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How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
Published in:
BMC Genomics, 2012, v. 13, n. 1, p. 734, doi. 10.1186/1471-2164-13-734
By:
- Haas, Brian J.;
- Chin, Melissa;
- Nusbaum, Chad;
- Birren, Bruce W.;
- Livny, Jonathan
Publication type:
Article
A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa.
Published in:
2009
By:
- Lambreghts, Randy;
- Mi Shi;
- Belden, William J.;
- deCaprio, David;
- Park, Danny;
- Henn, Matthew R.;
- Galagan, James E.;
- Baştürkmen, Meray;
- Birren, Bruce W.;
- Sachs, Matthew S.;
- Dunlap, Jay C.;
- Loros, Jennifer J.
Publication type:
Abstract
Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.
Published in:
Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0271-6
By:
- Yassour, Moran;
- Mi Young Lim;
- Hyun Sun Yun;
- Tickle, Timothy L.;
- Joohon Sung;
- Yun-Mi Song;
- Kayoung Lee;
- Franzosa, Eric A.;
- Morgan, Xochitl C.;
- Gevers, Dirk;
- Lander, Eric S.;
- Xavier, Ramnik J.;
- Birren., Bruce W.;
- GwangPyo Ko;
- Huttenhower, Curtis
Publication type:
Article
Staphylococcal Enterotoxin P Predicts Bacteremia in Hospitalized Patients Colonized With Methicillin-Resistant Staphylococcus aureus.
Published in:
Journal of Infectious Diseases, 2014, v. 209, n. 4, p. 571, doi. 10.1093/infdis/jit501
By:
- Calderwood, Michael S.;
- Desjardins, Christopher A.;
- Sakoulas, George;
- Nicol, Robert;
- DuBois, Andrea;
- Delaney, Mary L.;
- Kleinman, Ken;
- Cosimi, Lisa A.;
- Feldgarden, Michael;
- Onderdonk, Andrew B.;
- Birren, Bruce W.;
- Platt, Richard;
- Huang, Susan S.
Publication type:
Article
Whole Genome Pyrosequencing of Rare Hepatitis C Virus Genotypes Enhances Subtype Classification and Identification of Naturally Occurring Drug Resistance Variants.
Published in:
Journal of Infectious Diseases, 2013, v. 208, n. 1, p. 17, doi. 10.1093/infdis/jis679
By:
- Newman, Ruchi M.;
- Kuntzen, Thomas;
- Weiner, Brian;
- Berical, Andrew;
- Charlebois, Patrick;
- Kuiken, Carla;
- Murphy, Donald G.;
- Simmonds, Peter;
- Bennett, Phil;
- Lennon, Niall J.;
- Birren, Bruce W.;
- Zody, Michael C.;
- Allen, Todd M.;
- Henn, Matthew R.
Publication type:
Article
Reemergence and Decline of Dengue Virus Serotype 3 in Puerto Rico.
Published in:
Journal of Infectious Diseases, 2012, v. 206, n. 6, p. 893, doi. 10.1093/infdis/jis426
By:
- Santiago, Gilberto A.;
- McElroy-Horne, Kate;
- Lennon, Niall J.;
- Santiago, Luis M.;
- Birren, Bruce W.;
- Henn, Matthew R.;
- Muñoz-Jordán, Jorge L.
Publication type:
Article
Endemic Dengue Associated with the Co-Circulation of Multiple Viral Lineages and Localized Density- Dependent Transmission.
Published in:
PLoS Pathogens, 2011, v. 7, n. 6, p. 1, doi. 10.1371/journal.ppat.1002064
By:
- Raghwani, Jayna;
- Rambaut, Andrew;
- Holmes, Edward C.;
- Vu Ty Hang;
- Tran Tinh Hien;
- Farrar, Jeremy;
- Wills, Bridget;
- Lennon, Niall J.;
- Birren, Bruce W.;
- Henn, Matthew R.;
- Simmons, Cameron P.
Publication type:
Article
Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data.
Published in:
PLoS Computational Biology, 2012, v. 8, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002417
By:
- Macalalad, Alexander R.;
- Zody, Michael C.;
- Charlebois, Patrick;
- Lennon, Niall J.;
- Newman, Ruchi M.;
- Malboeuf, Christine M.;
- Ryan, Elizabeth M.;
- Boutwell, Christian L.;
- Power, Karen A.;
- Brackney, Doug E.;
- Pesko, Kendra N.;
- Levin, Joshua Z.;
- Ebel, Gregory D.;
- Allen, Todd M.;
- Birren, Bruce W.;
- Henn, Matthew R.
Publication type:
Article
PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.
Published in:
Bioinformatics, 2011, v. 27, n. 2, p. 266, doi. 10.1093/bioinformatics/btq624
By:
- Yu, Qing;
- Ryan, Elizabeth M.;
- Allen, Todd M.;
- Birren, Bruce W.;
- Henn, Matthew R.;
- Lennon, Niall J.
Publication type:
Article
Endurance, Refuge, and Reemergence of Dengue Virus Type 2, Puerto Rico, 1986-2007.
Published in:
Emerging Infectious Diseases, 2011, v. 17, n. 1, p. 64, doi. 10.3201/eid1701.100961
By:
- McElroy, Kate L.;
- Santiago, Gilberto A.;
- Lennon, Niall J.;
- Birren, Bruce W.;
- Henn, Matthew R.;
- Muñoz-Jordán, Jorge L.
Publication type:
Article
Hybrid selection for sequencing pathogen genomes from clinical samples.
Published in:
Genome Biology, 2011, v. 12, n. 8, p. 1, doi. 10.1186/gb-2011-12-8-r73
By:
- Melnikov, Alexandre;
- Galinsky, Kevin;
- Rogov, Peter;
- Fennell, Timothy;
- Van Tyne, Daria;
- Russ, Carsten;
- Daniels, Rachel;
- Barnes, Kayla G;
- Bochicchio, James;
- Ndiaye, Daouda;
- Sene, Papa D;
- Wirth, Dyann F;
- Nusbaum, Chad;
- Volkman, Sarah K;
- Birren, Bruce W;
- Gnirke, Andreas;
- Neafsey, Daniel E
Publication type:
Article
Emergence of the Asian 1 Genotype of Dengue Virus Serotype 2 in Viet Nam: In Vivo Fitness Advantage and Lineage Replacement in South-East Asia.
Published in:
PLoS Neglected Tropical Diseases, 2010, v. 4, n. 7, p. 1, doi. 10.1371/journal.pntd.0000757
By:
- Ty Hang, Vu Thi;
- Holmes, Edward C.;
- Veasna, Duong;
- Quy, Nguyen Thien;
- Tinh Hien, Tran;
- Quail, Michael;
- Churcher, Carol;
- Parkhill, Julian;
- Cardosa, Jane;
- Farrar, Jeremy;
- Wills, Bridget;
- Lennon, Niall J.;
- Birren, Bruce W.;
- Buchy, Philippe;
- Henn, Matthew R.;
- Simmons, Cameron P.
Publication type:
Article
Emergence of the Asian 1 Genotype of Dengue Virus Serotype 2 in Viet Nam: In Vivo Fitness Advantage and Lineage Replacement in South-East Asia.
Published in:
PLoS Neglected Tropical Diseases, 2010, v. 4, n. 7, p. 1, doi. 10.1371/journal.pntd.0000757
By:
- Vu Thi Ty Hang;
- Holmes, Edward C.;
- Veasna, Duong;
- Nguyen Thien Quy;
- Tran Tinh Hien;
- Quail, Michael;
- Churcher, Carol;
- Parkhill, Julian;
- Cardosa, Jane;
- Farrar, Jeremy;
- Wills, Bridget;
- Lennon, Niall J.;
- Birren, Bruce W.;
- Buchy, Philippe;
- Henn, Matthew R.;
- Simmons, Cameron P.
Publication type:
Article
Evolutionary Dynamics of the Accessory Genome of <i>Listeria monocytogenes</i>.
Published in:
PLoS ONE, 2013, v. 8, n. 6, p. 1, doi. 10.1371/journal.pone.0067511
By:
- den Bakker, Henk C.;
- Desjardins, Christopher A.;
- Griggs, Allison D.;
- Peters, Joseph E.;
- Zeng, Qiandong;
- Young, Sarah K.;
- Kodira, Chinnappa D.;
- Yandava, Chandri;
- Hepburn, Theresa A.;
- Haas, Brian J.;
- Birren, Bruce W.;
- Wiedmann, Martin
Publication type:
Article
The "Most Wanted" Taxa from the Human Microbiome for Whole Genome Sequencing.
Published in:
PLoS ONE, 2012, v. 7, n. 7, p. 1, doi. 10.1371/journal.pone.0041294
By:
- Fodor, Anthony A.;
- DeSantis, Todd Z.;
- Wylie, Kristine M.;
- Badger, Jonathan H.;
- Yuzhen Ye;
- Hepburn, Theresa;
- Ping Hu;
- Sodergren, Erica;
- Liolios, Konstantinos;
- Huot-Creasy, Heather;
- Birren, Bruce W.;
- Earl, Ashlee M.
Publication type:
Article
Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes.
Published in:
PLoS ONE, 2010, v. 5, n. 2, p. 1, doi. 10.1371/journal.pone.0009083
By:
- Henn, Matthew R.;
- Sullivan, Matthew B.;
- Stange-Thomann, Nicole;
- Osburne, Marcia S.;
- Berlin, Aaron M.;
- Kelly, Libusha;
- Yandava, Chandri;
- Kodira, Chinnappa;
- Qiandong Zeng;
- Weiand, Michael;
- Sparrow, Todd;
- Saif, Sakina;
- Giannoukos, Georgia;
- Young, Sarah K.;
- Nusbaum, Chad;
- Birren, Bruce W.;
- Chisholm, Sallie W.
Publication type:
Article
Whole Genome Amplification and De novo Assembly of Single Bacterial Cells.
Published in:
PLoS ONE, 2009, v. 4, n. 9, p. 1, doi. 10.1371/journal.pone.0006864
By:
- Rodrigue, Sébastien;
- Malmstrom, Rex R.;
- Berlin, Aaron M.;
- Birren, Bruce W.;
- Henn, Matthew R.;
- Chisholm, Sallie W.
Publication type:
Article
A novel member of the F-box/WD40 gene family, encoding dactylin, is disrupted in the mouse dactylaplasia mutant.
Published in:
Nature Genetics, 1999, v. 23, n. 1, p. 104, doi. 10.1038/12709
By:
- Sidow, Arend;
- Bulotsky, Monique S.;
- Kerrebrock, Anne W.;
- Birren, Bruce W.;
- Altshuler, David;
- Jaenisch, Rudolf;
- Johnson, Kenneth R.;
- Lander, Eric S.
Publication type:
Article
A YAC-based physical map of the mouse genome.
Published in:
Nature Genetics, 1999, v. 22, n. 4, p. 388, doi. 10.1038/11967
By:
- Nusbaum, Chad;
- Slonim, Donna K.;
- Harris, Katrina L.;
- Birren, Bruce W.;
- Steen, Robert G.;
- Stein, Lincoln D.;
- Miller, Joyce;
- Dietrich, William F.;
- Nahf, Robert;
- Wang, Victoria;
- Merport, Olga;
- Castle, Andrew B.;
- Husain, Zeeshan;
- Farino, Gail;
- Gray, Delphine;
- Anderson, Mechele O.;
- Devine, Richard;
- Horton, Lloyd T.;
- Ye, Wenjuan
Publication type:
Article
The mouse pudgy mutation disrupts Delta homologue Dll3 and initiation of early somite boundaries.
Published in:
Nature Genetics, 1998, v. 19, n. 3, p. 274, doi. 10.1038/961
By:
- Kusumi, Kenro;
- Sun, Eileen;
- Kerrebrock, Anne W.;
- Bronson, Roderick T.;
- Chi, Dow-Chung;
- Bulotsky, Monique;
- Spencer, Jessica B.;
- Birren, Bruce W.;
- Frankel, Wayne N.;
- Lander, Eric S.
Publication type:
Article
Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.
Published in:
Nature Methods, 2009, v. 6, n. 1, p. 67, doi. 10.1038/nmeth.1286
By:
- Nusbaum, Chad;
- Ohsumi, Toshiro K.;
- Gomez, James;
- Aquadro, John;
- Victor, Thomas C.;
- Warren, Robert M.;
- Hung, Deborah T.;
- Birren, Bruce W.;
- Lander, Eric S.;
- Jaffe, David B.
Publication type:
Article
Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development.
Published in:
PLoS Genetics, 2011, v. 7, n. 9, p. 1, doi. 10.1371/journal.pgen.1002219
By:
- Holder, Jason W.;
- Ulrich, Jil C.;
- DeBono, Anthony C.;
- Godfrey, Paul A.;
- Desjardins, Christopher A.;
- Zucker, Jeremy;
- Zeng, Qiandong;
- Leach, Alex L. B.;
- Ghiviriga, Ion;
- Dancel, Christine;
- Abeel, Thomas;
- Gevers, Dirk;
- Kodira, Chinnappa D.;
- Desany, Brian;
- Affourtit, Jason P.;
- Birren, Bruce W.;
- Sinskey, Anthony J.
Publication type:
Article
Pulsed field gel electrophoresis: Studies of DNA migration made with the programmable, autonomously-controlled electrode electrophoresis system.
Published in:
Electrophoresis, 1989, v. 10, n. 5/6, p. 302, doi. 10.1002/elps.1150100506
By:
- Birren, Bruce W.;
- Hood, Leroy;
- Lai, Eric
Publication type:
Article
Dynamics of Dengue Disease Severity Determined by the Interplay Between Viral Genetics and Serotype-Specific Immunity.
Published in:
Science Translational Medicine, 2011, v. 3, n. 114, p. 1, doi. 10.1126/scitranslmed.3003084
By:
- OhAinle, Molly;
- Balmaseda, Angel;
- Macalalad, Alexander R.;
- Tellez, Yolanda;
- Zody, Michael C.;
- Saborío, Saira;
- Nuñez, Andrea;
- Lennon, Niall J.;
- Birren, Bruce W.;
- Gordon, Aubree;
- Henn, Matthew R.;
- Harris, Eva
Publication type:
Article
Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota.
Published in:
ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2014, v. 8, n. 3, p. 493, doi. 10.1038/ismej.2013.167
By:
- Lee, Sunghee;
- Cantarel, Brandi;
- Henrissat, Bernard;
- Gevers, Dirk;
- Birren, Bruce W;
- Huttenhower, Curtis;
- Ko, GwangPyo
Publication type:
Article
Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.
Published in:
Nature Genetics, 2013, v. 45, n. 5, p. 495, doi. 10.1038/ng.2585
By:
- Desjardins, Christopher A;
- Cerqueira, Gustavo C;
- Goldberg, Jonathan M;
- Hotopp, Julie C Dunning;
- Haas, Brian J;
- Zucker, Jeremy;
- Ribeiro, José M C;
- Saif, Sakina;
- Levin, Joshua Z;
- Fan, Lin;
- Zeng, Qiandong;
- Russ, Carsten;
- Wortman, Jennifer R;
- Fink, Doran L;
- Birren, Bruce W;
- Nutman, Thomas B
Publication type:
Article
Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses.
Published in:
Nature Genetics, 2012, v. 44, n. 9, p. 1060, doi. 10.1038/ng.2372
By:
- O'Connell, Richard J;
- Thon, Michael R;
- Hacquard, Stéphane;
- Amyotte, Stefan G;
- Kleemann, Jochen;
- Torres, Maria F;
- Damm, Ulrike;
- Buiate, Ester A;
- Epstein, Lynn;
- Alkan, Noam;
- Altmüller, Janine;
- Alvarado-Balderrama, Lucia;
- Bauser, Christopher A;
- Becker, Christian;
- Birren, Bruce W;
- Chen, Zehua;
- Choi, Jaeyoung;
- Crouch, Jo Anne;
- Duvick, Jonathan P;
- Farman, Mark A
Publication type:
Article
The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum.
Published in:
Nature Genetics, 2012, v. 44, n. 9, p. 1046, doi. 10.1038/ng.2373
By:
- Neafsey, Daniel E;
- Galinsky, Kevin;
- Jiang, Rays H Y;
- Young, Lauren;
- Sykes, Sean M;
- Saif, Sakina;
- Gujja, Sharvari;
- Goldberg, Jonathan M;
- Young, Sarah;
- Zeng, Qiandong;
- Chapman, Sinéad B;
- Dash, Aditya P;
- Anvikar, Anupkumar R;
- Sutton, Patrick L;
- Birren, Bruce W;
- Escalante, Ananias A;
- Barnwell, John W;
- Carlton, Jane M
Publication type:
Article
The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome.
Published in:
PLoS Biology, 2012, v. 10, n. 8, p. 1, doi. 10.1371/journal.pbio.1001377
By:
- Gevers, Dirk;
- Knight, Rob;
- Petrosino, Joseph F.;
- Huang, Katherine;
- McGuire, Amy L.;
- Birren, Bruce W.;
- Nelson, Karen E.;
- White, Owen;
- Methé, Barbara A.;
- Huttenhower, Curtis
Publication type:
Article
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.
Published in:
Nature, 2004, v. 428, n. 6983, p. 617, doi. 10.1038/nature02424
By:
- Kellis, Manolis;
- Birren, Bruce W.;
- Lander, Eric S.
Publication type:
Article
Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance.
Published in:
Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1204-4
By:
- Cerqueira, Gustavo C.;
- Cheeseman, Ian H.;
- Schaffner, Steve F.;
- Nair, Shalini;
- McDew-White, Marina;
- Phyo, Aung Pyae;
- Ashley, Elizabeth A.;
- Melnikov, Alexandre;
- Rogov, Peter;
- Birren, Bruce W.;
- Nosten, François;
- Anderson, Timothy J. C.;
- Neafsey, Daniel E.
Publication type:
Article
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Published in:
Nature Biotechnology, 2011, v. 29, n. 7, p. 644, doi. 10.1038/nbt.1883
By:
- Grabherr, Manfred G;
- Haas, Brian J;
- Yassour, Moran;
- Levin, Joshua Z;
- Thompson, Dawn A;
- Amit, Ido;
- Adiconis, Xian;
- Fan, Lin;
- Raychowdhury, Raktima;
- Zeng, Qiandong;
- Chen, Zehua;
- Mauceli, Evan;
- Hacohen, Nir;
- Gnirke, Andreas;
- Rhind, Nicholas;
- di Palma, Federica;
- Birren, Bruce W;
- Nusbaum, Chad;
- Lindblad-Toh, Kerstin;
- Friedman, Nir
Publication type:
Article
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Published in:
2011
By:
- Yilmaz, Pelin;
- Kottmann, Renzo;
- Field, Dawn;
- Knight, Rob;
- Cole, James R.;
- Amaral-Zettler, Linda;
- Gilbert, Jack A.;
- Karsch-Mizrachi, Ilene;
- Johnston, Anjanette;
- Cochrane, Guy;
- Vaughan, Robert;
- Hunter, Christopher;
- Park, Joonhong;
- Morrison, Norman;
- Rocca-Serra, Philippe;
- Sterk, Peter;
- Arumugam, Manimozhiyan;
- Bailey, Mark;
- Baumgartner, Laura;
- Birren, Bruce W.
Publication type:
Opinion
A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame.
Published in:
Journal of Medical Virology, 2008, v. 80, n. 8, p. 1370, doi. 10.1002/jmv.21240
By:
- Kuntzen, Thomas;
- Berical, Andrew;
- Ndjomou, Jean;
- Bennett, Phil;
- Schneidewind, Arne;
- Lennon, Niall;
- Birren, Bruce W.;
- Kuiken, Carla;
- Henn, Matthew R.;
- Simmonds, Peter;
- Allen, Todd M.
Publication type:
Article

Found: 34