatures Associated with Steatohepatitis and Moderate to Severe Fibrosis in Children With Nonalcoholic Fatty Liver Disease.
Schwimmer, Jeffrey B; Johnson, Jethro S; Angeles, Jorge E; Behling, Cynthia; Belt, Patricia H; Borecki, Ingrid; Bross, Craig; Durelle, Janis; Goyal, Nidhi P; Hamilton, Gavin; Holtz, Mary L; Lavine, Joel E; Mitreva, Makedonka; Newton, Kimberly P; Pan, Amy; Simpson, Pippa M; Sirlin, Claude B; Sodergren, Erica; Tyagi, Rahul; Yates, Katherine P; Weinstock, George; Salzman, Nita H Gastroenterology 2019 Jun;
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A longitudinal big data approach for precision health.
Schüssler-Fiorenza Rose, Sophia Miryam; Contrepois, Kévin; Moneghetti, Kegan J; Zhou, Wenyu; Mishra, Tejaswini; Mataraso, Samson; Dagan-Rosenfeld, Orit; Ganz, Ariel B; Dunn, Jessilyn; Hornburg, Daniel; Rego, Shannon; Perelman, Dalia; Ahadi, Sara; Sailani, M Reza; Zhou, Yanjiao; Leopold, Shana R; Chen, Jieming; Ashland, Melanie; Christle, Jeffrey W; Avina, Monika; Limcaoco, Patricia; Ruiz, Camilo; Tan, Marilyn; Butte, Atul J; Weinstock, George M; Slavich, George M; Sodergren, Erica; McLaughlin, Tracey L; Haddad, Francois; Snyder, Michael P Nature medicine 2019 May;25(5):792-804
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Longitudinal multi-omics of host-microbe dynamics in prediabetes.
Zhou, Wenyu; Sailani, M Reza; Contrepois, Kévin; Zhou, Yanjiao; Ahadi, Sara; Leopold, Shana R; Zhang, Martin J; Rao, Varsha; Avina, Monika; Mishra, Tejaswini; Johnson, Jethro; Lee-McMullen, Brittany; Chen, Songjie; Metwally, Ahmed A; Tran, Thi Dong Binh; Nguyen, Hoan; Zhou, Xin; Albright, Brandon; Hong, Bo-Young; Petersen, Lauren; Bautista, Eddy; Hanson, Blake; Chen, Lei; Spakowicz, Daniel; Bahmani, Amir; Salins, Denis; Leopold, Benjamin; Ashland, Melanie; Dagan-Rosenfeld, Orit; Rego, Shannon; Limcaoco, Patricia; Colbert, Elizabeth; Allister, Candice; Perelman, Dalia; Craig, Colleen; Wei, Eric; Chaib, Hassan; Hornburg, Daniel; Dunn, Jessilyn; Liang, Liang; Rose, Sophia Miryam Schüssler-Fiorenza; Kukurba, Kim; Piening, Brian; Rost, Hannes; Tse, David; McLaughlin, Tracey; Sodergren, Erica; Weinstock, George M; Snyder, Michael Nature 2019 May;569(7758):663-671
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Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis.
Hong, Bo-Young; Sobue, Takanori; Choquette, Linda; Dupuy, Amanda K; Thompson, Angela; Burleson, Joseph A; Salner, Andrew L; Schauer, Peter K; Joshi, Pujan; Fox, Evan; Shin, Dong-Guk; Weinstock, George M; Strausbaugh, Linda D; Dongari-Bagtzoglou, Anna; Peterson, Douglas E; Diaz, Patricia I Microbiome 2019 Apr;7(1):66
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Association of the Infant Gut Microbiome With Early Childhood Neurodevelopmental Outcomes: An Ancillary Study to the VDAART Randomized Clinical Trial.
Sordillo, Joanne E; Korrick, Susan; Laranjo, Nancy; Carey, Vincent; Weinstock, George M; Gold, Diane R; O'Connor, George; Sandel, Megan; Bacharier, Leonard B; Beigelman, Avraham; Zeiger, Robert; Litonjua, Augusto A; Weiss, Scott T JAMA network open 2019 Mar;2(3):e190905
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Rapid growth is a dominant predictor of hepcidin suppression and declining ferritin in Gambian infants.
Armitage, Andrew E; Agbla, Schadrac C; Betts, Modupeh; Sise, Ebrima A; Jallow, Momodou W; Sambou, Ellen; Darboe, Bakary; Worwui, Archibald; Weinstock, George M; Antonio, Martin; Pasricha, Sant-Rayn; Prentice, Andrew M; Drakesmith, Hal; Darboe, Momodou K; Kwambana-Adams, Brenda Anna Haematologica 2019 Feb;
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MSC: a metagenomic sequence classification algorithm.
Saha, Subrata; Johnson, Jethro; Pal, Soumitra; Weinstock, George; Rajasekaran, Sanguthevar Bioinformatics (Oxford, England) 2019 Jan;
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Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.
Belcaid, Mahdi; Casaburi, Giorgio; McAnulty, Sarah J; Schmidbaur, Hannah; Suria, Andrea M; Moriano-Gutierrez, Silvia; Pankey, M Sabrina; Oakley, Todd H; Kremer, Natacha; Koch, Eric J; Collins, Andrew J; Nguyen, Hoan; Lek, Sai; Goncharenko-Foster, Irina; Minx, Patrick; Sodergren, Erica; Weinstock, George; Rokhsar, Daniel S; McFall-Ngai, Margaret; Simakov, Oleg; Foster, Jamie S; Nyholm, Spencer V Proceedings of the National Academy of Sciences of the United States of America 2019 Jan;
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Diet during Pregnancy and Infancy and the Infant Intestinal Microbiome.
Savage, Jessica H; Lee-Sarwar, Kathleen A; Sordillo, Joanne E; Lange, Nancy E; Zhou, Yanjiao; O'Connor, George T; Sandel, Megan; Bacharier, Leonard B; Zeiger, Robert; Sodergren, Erica; Weinstock, George M; Gold, Diane R; Weiss, Scott T; Litonjua, Augusto A The Journal of pediatrics 2018 Aug;20347-54.e4
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Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota.
Cignarella, Francesca; Cantoni, Claudia; Ghezzi, Laura; Salter, Amber; Dorsett, Yair; Chen, Lei; Phillips, Daniel; Weinstock, George M; Fontana, Luigi; Cross, Anne H; Zhou, Yanjiao*; Piccio, Laura* Cell metabolism 2018 Jun;27(6):1222-1235.e6 *Co-Corresponding Authors
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Oral microbiome in HIV-infected women: Shifts in the abundance of pathogenic and beneficial bacteria are associated with aging, HIV load, CD4 count, and ART.
Lewy, Tyler; Hong, Bo-Young; Weiser, Barbara; Burger, Harold; Tremain, Andrew; Weinstock, George; Anastos, Kathryn; George, Michael AIDS research and human retroviruses 2018 May;
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Extensive Gene Amplification as a Mechanism for Piperacillin-Tazobactam Resistance in Escherichia coli.
Schechter, Lisa M; Creely, David P; Garner, Cherilyn D; Shortridge, Dee; Nguyen, Hoan; Chen, Lei; Hanson, Blake M; Sodergren, Erica; Weinstock, George M; Dunne, W Michael; van Belkum, Alex; Leopold, Shana R mBio 2018 Apr;9(2):
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Meta-analysis of the lung microbiota in pulmonary tuberculosis.
Hong, Bo-Young; Paulson, Joseph N; Stine, O Colin; Weinstock, George M; Cervantes, Jorge L Tuberculosis (Edinburgh, Scotland) 2018 Mar;109102-108
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Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.
Piening, Brian D; Zhou, Wenyu; Contrepois, Kévin; Röst, Hannes; Gu Urban, Gucci Jijuan; Mishra, Tejaswini; Hanson, Blake M; Bautista, Eddy J; Leopold, Shana; Yeh, Christine Y; Spakowicz, Daniel; Banerjee, Imon; Chen, Cynthia; Kukurba, Kimberly; Perelman, Dalia; Craig, Colleen; Colbert, Elizabeth; Salins, Denis; Rego, Shannon; Lee, Sunjae; Zhang, Cheng; Wheeler, Jessica; Sailani, M Reza; Liang, Liang; Abbott, Charles; Gerstein, Mark; Mardinoglu, Adil; Smith, Ulf; Rubin, Daniel L; Pitteri, Sharon; Sodergren, Erica; McLaughlin, Tracey L; Weinstock, George M; Snyder, Michael P Cell systems 2018 Feb;6(2):157-170.e8
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Proteomics and metabolomics for analysis of the dynamics of microbiota.
Van Belkum, Alex; Broadwell, David; Lovern, Douglas; Petersen, Lauren; Weinstock, George; Dunne, W Michael Expert review of proteomics 2018 Feb;15(2):101-104
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An Analysis of the Epidemic of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae: Convergence of Two Evolutionary Mechanisms Creates the "Perfect Storm".
Rojas, Laura J; Weinstock, George M; De La Cadena, Elsa; Diaz, Lorena; Rios, Rafael; Hanson, Blake M; Brown, Joseph S; Vats, Purva; Phillips, Daniel S; Nguyen, Hoan; Hujer, Kristine M; Correa, Adriana; Adams, Mark D; Perez, Federico; Sodergren, Erica; Narechania, Apurva; Planet, Paul J; Villegas, Maria V; Bonomo, Robert A; Arias, Cesar A The Journal of infectious diseases 2017 Dec;217(1):82-92
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Obesity and obesogenic growth are both highly heritable and modified by diet in a nonhuman primate model, the African green monkey (Chlorocebus aethiops sabaeus).
Schmitt, C A; Service, S K; Jasinska, A J; Dyer, T D; Jorgensen, M J; Cantor, R M; Weinstock, G M; Blangero, J; Kaplan, J R; Freimer, N B International journal of obesity (2005) 2017 Dec;42765-774
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Ancient hybridization and strong adaptation to viruses across African vervet monkey populations.
Svardal, Hannes; Jasinska, Anna J; Apetrei, Cristian; Coppola, Giovanni; Huang, Yu; Schmitt, Christopher A; Jacquelin, Beatrice; Ramensky, Vasily; Müller-Trutwin, Michaela; Antonio, Martin; Weinstock, George; Grobler, J Paul; Dewar, Ken; Wilson, Richard K; Turner, Trudy R; Warren, Wesley C; Freimer, Nelson B; Nordborg, Magnus Nature genetics 2017 Oct;491705-1713
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Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.
Jasinska, Anna J; Zelaya, Ivette; Service, Susan K; Peterson, Christine B; Cantor, Rita M; Choi, Oi-Wa; DeYoung, Joseph; Eskin, Eleazar; Fairbanks, Lynn A; Fears, Scott; Furterer, Allison E; Huang, Yu S; Ramensky, Vasily; Schmitt, Christopher A; Svardal, Hannes; Jorgensen, Matthew J; Kaplan, Jay R; Villar, Diego; Aken, Bronwen L; Flicek, Paul; Nag, Rishi; Wong, Emily S; Blangero, John; Dyer, Thomas D; Bogomolov, Marina; Benjamini, Yoav; Weinstock, George M; Dewar, Ken; Sabatti, Chiara; Wilson, Richard K; Jentsch, J David; Warren, Wesley; Coppola, Giovanni; Woods, Roger P; Freimer, Nelson B Nature genetics 2017 Oct;491714-1721
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Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology.
Kwambana-Adams, Brenda; Hanson, Blake; Worwui, Archibald; Agbla, Schadrac; Foster-Nyarko, Ebenezer; Ceesay, Fatima; Ebruke, Chinelo; Egere, Uzochukwu; Zhou, Yanjiao; Ndukum, Maze; Sodergren, Erica; Barer, Michael; Adegbola, Richard; Weinstock, George; Antonio, Martin Scientific reports 2017 Aug;7(1):8127
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Community characteristics of the gut microbiomes of competitive cyclists.
Petersen, Lauren M; Bautista, Eddy J; Nguyen, Hoan; Hanson, Blake M; Chen, Lei; Lek, Sai H; Sodergren, Erica; Weinstock, George M Microbiome 2017 Aug;5(1):98
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers, Robert M; Kyrpides, Nikos C; Stepanauskas, Ramunas; Harmon-Smith, Miranda; Doud, Devin; Reddy, T B K; Schulz, Frederik; Jarett, Jessica; Rivers, Adam R; Eloe-Fadrosh, Emiley A; Tringe, Susannah G; Ivanova, Natalia N; Copeland, Alex; Clum, Alicia; Becraft, Eric D; Malmstrom, Rex R; Birren, Bruce; Podar, Mircea; Bork, Peer; Weinstock, George M; Garrity, George M; Dodsworth, Jeremy A; Yooseph, Shibu; Sutton, Granger; Glöckner, Frank O; Gilbert, Jack A; Nelson, William C; Hallam, Steven J; Jungbluth, Sean P; Ettema, Thijs J G; Tighe, Scott; Konstantinidis, Konstantinos T; Liu, Wen-Tso; Baker, Brett J; Rattei, Thomas; Eisen, Jonathan A; Hedlund, Brian; McMahon, Katherine D; Fierer, Noah; Knight, Rob; Finn, Rob; Cochrane, Guy; Karsch-Mizrachi, Ilene; Tyson, Gene W; Rinke, Christian; Genome Standards Consortium; Lapidus, Alla; Meyer, Folker; Yilmaz, Pelin; Parks, Donovan H; Eren, A M; Schriml, Lynn; Banfield, Jillian F; Hugenholtz, Philip; Woyke, Tanja Nature biotechnology 2017 Aug;35(8):725-731
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Molecular Epidemiology and Phylogenomics of Staphylococcus aureus Bacteremia in Latin-America: A Prospective Cohort Multicenter Study in Nine Countries.
Arias, Cesar A; Reyes, Jinnethe; Carvajal, Lina Paola; Rincon, Sandra; Diaz, Lorena; Panesso, Diana; Ibarra, Gabriel; Rios, Rafael; Munita, Jose M; Salles, Mauro J; Alvarez-Moreno, Carlos; Labarca, Jaime; Garcia, Coralith; Luna, Carlos M; Mejia-Villatoro, Carlos; Zurita, Jeannete; Guzman-Blanco, Manuel; Rodriguez-Noriega, Eduardo; Narechania, Apurva; Rojas, Laura J; Planet, Paul J; Weinstock, George M; Gotuzzo, Eduardo; Seas, Carlos Antimicrobial agents and chemotherapy 2017 Jul;61
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A prospective microbiome-wide association study of food sensitization and food allergy in early childhood.
Savage, Jessica H; Lee-Sarwar, Kathleen A; Sordillo, Joanne; Bunyavanich, Supinda; Zhou, Yanjiao; O'Connor, George; Sandel, Megan; Bacharier, Leonard; Zeiger, Robert; Sodergren, Erica; Weinstock, George M; Gold, Diane R; Weiss, Scott T; Litonjua, Augusto A Allergy 2017 Jun;73145-152
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Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.
Schlaberg, Robert; Chiu, Charles Y; Miller, Steve; Procop, Gary W; Weinstock, George; Professional Practice Committee and Committee on Laboratory Practices of the American Society for Microbiology; Microbiology Resource Committee of the College of American Pathologists Archives of pathology & laboratory medicine 2017 Jun;141(6):776-786
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Ceftaroline-Resistant, Daptomycin-Tolerant, and Heterogeneous Vancomycin-Intermediate Methicillin-Resistant Staphylococcus aureus Causing Infective Endocarditis.
Nigo, Masayuki; Diaz, Lorena; Carvajal, Lina P; Tran, Truc T; Rios, Rafael; Panesso, Diana; Garavito, Juan D; Miller, William R; Wanger, Audrey; Weinstock, George; Munita, Jose M; Arias, Cesar A; Chambers, Henry F Antimicrobial agents and chemotherapy 2017 Mar;61(3):
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Impact of Age, Caloric Restriction, and Influenza Infection on Mouse Gut Microbiome: An Exploratory Study of the Role of Age-Related Microbiome Changes on Influenza Responses.
Bartley, Jenna M; Zhou, Xin; Kuchel, George A; Weinstock, George M; Haynes, Laura Frontiers in immunology 2017 Jan;81164
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Isolation of Methicillin-resistant Staphylococcus aureus and Multidrug-resistant Elizabethkingia meningoseptica From Neonates Within Minutes of Birth.
Kwambana-Adams, Brenda A; Laxton, Claire S; Foster-Nyarko, Ebenezer; Laxton, Claire S; Weinstock, George; Antonio, Martin The Pediatric infectious disease journal 2017 Jan;36(1):123-124
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Factors Influencing the Infant Gut Microbiome at Age 3-6 months: Findings from the ethnically diverse Vitamin D Antenatal Asthma Reduction Trial (VDAART).
Sordillo, Joanne E; Zhou, Yanjiao; McGeachie, Michael J; Ziniti, John; Lange, Nancy; Laranjo, Nancy; Savage, Jessica R; Carey, Vincent; O'Connor, George; Sandel, Megan; Strunk, Robert; Bacharier, Leonard; Zeiger, Robert; Weiss, Scott T; Weinstock, George; Gold, Diane R; Litonjua, Augusto A The Journal of allergy and clinical immunology 2016 Oct;139482-491.e14
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Symbiotic Burkholderia species show diverse arrangements of nif/fix and nod genes, and lack typical high affinity cytochrome cbb3 oxidase genes.
De Meyer, Sofie Elisabeth; Briscoe, Leah; Martinez-Hidalgo, Pilar; Agapakis, Christina; Estrada de Los Santos, Paulina; Seshadri, Rekha; Reeve, Wayne; Weinstock, George; O'Hara, Graham; Howieson, John; Hirsch, Ann M Molecular plant-microbe interactions : MPMI 2016 Jun;29609-19
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Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study.
Hanson, Blake; Zhou, Yanjiao; Bautista, Eddy J; Urch, Bruce; Speck, Mary; Silverman, Frances; Muilenberg, Michael; Phipatanakul, Wanda; Weinstock, George; Sodergren, Erica; Gold, Diane R; Sordillo, Joanne E Environmental science. Processes & impacts 2016 May;18713-24
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Effects of walnut consumption on colon carcinogenesis and microbial community structure.
Nakanishi, Masako; Chen, Yanfei; Qendro, Veneta; Miyamoto, Shingo; Weinstock, Erica; Weinstock, George M; Rosenberg, Daniel W Cancer prevention research (Philadelphia, Pa.) 2016 May;9692-703
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Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study.
Warner, Barbara B; Deych, Elena; Zhou, Yanjiao; Hall-Moore, Carla; Weinstock, George M; Sodergren, Erica; Shaikh, Nurmohammad; Hoffmann, Julie A; Linneman, Laura A; Hamvas, Aaron; Khanna, Geetika; Rouggly-Nickless, Lucina C; Ndao, I Malick; Shands, Berkley A; Escobedo, Marilyn; Sullivan, Janice E; Radmacher, Paula G; Shannon, William D; Tarr, Phillip I Lancet (London, England) 2016 May;387(10031):1928-36
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Role of Clinicogenomics in Infectious Disease Diagnostics and Public Health Microbiology.
Westblade, Lars F; van Belkum, Alex; Grundhoff, Adam; Weinstock, George M; Pamer, Eric G; Pallen, Mark J; Dunne, Wm Michael Journal of clinical microbiology 2016 Feb;541686-1693
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R2d2 Drives Selfish Sweeps in the House Mouse.
Didion, John P; Morgan, Andrew P; Yadgary, Liran; Bell, Timothy A; McMullan, Rachel C; Ortiz de Solorzano, Lydia; Britton-Davidian, Janice; Bult, Carol J; Campbell, Karl J; Castiglia, Riccardo; Ching, Yung-Hao; Chunco, Amanda J; Crowley, James J; Chesler, Elissa J; Förster, Daniel W; French, John E; Gabriel, Sofia I; Gatti, Daniel M; Garland, Theodore; Giagia-Athanasopoulou, Eva B; Giménez, Mabel D; Grize, Sofia A; Gündüz, Islam; Holmes, Andrew; Hauffe, Heidi C; Herman, Jeremy S; Holt, James M; Hua, Kunjie; Jolley, Wesley J; Lindholm, Anna K; López-Fuster, María J; Mitsainas, George; da Luz Mathias, Maria; McMillan, Leonard; Ramalhinho, Maria da Graça Morgado; Rehermann, Barbara; Rosshart, Stephan P; Searle, Jeremy B; Shiao, Meng-Shin; Solano, Emanuela; Svenson, Karen L; Thomas-Laemont, Patricia; Threadgill, David W; Ventura, Jacint; Weinstock, George M; Pomp, Daniel; Churchill, Gary A; Pardo-Manuel de Villena, Fernando Molecular biology and evolution 2016 Feb;331381-95
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Effect of Advanced HIV Infection on the Respiratory Microbiome.
Twigg Iii, Homer L; Knox, Kenneth S; Zhou, Jin; Crothers, Kristina A; Nelson, David E; Toh, Evelyn; Day, Richard B; Lin, Huaiying; Gao, Xiang; Dong, Qunfeng; Mi, Deming; Katz, Barry P; Sodergren, Erica; Weinstock, George M American journal of respiratory and critical care medicine 2016 Feb;194226-35
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Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens.
Zhou, Yanjiao; Wylie, Kristine M; El Feghaly, Rana E; Mihindukulasuriya, Kathie A; Elward, Alexis; Haslam, David B; Storch, Gregory A; Weinstock, George M Journal of clinical microbiology 2016 Feb;54(2):368-75
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Household air pollution and the lung microbiome of healthy adults in Malawi: a cross-sectional study.
Rylance, Jamie; Kankwatira, Anstead; Nelson, David E; Toh, Evelyn; Day, Richard B; Lin, Huaiying; Gao, Xiang; Dong, Qunfeng; Sodergren, Erica; Weinstock, George M; Heyderman, Robert S; Twigg, Homer L; Gordon, Stephen B BMC microbiology 2016 Jan;16(1):182
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Identification of a Novel Gene on 10q22.1 Causing Autosomal Dominant Retinitis Pigmentosa (adRP).
Daiger, Stephen P; Sullivan, Lori S; Bowne, Sara J; Koboldt, Daniel C; Blanton, Susan H; Wheaton, Dianna K; Avery, Cheryl E; Cadena, Elizabeth D; Koenekoop, Robert K; Fulton, Robert S; Wilson, Richard K; Weinstock, George M; Lewis, Richard A; Birch, David G Advances in experimental medicine and biology 2016 Jan;854193-200
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Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks.
McGeachie, Michael J; Sordillo, Joanne E; Gibson, Travis; Weinstock, George M; Liu, Yang-Yu; Gold, Diane R; Weiss, Scott T; Litonjua, Augusto Scientific reports 2016 Jan;620359
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The real cost of sequencing: scaling computation to keep pace with data generation.
Muir, Paul; Li, Shantao; Lou, Shaoke; Wang, Daifeng; Spakowicz, Daniel J; Salichos, Leonidas; Zhang, Jing; Weinstock, George M; Isaacs, Farren; Rozowsky, Joel; Gerstein, Mark Genome biology 2016 Jan;17(1):53
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Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America.
Planet, Paul J; Diaz, Lorena; Kolokotronis, Sergios-Orestis; Narechania, Apurva; Reyes, Jinnethe; Xing, Galen; Rincon, Sandra; Smith, Hannah; Panesso, Diana; Ryan, Chanelle; Smith, Dylan P; Guzman, Manuel; Zurita, Jeannete; Sebra, Robert; Deikus, Gintaras; Nolan, Rathel L; Tenover, Fred C; Weinstock, George M; Robinson, D Ashley; Arias, Cesar A The Journal of infectious diseases 2015 Dec;212(12):1874-82
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The genome of the vervet (Chlorocebus aethiops sabaeus).
Warren, Wesley C; Jasinska, Anna J; García-Pérez, Raquel; Svardal, Hannes; Tomlinson, Chad; Rocchi, Mariano; Archidiacono, Nicoletta; Capozzi, Oronzo; Minx, Patrick; Montague, Michael J; Kyung, Kim; Hillier, LaDeana W; Kremitzki, Milinn; Graves, Tina; Chiang, Colby; Hughes, Jennifer; Tran, Nam; Huang, Yu; Ramensky, Vasily; Choi, Oi-Wa; Jung, Yoon J; Schmitt, Christopher A; Juretic, Nikoleta; Wasserscheid, Jessica; Turner, Trudy R; Wiseman, Roger W; Tuscher, Jennifer J; Karl, Julie A; Schmitz, Jörn E; Zahn, Roland; O'Connor, David H; Redmond, Eugene; Nisbett, Alex; Jacquelin, Béatrice; Müller-Trutwin, Michaela C; Brenchley, Jason M; Dione, Michel; Antonio, Martin; Schroth, Gary P; Kaplan, Jay R; Jorgensen, Matthew J; Thomas, Gregg W C; Hahn, Matthew W; Raney, Brian J; Aken, Bronwen; Nag, Rishi; Schmitz, Juergen; Churakov, Gennady; Noll, Angela; Stanyon, Roscoe; Webb, David; Thibaud-Nissen, Francoise; Nordborg, Magnus; Marques-Bonet, Tomas; Dewar, Ken; Weinstock, George M; Wilson, Richard K; Freimer, Nelson B Genome research 2015 Dec;25(12):1921-33
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A Glimpse of Microbial Power in Preventive Medicine.
Weinstock, George M JAMA pediatrics 2015 Nov;17011
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Discriminatory Indices of Typing Methods for Epidemiologic Analysis of Contemporary Staphylococcus aureus Strains.
Rodriguez, Marcela; Hogan, Patrick G; Satola, Sarah W; Crispell, Emily; Wylie, Todd; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Burnham, Carey-Ann D; Fritz, Stephanie A Medicine 2015 Sep;94(37):e1534
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Multi-center Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.
Beck, James M; Schloss, Patrick D; Venkataraman, Arvind; Twigg Iii, Homer; Jablonski, Kathleen A; Bushman, Frederic D; Campbell, Thomas B; Charlson, Emily S; Collman, Ronald G; Crothers, Kristina; Curtis, Jeffrey L; Drews, Kimberly L; Flores, Sonia C; Fontenot, Andrew P; Foulkes, Mary A; Frank, Ian; Ghedin, Elodie; Huang, Laurence; Lynch, Susan V; Morris, Alison; Palmer, Brent E; Schmidt, Thomas M; Sodergren, Erica; Weinstock, George M; Young, Vincent B American journal of respiratory and critical care medicine 2015 Aug;1921335-44
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Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci.
Leslie, Elizabeth J; Taub, Margaret A; Liu, Huan; Steinberg, Karyn Meltz; Koboldt, Daniel C; Zhang, Qunyuan; Carlson, Jenna C; Hetmanski, Jacqueline B; Wang, Hang; Larson, David E; Fulton, Robert S; Kousa, Youssef A; Fakhouri, Walid D; Naji, Ali; Ruczinski, Ingo; Begum, Ferdouse; Parker, Margaret M; Busch, Tamara; Standley, Jennifer; Rigdon, Jennifer; Hecht, Jacqueline T; Scott, Alan F; Wehby, George L; Christensen, Kaare; Czeizel, Andrew E; Deleyiannis, Frederic W-B; Schutte, Brian C; Wilson, Richard K; Cornell, Robert A; Lidral, Andrew C; Weinstock, George M; Beaty, Terri H; Marazita, Mary L; Murray, Jeffrey C American journal of human genetics 2015 Feb;96(3):397-411
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A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2.
Didion, John P; Morgan, Andrew P; Clayshulte, Amelia M-F; Mcmullan, Rachel C; Yadgary, Liran; Petkov, Petko M; Bell, Timothy A; Gatti, Daniel M; Crowley, James J; Hua, Kunjie; Aylor, David L; Bai, Ling; Calaway, Mark; Chesler, Elissa J; French, John E; Geiger, Thomas R; Gooch, Terry J; Garland, Theodore; Harrill, Alison H; Hunter, Kent; McMillan, Leonard; Holt, Matt; Miller, Darla R; O'Brien, Deborah A; Paigen, Kenneth; Pan, Wenqi; Rowe, Lucy B; Shaw, Ginger D; Simecek, Petr; Sullivan, Patrick F; Svenson, Karen L; Weinstock, George M; Threadgill, David W; Pomp, Daniel; Churchill, Gary A; Pardo-Manuel de Villena, Fernando PLoS genetics 2015 Feb;11(2):e1004850
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Selection of models for the analysis of risk-factor trees: leveraging biological knowledge to mine large sets of risk factors with application to microbiome data.
Zhang, Qunyuan; Abel, Haley; Wells, Alan; Lenzini, Petra; Gomez, Felicia; Province, Michael A; Templeton, Alan A; Weinstock, George M; Salzman, Nita H; Borecki, Ingrid B Bioinformatics (Oxford, England) 2015 Jan;31(10):1607-13
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Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis.
Shi, Baochen; Chang, Michaela; Martin, John; Mitreva, Makedonka; Lux, Renate; Klokkevold, Perry; Sodergren, Erica; Weinstock, George M; Haake, Susan K; Li, Huiying mBio 2015 Jan;6(1):e01926-14
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Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study.
Zhou, Yanjiao; Shan, Gururaj; Sodergren, Erica; Weinstock, George; Walker, W Allan; Gregory, Katherine E PloS one 2015 Jan;10(3):e0118632
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Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment.
Nobel, Yael R; Cox, Laura M; Kirigin, Francis F; Bokulich, Nicholas A; Yamanishi, Shingo; Teitler, Isabel; Chung, Jennifer; Sohn, Jiho; Barber, Cecily M; Goldfarb, David S; Raju, Kartik; Abubucker, Sahar; Zhou, Yanjiao; Ruiz, Victoria E; Li, Huilin; Mitreva, Makedonka; Alekseyenko, Alexander V; Weinstock, George M; Sodergren, Erica; Blaser, Martin J Nature communications 2015 Jan;67486
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Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits.
Huang, Yu S; Ramensky, Vasily; Service, Susan K; Jasinska, Anna J; Jung, Yoon; Choi, Oi-Wa; Cantor, Rita M; Juretic, Nikoleta; Wasserscheid, Jessica; Kaplan, Jay R; Jorgensen, Matthew J; Dyer, Thomas D; Dewar, Ken; Blangero, John; Wilson, Richard K; Warren, Wesley; Weinstock, George M; Freimer, Nelson B BMC biology 2015 Jan;1341
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Small bowel resection induces long-term changes in the enteric microbiota of mice.
Sommovilla, J; Zhou, Y; Sun, R C; Choi, P M; Diaz-Miron, J; Shaikh, N; Sodergren, E; Warner, B B; Weinstock, G M; Tarr, P I; Warner, B W Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract 2015 Jan;19(1):56-64; discussion 64
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The transcriptional profile of coronary arteritis in Kawasaki disease.
Rowley, Anne H; Wylie, Kristine M; Kim, Kwang-Youn A; Pink, Adam J; Yang, Amy; Reindel, Rebecca; Baker, Susan C; Shulman, Stanford T; Orenstein, Jan M; Lingen, Mark W; Weinstock, George M; Wylie, Todd N BMC genomics 2015 Jan;16(1):1076
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HCoDES reveals chromosomal DNA end structures with single-nucleotide resolution.
Dorsett, Yair; Zhou, Yanjiao; Tubbs, Anthony T; Chen, Bo-Ruei; Purman, Caitlin; Lee, Baeck-Seung; George, Rosmy; Bredemeyer, Andrea L; Zhao, Jiang-Yang; Sodergen, Erica; Weinstock, George M; Han, Nathan D; Reyes, Alejandro; Oltz, Eugene M; Dorsett, Dale; Misulovin, Ziva; Payton, Jacqueline E; Sleckman, Barry P Molecular cell 2014 Dec;56(6):808-18
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High-resolution genetic mapping in the diversity outbred mouse population identifies Apobec1 as a candidate gene for atherosclerosis.
Smallwood, Tangi L; Gatti, Daniel M; Quizon, Pamela; Weinstock, George M; Jung, Kuo-Chen; Zhao, Liyang; Hua, Kunjie; Pomp, Daniel; Bennett, Brian J G3 (Bethesda, Md.) 2014 Dec;4(12):2353-63
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Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study.
Zhou, Yanjiao; Burnham, Carey-Ann D; Hink, Tiffany; Chen, Lei; Shaikh, Nurmohammad; Wollam, Aye; Sodergren, Erica; Weinstock, George M; Tarr, Phillip I; Dubberke, Erik R Journal of clinical microbiology 2014 Dec;52(12):4260-6
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A dominant mutation in hexokinase 1 (HK1) causes retinitis pigmentosa.
Sullivan, Lori S; Koboldt, Daniel C; Bowne, Sara J; Lang, Steven; Blanton, Susan H; Cadena, Elizabeth; Avery, Cheryl E; Lewis, Richard A; Webb-Jones, Kaylie; Wheaton, Dianna H; Birch, David G; Coussa, Razck; Ren, Huanan; Lopez, Irma; Chakarova, Christina; Koenekoop, Robert K; Garcia, Charles A; Fulton, Robert S; Wilson, Richard K; Weinstock, George M; Daiger, Stephen P Investigative ophthalmology & visual science 2014 Nov;55(11):7147-58
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Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes.
Staudová, Barbora; Strouhal, Michal; Zobaníková, Marie; Cejková, Darina; Fulton, Lucinda L; Chen, Lei; Giacani, Lorenzo; Centurion-Lara, Arturo; Bruisten, Sylvia M; Sodergren, Erica; Weinstock, George M; Smajs, David PLoS neglected tropical diseases 2014 Nov;8(11):e3261
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The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease.
Proctor, Lita M; Sechi, Salvatore; DiGiacomo, Nicholas D; Fettweis, Jennifer M; Jefferson, Kimberly K; Strauss, Jerome F; Rubens, Craig E; Brooks, J Paul; Girerd, Phillipe P; Huang, Bernice; Serrano, Myrna G; Sheth, Nihar U; Vivadelli, Stephany C; Asmussen, Niels C; Borzelleca, Joseph F; Bradley, Steven P; Brooks, Jamie L; Chalfant, Charles E; Dickinson, Molly R; Drake, Jennifer I; Edwards, David J; El Khoury, Joseph; Glascock, Abigail L; Gravett, Michael G; Hendricks-Muñoz, Karen D; Koparde, Vishal N; Lanni, Susan M; Lara, Ana M; Lee, Vladimir; Matveyev, Andrey V; Ozaki, Luiz V; Sexton, Amber S; Shyu, Conrad; Tran, Ann; Uetz, Peter H; Wijesinghe, Dayanjan S; Wijesooriya, Niran R; Xu, Jie; Buck, Gregory A; Huttenhower, Curtis; Gevers, Dirk; Sirota-Madi, Alexandra; Bayer, Keith; Braun, Jonathan; Denson, Lee A; Jansson, Janet K; Knight, Rob; Kugathasan, Subra; McGovern, Dermot P B; Petrosino, Joseph F; Stappenbeck, Thaddeus S; Birren, Bruce W; Clish, Clary B; Gonzalez, Antonio; Graeber, Thomas G; Lake, Kathleen; Li, Xiaoxiao; Loo, Joseph; McDonald, Daniel; Nicol, Rob; Nusbaum, Chad; Prasad, Mahadev; Ryu, Stacy; Sauk, Jenny; Schwager, Randall; Sturgeon, Holly; Tas, Neslihan; VanDussen, Kelli L; Wilson, Robin G; Yassour, Moran; Xavier, Ramnik J; Weinstock, George; McLaughlin, Tracey; Bernstein, Jonathan A; Zhou, Wenyu; Piening, Brian D; Kukurba, Kimberly; Allister, Candice; Butte, Atul J; Boyle, Sean M; Cao, Lulu; Chen, Rui; Contrepois, Kevin; Cooper, Breanna; Craig, Colleen; Datta, Somalee; Fan-Minogue, Hua; Gu, Gucci J; Hanson, Blake; Jiang, Lihua; Lek, Sai; Leopold, Benjamin; Leopold, Shana; Li-Pook-Than, Jennifer; Mitra, Siddhartha; Rego, Shannon; Sailani, M Reza; Salins, Denis; Sodergren, Erica; Soto Pérez, Paola; Takahashi, Shinichi; Snyder, Michael P; White, Owen; Mahurkar, Anup; Gwinn Giglio, Michelle Cell host & microbe 2014 Sep;16(3):276-89
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CcpA is important for growth and virulence of Enterococcus faecium.
Somarajan, Sudha R; Roh, Jung H; Singh, Kavindra V; Weinstock, George M; Murray, Barbara E Infection and immunity 2014 Sep;82(9):3580-7
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Characterization of mutations in the PAS domain of the EvgS sensor kinase selected by laboratory evolution for acid resistance in Escherichia coli.
Johnson, Matthew D; Bell, James; Clarke, Kim; Chandler, Rachel; Pathak, Prachi; Xia, Yandong; Marshall, Robert L; Weinstock, George M; Loman, Nicholas J; Winn, Peter J; Lund, Peter A Molecular microbiology 2014 Sep;93(5):911-27
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Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages.
Deng, Xiangyu; Desai, Prerak T; den Bakker, Henk C; Mikoleit, Matthew; Tolar, Beth; Trees, Eija; Hendriksen, Rene S; Frye, Jonathan G; Porwollik, Steffen; Weimer, Bart C; Wiedmann, Martin; Weinstock, George M; Fields, Patricia I; McClelland, Michael Emerging infectious diseases 2014 Sep;20(9):1481-9
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Patterned progression of bacterial populations in the premature infant gut.
La Rosa, Patricio S; Warner, Barbara B; Zhou, Yanjiao; Weinstock, George M; Sodergren, Erica; Hall-Moore, Carla M; Stevens, Harold J; Bennett, William E; Shaikh, Nurmohammad; Linneman, Laura A; Hoffmann, Julie A; Hamvas, Aaron; Deych, Elena; Shands, Berkley A; Shannon, William D; Tarr, Phillip I Proceedings of the National Academy of Sciences of the United States of America 2014 Aug;111(34):12522-7
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Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.
Kyrpides, Nikos C; Hugenholtz, Philip; Eisen, Jonathan A; Woyke, Tanja; Göker, Markus; Parker, Charles T; Amann, Rudolf; Beck, Brian J; Chain, Patrick S G; Chun, Jongsik; Colwell, Rita R; Danchin, Antoine; Dawyndt, Peter; Dedeurwaerdere, Tom; DeLong, Edward F; Detter, John C; De Vos, Paul; Donohue, Timothy J; Dong, Xiu-Zhu; Ehrlich, Dusko S; Fraser, Claire; Gibbs, Richard; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Jansson, Janet K; Keasling, Jay D; Knight, Rob; Labeda, David; Lapidus, Alla; Lee, Jung-Sook; Li, Wen-Jun; Ma, Juncai; Markowitz, Victor; Moore, Edward R B; Morrison, Mark; Meyer, Folker; Nelson, Karen E; Ohkuma, Moriya; Ouzounis, Christos A; Pace, Norman; Parkhill, Julian; Qin, Nan; Rossello-Mora, Ramon; Sikorski, Johannes; Smith, David; Sogin, Mitch; Stevens, Rick; Stingl, Uli; Suzuki, Ken-Ichiro; Taylor, Dorothea; Tiedje, Jim M; Tindall, Brian; Wagner, Michael; Weinstock, George; Weissenbach, Jean; White, Owen; Wang, Jun; Zhang, Lixin; Zhou, Yu-Guang; Field, Dawn; Whitman, William B; Garrity, George M; Klenk, Hans-Peter PLoS biology 2014 Aug;12(8):e1001920
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The common marmoset genome provides insight into primate biology and evolution.
Worley, Kim C; Warren, Wesley C; Rogers, Jeffrey; Locke, Devin; Muzny, Donna M; Mardis, Elaine R; Weinstock, George M; Tardif, Suzette D; Aagaard, Kjersti M; Archidiacono, Nicoletta; Rayan, Nirmala Arul; Batzer, Mark A; Beal, Kathryn; Brejova, Brona; Capozzi, Oronzo; Capuano, Saverio B; Casola, Claudio; Chandrabose, Mimi M; Cree, Andrew; Dao, Marvin Diep; de Jong, Pieter J; Del Rosario, Ricardo Cruz-Herrera; Delehaunty, Kim D; Dinh, Huyen H; Eichler, Evan E; Fitzgerald, Stephen; Flicek, Paul; Fontenot, Catherine C; Fowler, R Gerald; Fronick, Catrina; Fulton, Lucinda A; Fulton, Robert S; Gabisi, Ramatu Ayiesha; Gerlach, Daniel; Graves, Tina A; Gunaratne, Preethi H; Hahn, Matthew W; Haig, David; Han, Yi; Harris, R Alan; Herrero, Javier; Hillier, LaDeana W; Hubley, Robert; Hughes, Jennifer F; Hume, Jennifer; Jhangiani, Shalini N; Jorde, Lynn B; Joshi, Vandita; Karakor, Emre; Konkel, Miriam K; Kosiol, Carolin; Kovar, Christie L; Kriventseva, Evgenia V; Lee, Sandra L; Lewis, Lora R; Liu, Yih-Shin; Lopez, John; Lopez-Otin, Carlos; Lorente-Galdos, Belen; Mansfield, Keith G; Marques-Bonet, Tomas; Minx, Patrick; Misceo, Doriana; Moncrieff, J Scott; Morgan, Margaret B; Nazareth, Lynne V; Newsham, Irene; Nguyen, Ngoc Bich; Okwuonu, Geoffrey O; Prabhakar, Shyam; Perales, Lora; Pu, Ling-Ling; Puente, Xose S; Quesada, Victor; Ranck, Megan C; Raney, Brian J; Raveendran, Muthuswamy; Deiros, David Rio; Rocchi, Mariano; Rodriguez, David; Ross, Corinna; Ruffier, Magali; Ruiz, San Juana; Sajjadian, Saba; Santibanez, Jireh; Schrider, Daniel R; Searle, Steve; Skaletsky, Helen; Soibam, Benjamin; Smit, Arian F A; Tennakoon, Jayantha B; Tomaska, Lubomir; Ullmer, Brygg; Vejnar, Charles E; Ventura, Mario; Vilella, Albert J; Vinar, Tomas; Vogel, Jan-Hinnerk; Walker, Jerilyn A; Wang, Qing; Warner, Crystal M; Wildman, Derek E; Witherspoon, David J; Wright, Rita A; Wu, Yuanqing; Xiao, Weimin; Xing, Jinchuan; Zdobnov, Evgeny M; Zhu, Baoli; Gibbs, Richard A; Wilson, Richard K Nature genetics 2014 Aug;46(8):850-7
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Whole-genome analyses of Enterococcus faecium isolates with diverse daptomycin MICs.
Diaz, Lorena; Tran, Truc T; Munita, Jose M; Miller, William R; Rincon, Sandra; Carvajal, Lina P; Wollam, Aye; Reyes, Jinnethe; Panesso, Diana; Rojas, Natalia L; Shamoo, Yousif; Murray, Barbara E; Weinstock, George M; Arias, Cesar A Antimicrobial agents and chemotherapy 2014 Aug;58(8):4527-34
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Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections.
Carl, Mike A; Ndao, I Malick; Springman, A Cody; Manning, Shannon D; Johnson, James R; Johnston, Brian D; Burnham, Carey-Ann D; Weinstock, Erica Sodergren; Weinstock, George M; Wylie, Todd N; Mitreva, Makedonka; Abubucker, Sahar; Zhou, Yanjiao; Stevens, Harold J; Hall-Moore, Carla; Julian, Samuel; Shaikh, Nurmohammad; Warner, Barbara B; Tarr, Phillip I Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2014 May;58(9):1211-8
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Phylogenomics and the dynamic genome evolution of the genus Streptococcus.
Richards, Vincent P; Palmer, Sara R; Pavinski Bitar, Paulina D; Qin, Xiang; Weinstock, George M; Highlander, Sarah K; Town, Christopher D; Burne, Robert A; Stanhope, Michael J Genome biology and evolution 2014 Apr;6(4):741-53
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The relationships between environmental bacterial exposure, airway bacterial colonization, and asthma.
Beigelman, Avraham; Weinstock, George M; Bacharier, Leonard B Current opinion in allergy and clinical immunology 2014 Apr;14(2):137-42
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Exome-based mapping and variant prioritization for inherited Mendelian disorders.
Koboldt, Daniel C; Larson, David E; Sullivan, Lori S; Bowne, Sara J; Steinberg, Karyn M; Churchill, Jennifer D; Buhr, Aimee C; Nutter, Nathan; Pierce, Eric A; Blanton, Susan H; Weinstock, George M; Wilson, Richard K; Daiger, Stephen P American journal of human genetics 2014 Mar;94(3):373-84
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TIGRA: a targeted iterative graph routing assembler for breakpoint assembly.
Chen, Ken; Chen, Lei; Fan, Xian; Wallis, John; Ding, Li; Weinstock, George Genome research 2014 Feb;24(2):310-7
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Application of next-generation sequencing to identify genes and mutations causing autosomal dominant retinitis pigmentosa (adRP).
Daiger, Stephen P; Bowne, Sara J; Sullivan, Lori S; Blanton, Susan H; Weinstock, George M; Koboldt, Daniel C; Fulton, Robert S; Larsen, David; Humphries, Peter; Humphries, Marian M; Pierce, Eric A; Chen, Rui; Li, Yumei Advances in experimental medicine and biology 2014 Jan;801123-9
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Exploration of bacterial community classes in major human habitats.
Zhou, Yanjiao; Mihindukulasuriya, Kathie A; Gao, Hongyu; La Rosa, Patricio S; Wylie, Kristine M; Martin, John C; Kota, Karthik; Shannon, William D; Mitreva, Makedonka; Sodergren, Erica; Weinstock, George M Genome biology 2014 Jan;15(5):R66
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High-resolution quantification of hepatitis C virus genome-wide mutation load and its correlation with the outcome of peginterferon-alpha2a and ribavirin combination therapy.
Wang, Weihua; Zhang, Xiaoan; Xu, Yanjuan; Weinstock, George M; Di Bisceglie, Adrian M; Fan, Xiaofeng PloS one 2014 Jan;9(6):e100131
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Inactivation of SAM-methyltransferase is the mechanism of attenuation of a historic louse borne typhus vaccine strain.
Liu, Yan; Wu, Bin; Weinstock, George; Walker, David H; Yu, Xue-Jie PloS one 2014 Jan;9(11):e113285
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Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
Delaneau, Olivier; Marchini, Jonathan; 1000 Genomes Project Consortium; 1000 Genomes Project Consortium Nature communications 2014 Jan;53934
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Metagenomic analysis of double-stranded DNA viruses in healthy adults.
Wylie, Kristine M; Mihindukulasuriya, Kathie A; Zhou, Yanjiao; Sodergren, Erica; Storch, Gregory A; Weinstock, George M BMC biology 2014 Jan;1271
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Microbial sequencing to improve individual and population health.
Peacock, Sharon J; Weinstock, George M Genome medicine 2014 Jan;6(11):103
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Plant-associated symbiotic Burkholderia species lack hallmark strategies required in mammalian pathogenesis.
Angus, Annette A; Agapakis, Christina M; Fong, Stephanie; Yerrapragada, Shailaja; Estrada-de los Santos, Paulina; Yang, Paul; Song, Nannie; Kano, Stephanie; Caballero-Mellado, Jésus; de Faria, Sergio M; Dakora, Felix D; Weinstock, George; Hirsch, Ann M PloS one 2014 Jan;9(1):e83779
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The conjunctival microbiome in health and trachomatous disease: a case control study.
Zhou, Yanjiao; Holland, Martin J; Makalo, Pateh; Joof, Hassan; Roberts, Chrissy H; Mabey, David Cw; Bailey, Robin L; Burton, Matthew J; Weinstock, George M; Burr, Sarah E Genome medicine 2014 Jan;6(11):99
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Whole-Genome Sequencing of Salmonella enterica subsp. enterica Serovar Cubana Strains Isolated from Agricultural Sources.
Benahmed, Faiza H; Gopinath, Gopal R; Wang, Hua; Jean-Gilles Beaubrun, Junia; Grim, Christopher; Cheng, Chorng-Ming; McClelland, Michael; Ayers, Sherry; Abbott, Jason; Desai, Prerak; Frye, Jonathan G; Weinstock, George; Hammack, Thomas S; Hanes, Darcy E; Rasmussen, Mark A; Davidson, Maureen K Genome announcements 2014 Jan;2(1):
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A novel intronic single nucleotide polymorphism in the myosin heavy polypeptide 4 gene is responsible for the mini-muscle phenotype characterized by major reduction in hind-limb muscle mass in mice.
Kelly, Scott A; Bell, Timothy A; Selitsky, Sara R; Buus, Ryan J; Hua, Kunjie; Weinstock, George M; Garland, Theodore; Pardo-Manuel de Villena, Fernando; Pomp, Daniel Genetics 2013 Dec;195(4):1385-95
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Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis.
Turabelidze, George; Lawrence, Steven J; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Abubucker, Sahar; Wylie, Todd; Mitreva, Makedonka; Shaikh, Nurmohammad; Gautom, Romesh; Tarr, Phillip I Journal of clinical microbiology 2013 Dec;51(12):3950-4
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Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem.
Wendl, Michael C; Kota, Karthik; Weinstock, George M; Mitreva, Makedonka Journal of mathematical biology 2013 Nov;67(5):1141-61
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Integrative annotation of variants from 1092 humans: application to cancer genomics.
Khurana, Ekta; Fu, Yao; Colonna, Vincenza; Mu, Xinmeng Jasmine; Kang, Hyun Min; Lappalainen, Tuuli; Sboner, Andrea; Lochovsky, Lucas; Chen, Jieming; Harmanci, Arif; Das, Jishnu; Abyzov, Alexej; Balasubramanian, Suganthi; Beal, Kathryn; Chakravarty, Dimple; Challis, Daniel; Chen, Yuan; Clarke, Declan; Clarke, Laura; Cunningham, Fiona; Evani, Uday S; Flicek, Paul; Fragoza, Robert; Garrison, Erik; Gibbs, Richard; Gümüs, Zeynep H; Herrero, Javier; Kitabayashi, Naoki; Kong, Yong; Lage, Kasper; Liluashvili, Vaja; Lipkin, Steven M; MacArthur, Daniel G; Marth, Gabor; Muzny, Donna; Pers, Tune H; Ritchie, Graham R S; Rosenfeld, Jeffrey A; Sisu, Cristina; Wei, Xiaomu; Wilson, Michael; Xue, Yali; Yu, Fuli; 1000 Genomes Project Consortium; Dermitzakis, Emmanouil T; Yu, Haiyuan; Rubin, Mark A; Tyler-Smith, Chris; Gerstein, Mark Science (New York, N.Y.) 2013 Oct;342(6154):1235587
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Propionibacterium acnes strain populations in the human skin microbiome associated with acne.
Fitz-Gibbon, Sorel; Tomida, Shuta; Chiu, Bor-Han; Nguyen, Lin; Du, Christine; Liu, Minghsun; Elashoff, David; Erfe, Marie C; Loncaric, Anya; Kim, Jenny; Modlin, Robert L; Miller, Jeff F; Sodergren, Erica; Craft, Noah; Weinstock, George M; Li, Huiying The Journal of investigative dermatology 2013 Sep;133(9):2152-60
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Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations.
Lang, Gregory I; Rice, Daniel P; Hickman, Mark J; Sodergren, Erica; Weinstock, George M; Botstein, David; Desai, Michael M Nature 2013 Aug;500(7464):571-4
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Virome genomics: a tool for defining the human virome.
Wylie, Kristine M; Weinstock, George M; Storch, Gregory A Current opinion in microbiology 2013 Aug;16(4):479-84
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Use of bronchoalveolar lavage to assess the respiratory microbiome: signal in the noise.
Twigg, Homer L; Morris, Alison; Ghedin, Elodie; Curtis, Jeffrey L; Huffnagle, Gary B; Crothers, Kristina; Campbell, Thomas B; Flores, Sonia C; Fontenot, Andrew P; Beck, James M; Huang, Laurence; Lynch, Susan; Knox, Kenneth S; Weinstock, George The Lancet. Respiratory medicine 2013 Jul;1(5):354-6
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Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens.
Aylward, Frank O; Burnum-Johnson, Kristin E; Tringe, Susannah G; Teiling, Clotilde; Tremmel, Daniel M; Moeller, Joseph A; Scott, Jarrod J; Barry, Kerrie W; Piehowski, Paul D; Nicora, Carrie D; Malfatti, Stephanie A; Monroe, Matthew E; Purvine, Samuel O; Goodwin, Lynne A; Smith, Richard D; Weinstock, George M; Gerardo, Nicole M; Suen, Garret; Lipton, Mary S; Currie, Cameron R Applied and environmental microbiology 2013 Jun;79(12):3770-8
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Comparison of the respiratory microbiome in healthy nonsmokers and smokers.
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Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men.
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Candidate genes that may be responsible for the unusual resistances exhibited by Bacillus pumilus SAFR-032 spores.
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Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome.
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Systems biology of the vervet monkey.
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Complete genome sequence of Treponema pallidum strain DAL-1.
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Evaluation of 16S rDNA-based community profiling for human microbiome research.
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Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa.
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Graph accordance of next-generation sequence assemblies.
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Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges.
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Sequence analysis of the human virome in febrile and afebrile children.
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Statistical object data analysis of taxonomic trees from human microbiome data.
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Whole genome sequence of Treponema pallidum ssp. pallidum, strain Mexico A, suggests recombination between yaws and syphilis strains.
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Astrovirus MLB2 viremia in febrile child.
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Conservation of Ebp-type pilus genes among Enterococci and demonstration of their role in adherence of Enterococcus faecalis to human platelets.
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Integrated genomic analyses of ovarian carcinoma.
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Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
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Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
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Mapping copy number variation by population-scale genome sequencing.
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Comparative and demographic analysis of orang-utan genomes.
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A vertebrate case study of the quality of assemblies derived from next-generation sequences.
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Complete genome sequence of Treponema paraluiscuniculi, strain Cuniculi A: the loss of infectivity to humans is associated with genome decay.
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Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
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Identification of disease-causing mutations in autosomal dominant retinitis pigmentosa (adRP) using next-generation DNA sequencing.
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The functional spectrum of low-frequency coding variation.
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The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle.
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The volatile microbiome.
Weinstock, George M Genome biology 2011 Jan;12(5):114
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Diversity of human copy number variation and multicopy genes.
Sudmant, Peter H; Kitzman, Jacob O; Antonacci, Francesca; Alkan, Can; Malig, Maika; Tsalenko, Anya; Sampas, Nick; Bruhn, Laurakay; Shendure, Jay; 1000 Genomes Project; Eichler, Evan E Science (New York, N.Y.) 2010 Oct;330(6004):641-6
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A map of human genome variation from population-scale sequencing.
1000 Genomes Project Consortium; Abecasis, Gonçalo R; Altshuler, David; Auton, Adam; Brooks, Lisa D; Durbin, Richard M; Gibbs, Richard A; Hurles, Matt E; McVean, Gil A Nature 2010 Oct;467(7319):1061-73
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A catalog of reference genomes from the human microbiome.
Nelson, Karen E; Weinstock, George M; Highlander, Sarah K; Worley, Kim C; Creasy, Heather Huot; Wortman, Jennifer Russo; Rusch, Douglas B; Mitreva, Makedonka; Sodergren, Erica; Chinwalla, Asif T; Feldgarden, Michael; Gevers, Dirk; Haas, Brian J; Madupu, Ramana; Ward, Doyle V; Birren, Bruce W; Gibbs, Richard A; Methe, Barbara; Petrosino, Joseph F; Strausberg, Robert L; Sutton, Granger G; White, Owen R; Wilson, Richard K; Durkin, Scott; Giglio, Michelle Gwinn; Gujja, Sharvari; Howarth, Clint; Kodira, Chinnappa D; Kyrpides, Nikos; Mehta, Teena; Muzny, Donna M; Pearson, Matthew; Pepin, Kymberlie; Pati, Amrita; Qin, Xiang; Yandava, Chandri; Zeng, Qiandong; Zhang, Lan; Berlin, Aaron M; Chen, Lei; Hepburn, Theresa A; Johnson, Justin; McCorrison, Jamison; Miller, Jason; Minx, Pat; Nusbaum, Chad; Russ, Carsten; Sykes, Sean M; Tomlinson, Chad M; Young, Sarah; Warren, Wesley C; Badger, Jonathan; Crabtree, Jonathan; Markowitz, Victor M; Orvis, Joshua; Cree, Andrew; Ferriera, Steve; Fulton, Lucinda L; Fulton, Robert S; Gillis, Marcus; Hemphill, Lisa D; Joshi, Vandita; Kovar, Christie; Torralba, Manolito; Wetterstrand, Kris A; Abouellleil, Amr; Wollam, Aye M; Buhay, Christian J; Ding, Yan; Dugan, Shannon; FitzGerald, Michael G; Holder, Mike; Hostetler, Jessica; Clifton, Sandra W; Allen-Vercoe, Emma; Earl, Ashlee M; Farmer, Candace N; Liolios, Konstantinos; Surette, Michael G; Xu, Qiang; Pohl, Craig; Wilczek-Boney, Katarzyna; Zhu, Dianhui Science (New York, N.Y.) 2010 May;328(5981):994-9
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High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak.
Lewis, T; Loman, N J; Bingle, L; Jumaa, P; Weinstock, G M; Mortiboy, D; Pallen, M J The Journal of hospital infection 2010 May;75(1):37-41
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Genome remodelling in a basal-like breast cancer metastasis and xenograft.
Ding, Li; Ellis, Matthew J; Li, Shunqiang; Larson, David E; Chen, Ken; Wallis, John W; Harris, Christopher C; McLellan, Michael D; Fulton, Robert S; Fulton, Lucinda L; Abbott, Rachel M; Hoog, Jeremy; Dooling, David J; Koboldt, Daniel C; Schmidt, Heather; Kalicki, Joelle; Zhang, Qunyuan; Chen, Lei; Lin, Ling; Wendl, Michael C; McMichael, Joshua F; Magrini, Vincent J; Cook, Lisa; McGrath, Sean D; Vickery, Tammi L; Appelbaum, Elizabeth; Deschryver, Katherine; Davies, Sherri; Guintoli, Therese; Lin, Li; Crowder, Robert; Tao, Yu; Snider, Jacqueline E; Smith, Scott M; Dukes, Adam F; Sanderson, Gabriel E; Pohl, Craig S; Delehaunty, Kim D; Fronick, Catrina C; Pape, Kimberley A; Reed, Jerry S; Robinson, Jody S; Hodges, Jennifer S; Schierding, William; Dees, Nathan D; Shen, Dong; Locke, Devin P; Wiechert, Madeline E; Eldred, James M; Peck, Josh B; Oberkfell, Benjamin J; Lolofie, Justin T; Du, Feiyu; Hawkins, Amy E; O'Laughlin, Michelle D; Bernard, Kelly E; Cunningham, Mark; Elliott, Glendoria; Mason, Mark D; Thompson, Dominic M; Ivanovich, Jennifer L; Goodfellow, Paul J; Perou, Charles M; Weinstock, George M; Aft, Rebecca; Watson, Mark; Ley, Timothy J; Wilson, Richard K; Mardis, Elaine R Nature 2010 Apr;464(7291):999-1005
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A SNP discovery method to assess variant allele probability from next-generation resequencing data.
Shen, Yufeng; Wan, Zhengzheng; Coarfa, Cristian; Drabek, Rafal; Chen, Lei; Ostrowski, Elizabeth A; Liu, Yue; Weinstock, George M; Wheeler, David A; Gibbs, Richard A; Yu, Fuli Genome research 2010 Feb;20(2):273-80
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Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection.
Nelson, David E; Van Der Pol, Barbara; Dong, Qunfeng; Revanna, Kashi V; Fan, Baochang; Easwaran, Shraddha; Sodergren, Erica; Weinstock, George M; Diao, Lixia; Fortenberry, J Dennis PloS one 2010 Jan;5(11):e14116
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Enteric defensins are essential regulators of intestinal microbial ecology.
Salzman, Nita H; Hung, Kuiechun; Haribhai, Dipica; Chu, Hiutung; Karlsson-Sjöberg, Jenny; Amir, Elad; Teggatz, Paul; Barman, Melissa; Hayward, Michael; Eastwood, Daniel; Stoel, Maaike; Zhou, Yanjiao; Sodergren, Erica; Weinstock, George M; Bevins, Charles L; Williams, Calvin B; Bos, Nicolaas A Nature immunology 2010 Jan;11(1):76-83
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Genome analysis of Treponema pallidum subsp. pallidum and subsp. pertenue strains: most of the genetic differences are localized in six regions.
Mikalová, Lenka; Strouhal, Michal; Cejková, Darina; Zobaníková, Marie; Pospíšilová, Petra; Norris, Steven J; Sodergren, Erica; Weinstock, George M; Šmajs, David PloS one 2010 Jan;5(12):e15713
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Genome sequencing reveals widespread virulence gene exchange among human Neisseria species.
Marri, Pradeep Reddy; Paniscus, Mary; Weyand, Nathan J; Rendón, María A; Calton, Christine M; Hernández, Diana R; Higashi, Dustin L; Sodergren, Erica; Weinstock, George M; Rounsley, Steven D; So, Magdalene PloS one 2010 Jan;5(7):e11835
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Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching.
Snyder, Lori A S; Loman, Nicholas J; Linton, James D; Langdon, Rebecca R; Weinstock, George M; Wren, Brendan W; Pallen, Mark J BMC genomics 2010 Jan;1167
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Targeted high-throughput DNA sequencing for gene discovery in retinitis pigmentosa.
Daiger, Stephen P; Sullivan, Lori S; Bowne, Sara J; Birch, David G; Heckenlively, John R; Pierce, Eric A; Weinstock, George M Advances in experimental medicine and biology 2010 Jan;664325-31
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A collagen-binding adhesin, Acb, and ten other putative MSCRAMM and pilus family proteins of Streptococcus gallolyticus subsp. gallolyticus (Streptococcus bovis Group, biotype I).
Sillanpää, Jouko; Nallapareddy, Sreedhar R; Qin, Xiang; Singh, Kavindra V; Muzny, Donna M; Kovar, Christie L; Nazareth, Lynne V; Gibbs, Richard A; Ferraro, Mary J; Steckelberg, James M; Weinstock, George M; Murray, Barbara E Journal of bacteriology 2009 Nov;191(21):6643-53
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Genomics. Genome project standards in a new era of sequencing.
Chain, P S G; Grafham, D V; Fulton, R S; Fitzgerald, M G; Hostetler, J; Muzny, D; Ali, J; Birren, B; Bruce, D C; Buhay, C; Cole, J R; Ding, Y; Dugan, S; Field, D; Garrity, G M; Gibbs, R; Graves, T; Han, C S; Harrison, S H; Highlander, S; Hugenholtz, P; Khouri, H M; Kodira, C D; Kolker, E; Kyrpides, N C; Lang, D; Lapidus, A; Malfatti, S A; Markowitz, V; Metha, T; Nelson, K E; Parkhill, J; Pitluck, S; Qin, X; Read, T D; Schmutz, J; Sozhamannan, S; Sterk, P; Strausberg, R L; Sutton, G; Thomson, N R; Tiedje, J M; Weinstock, G; Wollam, A; Detter, J C Science (New York, N.Y.) 2009 Oct;326(5950):236-7
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Prepublication data sharing.
Birney, Ewan; Hudson, Thomas J; Green, Eric D; Gunter, Chris; Eddy, Sean; Rogers, Jane; Harris, Jennifer R; Ehrlich, S Dusko; Apweiler, Rolf; Austin, Christopher P; Berglund, Lisa; Bobrow, Martin; Bountra, Chas; Brookes, Anthony J; Cambon-Thomsen, Anne; Carter, Nigel P; Chisholm, Rex L; Contreras, Jorge L; Cooke, Robert M; Crosby, William L; Dewar, Ken; Durbin, Richard; Dyke, Stephanie O M; Ecker, Joseph R; El Emam, Khaled; Feuk, Lars; Gabriel, Stacey B; Gallacher, John; Gelbart, William M; Granell, Antoni; Guarner, Francisco; Hubbard, Tim; Jackson, Scott A; Jennings, Jennifer L; Joly, Yann; Jones, Steven M; Kaye, Jane; Kennedy, Karen L; Knoppers, Bartha Maria; Kyrpides, Nikos C; Lowrance, William W; Luo, Jingchu; MacKay, John J; Martín-Rivera, Luis; McCombie, W Richard; McPherson, John D; Miller, Linda; Miller, Webb; Moerman, Don; Mooser, Vincent; Morton, Cynthia C; Ostell, James M; Ouellette, B F Francis; Parkhill, Julian; Raina, Parminder S; Rawlings, Christopher; Scherer, Steven E; Scherer, Stephen W; Schofield, Paul N; Sensen, Christoph W; Stodden, Victoria C; Sussman, Michael R; Tanaka, Toshihiro; Thornton, Janet; Tsunoda, Tatsuhiko; Valle, David; Vuorio, Eero I; Walker, Neil M; Wallace, Susan; Weinstock, George; Whitman, William B; Worley, Kim C; Wu, Cathy; Wu, Jiayan; Yu, Jun Nature 2009 Sep;461(7261):168-70
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Genome sequence of the emerging pathogen Helicobacter canadensis.
Loman, N J; Snyder, L A S; Linton, J D; Langdon, R; Lawson, A J; Weinstock, G M; Wren, B W; Pallen, M J Journal of bacteriology 2009 Sep;191(17):5566-7
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VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
Koboldt, Daniel C; Chen, Ken; Wylie, Todd; Larson, David E; McLellan, Michael D; Mardis, Elaine R; Weinstock, George M; Wilson, Richard K; Ding, Li Bioinformatics (Oxford, England) 2009 Sep;25(17):2283-5
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Macrolide treatment failure in a case of secondary syphilis: a novel A2059G mutation in the 23S rRNA gene of Treponema pallidum subsp. pallidum.
Matejková, Petra; Flasarová, Magdalena; Zákoucká, Hana; Borek, Milan; Kremenová, Sona; Arenberger, Petr; Woznicová, Vladana; Weinstock, George M; Smajs, David Journal of medical microbiology 2009 Jun;58(Pt 6):832-6
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Lineage-specific biology revealed by a finished genome assembly of the mouse.
Church, Deanna M; Goodstadt, Leo; Hillier, Ladeana W; Zody, Michael C; Goldstein, Steve; She, Xinwe; Bult, Carol J; Agarwala, Richa; Cherry, Joshua L; DiCuccio, Michael; Hlavina, Wratko; Kapustin, Yuri; Meric, Peter; Maglott, Donna; Birtle, Zoë; Marques, Ana C; Graves, Tina; Zhou, Shiguo; Teague, Brian; Potamousis, Konstantinos; Churas, Christopher; Place, Michael; Herschleb, Jill; Runnheim, Ron; Forrest, Daniel; Amos-Landgraf, James; Schwartz, David C; Cheng, Ze; Lindblad-Toh, Kerstin; Eichler, Evan E; Ponting, Chris P; Muzny, Donna M; Dugan-Rocha, Shannon; Ding, Yan; Scherer, Steven E; Buhay, Christian J; Cree, Andrew; Hernandez, Judith; Holder, Michael; Hume, Jennifer; Jackson, Laronda R; Kovar, Christie; Lee, Sandra L; Lewis, Lora R; Metzker, Michael L; Narareth, Lynne V; Sabo, Aniko; Sodergren, Erica; Gibbs, Richard A; Zody, Michael C; FitzGerald, Michael; Cook, April; Jaffe, David B; Garber, Manuel; Zimmer, Andrew R; Pirun, Mono; Russell, Lyndsey; Sharpe, Ted; Chaturvedi, Michael Kamal-Kabir; Wilkinson, Jane; LaButti, Kurt; Yang, Xiaoping; Bessette, Daniel; Allen, Nicole R; Nguyen, Cindy; Nguyen, Thu; Dunbar, Chelsea; Lubonja, Rakela; Matthews, Charles; Liu, Xiaohong; Benamara, Mostafa; Negash, Tamrat; Lokyitsang, Tashi; Decktor, Karin; Piqani, Bruno; Munson, Glen; Tenzin, Pema; Stone, Sabrina; Macdonald, Pendexter; Arachchi, Harindra; Abouelleil, Amr; Lui, Annie; Priest, Margaret; Gearin, Gary; Brown, Adam; Aftuck, Lynne; Shea, Terrance; Sykes, Sean; Berlin, Aaron; Chu, Jeff; Dooley, Kathleen; Hagopian, Daniel; Hall, Jennifer; Hafez, Nabil; Smith, Cherylyn L; Olandt, Peter; Miller, Karen; Ventkataraman, Vijay; Rachupka, Anthony; Dorris, Lester; Ayotte, Laura; Mabbitt, Richard; Erickson, Jeffrey; Horn, Andrea; An, Peter; Naylor, Jerome W; Settipalli, Sampath; Lander, Eric S; Lindblad-Toh, Kerstin; Wilson, Richard K; Graves, Tina A; Fulton, Robert S; Rock, Susan M; Hillier, LaDeana W; Chinwalla, Asif T; Bernard, Kelly; Courtney, Laura P; Fronick, Catrina; Fulton, Lucinda L; O'Laughlin, Michelle; Kremitzki, Colin L; Minx, Patrick J; Nelson, Joanne O; Schatzkamer, Kyriena L; Strong, Cynthia; Wollam, Aye M; Weinstock, George M; Yang, Shiaw-Pyng; Rogers, Jane; Grafham, Darren; Humphray, Sean; Nicholson, Christine; Bird, Christine; Brown, Andrew J; Burton, John; Clee, Chris; Hunt, Adrienne; Jones, Matt C; Lloyd, Christine; Matthews, Lucy; Mclaren, Karen; Mclaren, Stuart; McLay, Kirsten; Palmer, Sophie A; Plumb, Robert; Shownkeen, Ratna; Sims, Sarah; Quail, Mike A; Whitehead, Siobhan L; Willey, David L PLoS biology 2009 May;7(5):e1000112
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Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.
Gibbs, Richard A; Taylor, Jeremy F; Van Tassell, Curtis P; Barendse, William; Eversole, Kellye A; Gill, Clare A; Green, Ronnie D; Hamernik, Debora L; Kappes, Steven M; Lien, Sigbjørn; Matukumalli, Lakshmi K; McEwan, John C; Nazareth, Lynne V; Schnabel, Robert D; Weinstock, George M; Wheeler, David A; Ajmone-Marsan, Paolo; Boettcher, Paul J; Caetano, Alexandre R; Garcia, Jose Fernando; Hanotte, Olivier; Mariani, Paola; Skow, Loren C; Sonstegard, Tad S; Williams, John L; Diallo, Boubacar; Hailemariam, Lemecha; Martinez, Mario L; Morris, Chris A; Silva, Luiz O C; Spelman, Richard J; Mulatu, Woudyalew; Zhao, Keyan; Abbey, Colette A; Agaba, Morris; Araujo, Flábio R; Bunch, Rowan J; Burton, James; Gorni, Chiara; Olivier, Hanotte; Harrison, Blair E; Luff, Bill; Machado, Marco A; Mwakaya, Joel; Plastow, Graham; Sim, Warren; Smith, Timothy; Thomas, Merle B; Valentini, Alessio; Williams, Paul; Womack, James; Woolliams, John A; Liu, Yue; Qin, Xiang; Worley, Kim C; Gao, Chuan; Jiang, Huaiyang; Moore, Stephen S; Ren, Yanru; Song, Xing-Zhi; Bustamante, Carlos D; Hernandez, Ryan D; Muzny, Donna M; Patil, Shobha; San Lucas, Anthony; Fu, Qing; Kent, Matthew P; Vega, Richard; Matukumalli, Aruna; McWilliam, Sean; Sclep, Gert; Bryc, Katarzyna; Choi, Jungwoo; Gao, Hong; Grefenstette, John J; Murdoch, Brenda; Stella, Alessandra; Villa-Angulo, Rafael; Wright, Mark; Aerts, Jan; Jann, Oliver; Negrini, Riccardo; Goddard, Mike E; Hayes, Ben J; Bradley, Daniel G; Barbosa da Silva, Marcos; Lau, Lilian P L; Liu, George E; Lynn, David J; Panzitta, Francesca; Dodds, Ken G Science (New York, N.Y.) 2009 Apr;324(5926):528-32
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The genome sequence of taurine cattle: a window to ruminant biology and evolution.
Elsik, Christine G; Tellam, Ross L; Worley, Kim C; Gibbs, Richard A; Muzny, Donna M; Weinstock, George M; Adelson, David L; Eichler, Evan E; Elnitski, Laura; Guigó, Roderic; Hamernik, Debora L; Kappes, Steve M; Lewin, Harris A; Lynn, David J; Nicholas, Frank W; Reymond, Alexandre; Rijnkels, Monique; Skow, Loren C; Zdobnov, Evgeny M; Schook, Lawrence; Womack, James; Alioto, Tyler; Antonarakis, Stylianos E; Astashyn, Alex; Chapple, Charles E; Chen, Hsiu-Chuan; Chrast, Jacqueline; Câmara, Francisco; Ermolaeva, Olga; Henrichsen, Charlotte N; Hlavina, Wratko; Kapustin, Yuri; Kiryutin, Boris; Kitts, Paul; Kokocinski, Felix; Landrum, Melissa; Maglott, Donna; Pruitt, Kim; Sapojnikov, Victor; Searle, Stephen M; Solovyev, Victor; Souvorov, Alexandre; Ucla, Catherine; Wyss, Carine; Anzola, Juan M; Gerlach, Daniel; Elhaik, Eran; Graur, Dan; Reese, Justin T; Edgar, Robert C; McEwan, John C; Payne, Gemma M; Raison, Joy M; Junier, Thomas; Kriventseva, Evgenia V; Eyras, Eduardo; Plass, Mireya; Donthu, Ravikiran; Larkin, Denis M; Reecy, James; Yang, Mary Q; Chen, Lin; Cheng, Ze; Chitko-McKown, Carol G; Liu, George E; Matukumalli, Lakshmi K; Song, Jiuzhou; Zhu, Bin; Bradley, Daniel G; Brinkman, Fiona S L; Lau, Lilian P L; Whiteside, Matthew D; Walker, Angela; Wheeler, Thomas T; Casey, Theresa; German, J Bruce; Lemay, Danielle G; Maqbool, Nauman J; Molenaar, Adrian J; Seo, Seongwon; Stothard, Paul; Baldwin, Cynthia L; Baxter, Rebecca; Brinkmeyer-Langford, Candice L; Brown, Wendy C; Childers, Christopher P; Connelley, Timothy; Ellis, Shirley A; Fritz, Krista; Glass, Elizabeth J; Herzig, Carolyn T A; Iivanainen, Antti; Lahmers, Kevin K; Bennett, Anna K; Dickens, C Michael; Gilbert, James G R; Hagen, Darren E; Salih, Hanni; Aerts, Jan; Caetano, Alexandre R; Dalrymple, Brian; Garcia, Jose Fernando; Gill, Clare A; Hiendleder, Stefan G; Memili, Erdogan; Spurlock, Diane; Williams, John L; Alexander, Lee; Brownstein, Michael J; Guan, Leluo; Holt, Robert A; Jones, Steven J M; Marra, Marco A; Moore, Richard; Moore, Stephen S; Roberts, Andy; Taniguchi, Masaaki; Waterman, Richard C; Chacko, Joseph; Chandrabose, Mimi M; Cree, Andy; Dao, Marvin Diep; Dinh, Huyen H; Gabisi, Ramatu Ayiesha; Hines, Sandra; Hume, Jennifer; Jhangiani, Shalini N; Joshi, Vandita; Kovar, Christie L; Lewis, Lora R; Liu, Yih-Shin; Lopez, John; Morgan, Margaret B; Nguyen, Ngoc Bich; Okwuonu, Geoffrey O; Ruiz, San Juana; Santibanez, Jireh; Wright, Rita A; Buhay, Christian; Ding, Yan; Dugan-Rocha, Shannon; Herdandez, Judith; Holder, Michael; Sabo, Aniko; Egan, Amy; Goodell, Jason; Wilczek-Boney, Katarzyna; Fowler, Gerald R; Hitchens, Matthew Edward; Lozado, Ryan J; Moen, Charles; Steffen, David; Warren, James T; Zhang, Jingkun; Chiu, Readman; Schein, Jacqueline E; Durbin, K James; Havlak, Paul; Jiang, Huaiyang; Liu, Yue; Qin, Xiang; Ren, Yanru; Shen, Yufeng; Song, Henry; Bell, Stephanie Nicole; Davis, Clay; Johnson, Angela Jolivet; Lee, Sandra; Nazareth, Lynne V; Patel, Bella Mayurkumar; Pu, Ling-Ling; Vattathil, Selina; Williams, Rex Lee; Curry, Stacey; Hamilton, Cerissa; Sodergren, Erica; Wheeler, David A; Barris, Wes; Bennett, Gary L; Eggen, André; Green, Ronnie D; Harhay, Gregory P; Hobbs, Matthew; Jann, Oliver; Keele, John W; Kent, Matthew P; Lien, Sigbjørn; McKay, Stephanie D; McWilliam, Sean; Ratnakumar, Abhirami; Schnabel, Robert D; Smith, Timothy; Snelling, Warren M; Sonstegard, Tad S; Stone, Roger T; Sugimoto, Yoshikazu; Takasuga, Akiko; Taylor, Jeremy F; Van Tassell, Curtis P; Macneil, Michael D; Abatepaulo, Antonio R R; Abbey, Colette A; Ahola, Virpi; Almeida, Iassudara G; Amadio, Ariel F; Anatriello, Elen; Bahadue, Suria M; Biase, Fernando H; Boldt, Clayton R; Carroll, Jeffery A; Carvalho, Wanessa A; Cervelatti, Eliane P; Chacko, Elsa; Chapin, Jennifer E; Cheng, Ye; Choi, Jungwoo; Colley, Adam J; de Campos, Tatiana A; De Donato, Marcos; Santos, Isabel K F de Miranda; de Oliveira, Carlo J F; Deobald, Heather; Devinoy, Eve; Donohue, Kaitlin E; Dovc, Peter; Eberlein, Annett; Fitzsimmons, Carolyn J; Franzin, Alessandra M; Garcia, Gustavo R; Genini, Sem; Gladney, Cody J; Grant, Jason R; Greaser, Marion L; Green, Jonathan A; Hadsell, Darryl L; Hakimov, Hatam A; Halgren, Rob; Harrow, Jennifer L; Hart, Elizabeth A; Hastings, Nicola; Hernandez, Marta; Hu, Zhi-Liang; Ingham, Aaron; Iso-Touru, Terhi; Jamis, Catherine; Jensen, Kirsty; Kapetis, Dimos; Kerr, Tovah; Khalil, Sari S; Khatib, Hasan; Kolbehdari, Davood; Kumar, Charu G; Kumar, Dinesh; Leach, Richard; Lee, Justin C-M; Li, Changxi; Logan, Krystin M; Malinverni, Roberto; Marques, Elisa; Martin, William F; Martins, Natalia F; Maruyama, Sandra R; Mazza, Raffaele; McLean, Kim L; Medrano, Juan F; Moreno, Barbara T; Moré, Daniela D; Muntean, Carl T; Nandakumar, Hari P; Nogueira, Marcelo F G; Olsaker, Ingrid; Pant, Sameer D; Panzitta, Francesca; Pastor, Rosemeire C P; Poli, Mario A; Poslusny, Nathan; Rachagani, Satyanarayana; Ranganathan, Shoba; Razpet, Andrej; Riggs, Penny K; Rincon, Gonzalo; Rodriguez-Osorio, Nelida; Rodriguez-Zas, Sandra L; Romero, Natasha E; Rosenwald, Anne; Sando, Lillian; Schmutz, Sheila M; Shen, Libing; Sherman, Laura; Southey, Bruce R; Lutzow, Ylva Strandberg; Sweedler, Jonathan V; Tammen, Imke; Telugu, Bhanu Prakash V L; Urbanski, Jennifer M; Utsunomiya, Yuri T; Verschoor, Chris P; Waardenberg, Ashley J; Wang, Zhiquan; Ward, Robert; Weikard, Rosemarie; Welsh, Thomas H; White, Stephen N; Wilming, Laurens G; Wunderlich, Kris R; Yang, Jianqi; Zhao, Feng-Qi Science (New York, N.Y.) 2009 Apr;324(5926):522-8
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Bos taurus genome assembly.
Liu, Yue; Qin, Xiang; Song, Xing-Zhi Henry; Jiang, Huaiyang; Shen, Yufeng; Durbin, K James; Lien, Sigbjørn; Kent, Matthew Peter; Sodeland, Marte; Ren, Yanru; Zhang, Lan; Sodergren, Erica; Havlak, Paul; Worley, Kim C; Weinstock, George M; Gibbs, Richard A BMC genomics 2009 Jan;10180
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Somatic mutations affect key pathways in lung adenocarcinoma.
Ding, Li; Getz, Gad; Wheeler, David A; Mardis, Elaine R; McLellan, Michael D; Cibulskis, Kristian; Sougnez, Carrie; Greulich, Heidi; Muzny, Donna M; Morgan, Margaret B; Fulton, Lucinda; Fulton, Robert S; Zhang, Qunyuan; Wendl, Michael C; Lawrence, Michael S; Larson, David E; Chen, Ken; Dooling, David J; Sabo, Aniko; Hawes, Alicia C; Shen, Hua; Jhangiani, Shalini N; Lewis, Lora R; Hall, Otis; Zhu, Yiming; Mathew, Tittu; Ren, Yanru; Yao, Jiqiang; Scherer, Steven E; Clerc, Kerstin; Metcalf, Ginger A; Ng, Brian; Milosavljevic, Aleksandar; Gonzalez-Garay, Manuel L; Osborne, John R; Meyer, Rick; Shi, Xiaoqi; Tang, Yuzhu; Koboldt, Daniel C; Lin, Ling; Abbott, Rachel; Miner, Tracie L; Pohl, Craig; Fewell, Ginger; Haipek, Carrie; Schmidt, Heather; Dunford-Shore, Brian H; Kraja, Aldi; Crosby, Seth D; Sawyer, Christopher S; Vickery, Tammi; Sander, Sacha; Robinson, Jody; Winckler, Wendy; Baldwin, Jennifer; Chirieac, Lucian R; Dutt, Amit; Fennell, Tim; Hanna, Megan; Johnson, Bruce E; Onofrio, Robert C; Thomas, Roman K; Tonon, Giovanni; Weir, Barbara A; Zhao, Xiaojun; Ziaugra, Liuda; Zody, Michael C; Giordano, Thomas; Orringer, Mark B; Roth, Jack A; Spitz, Margaret R; Wistuba, Ignacio I; Ozenberger, Bradley; Good, Peter J; Chang, Andrew C; Beer, David G; Watson, Mark A; Ladanyi, Marc; Broderick, Stephen; Yoshizawa, Akihiko; Travis, William D; Pao, William; Province, Michael A; Weinstock, George M; Varmus, Harold E; Gabriel, Stacey B; Lander, Eric S; Gibbs, Richard A; Meyerson, Matthew; Wilson, Richard K Nature 2008 Oct;455(7216):1069-75
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A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery.
Wang, Xiaohu; Gao, Haichun; Shen, Yufeng; Weinstock, George M; Zhou, Jizhong; Palzkill, Timothy Nucleic acids research 2008 Sep;36(15):4863-71
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Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF.
Bourgogne, Agathe; Garsin, Danielle A; Qin, Xiang; Singh, Kavindra V; Sillanpaa, Jouko; Yerrapragada, Shailaja; Ding, Yan; Dugan-Rocha, Shannon; Buhay, Christian; Shen, Hua; Chen, Guan; Williams, Gabrielle; Muzny, Donna; Maadani, Arash; Fox, Kristina A; Gioia, Jason; Chen, Lei; Shang, Yue; Arias, Cesar A; Nallapareddy, Sreedhar R; Zhao, Meng; Prakash, Vittal P; Chowdhury, Shahreen; Jiang, Huaiyang; Gibbs, Richard A; Murray, Barbara E; Highlander, Sarah K; Weinstock, George M Genome biology 2008 Jan;9(7):R110
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Identification of novel and cross-species seroreactive proteins from Bacillus anthracis using a ligation-independent cloning-based, SOS-inducible expression system.
McWilliams, Brian D; Palzkill, Timothy; Weinstock, George M; Petrosino, Joseph F Microbial pathogenesis 53(5-6):250-8