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1

Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome

Zarrinpar, Amir, Chaix, Amandine, Yooseph, Shibu, Panda, Satchidananda

Journal:

Cell Metabolism

Year:

2014

Language:

english

File:

PDF, 2.05 MB

english, 2014

2

803 Diet and Time Restricted Feeding Modulate Cyclical Changes in the Gut Microbiome and Can Affect Metabolic Homeostasis Through Bile Acid Signaling

Zarrinpar, Amir, Yooseph, Shibu, Chaix, Amandine, Adams, Mark D., Panda, Satchidananda

Journal:

Gastroenterology

Year:

2014

Language:

english

File:

PDF, 65 KB

english, 2014

3

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering

Shibu Yooseph, Weizhong Li, Granger Sutton

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 815 KB

english, 2008

4

Library preparation methodology can influence genomic and functional predictions in human microbiome research

Jones, Marcus B., Highlander, Sarah K., Anderson, Ericka L., Li, Weizhong, Dayrit, Mark, Klitgord, Niels, Fabani, Martin M., Seguritan, Victor, Green, Jessica, Pride, David T., Yooseph, Shibu, Biggs,

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 878 KB

english, 2015

5

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome

Anderson, Ericka L., Li, Weizhong, Klitgord, Niels, Highlander, Sarah K., Dayrit, Mark, Seguritan, Victor, Yooseph, Shibu, Biggs, William, Venter, J. Craig, Nelson, Karen E., Jones, Marcus B.

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.20 MB

english, 2016

6

Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy

Rosas-Salazar, Christian, Shilts, Meghan H., Tovchigrechko, Andrey, Schobel, Seth, Chappell, James D., Larkin, Emma K., Shankar, Jyoti, Yooseph, Shibu, Nelson, Karen E., Halpin, Rebecca A., Moore, Mar

Journal:

The Journal of Infectious Diseases

Year:

2016

Language:

english

File:

PDF, 295 KB

english, 2016

7

A Metagenomic Framework for the Study of Airborne Microbial Communities

Yooseph, Shibu, Andrews-Pfannkoch, Cynthia, Tenney, Aaron, McQuaid, Jeff, Williamson, Shannon, Thiagarajan, Mathangi, Brami, Daniel, Zeigler-Allen, Lisa, Hoffman, Jeff, Goll, Johannes B., Fadrosh, Dou

Journal:

Year:

2013

Language:

english

File:

PDF, 1.59 MB

english, 2013

8

TAL Recognition inO(M(n2)) Time

Sanguthevar Rajasekaran, Shibu Yooseph

Journal:

Journal of Computer and System Sciences

Year:

1998

Language:

english

File:

PDF, 240 KB

english, 1998

9

Unifying Themes for Selection on Any Network

Sanguthevar Rajasekaran, Wang Chen, Shibu Yooseph

Journal:

Journal of Parallel and Distributed Computing

Year:

1997

Language:

english

File:

PDF, 102 KB

english, 1997

10

Viral photosynthetic reaction center genes and transcripts in the marine environment

Sharon, Itai, Tzahor, Shani, Williamson, Shannon, Shmoish, Michael, Man-Aharonovich, Dikla, Rusch, Douglas B, Yooseph, Shibu, Zeidner, Gil, Golden, Susan S, Mackey, Shannon R

Journal:

The ISME Journal

Year:

2007

Language:

english

File:

PDF, 500 KB

english, 2007

11

Genomic and functional adaptation in surface ocean planktonic prokaryotes

Yooseph, Shibu, Nealson, Kenneth H., Rusch, Douglas B., McCrow, John P., Dupont, Christopher L., Kim, Maria, Johnson, Justin, Montgomery, Robert, Ferriera, Steve, Beeson, Karen

Journal:

Year:

2010

Language:

english

File:

PDF, 445 KB

english, 2010

12

A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

Kerstin Röske, Mark F Foecking, Shibu Yooseph, John I Glass, Michael J Calcutt, Kim S Wise

Journal:

Year:

2010

Language:

english

File:

PDF, 1.32 MB

english, 2010

13

ANDES: Statistical tools for the ANalyses of DEep Sequencing

Kelvin Li, Eli Venter, Shibu Yooseph, Timothy B Stockwell, Lance D Eckerle, Mark R Denison, David J Spiro, Barbara A Methé

Journal:

BMC Research Notes

Year:

2010

Language:

english

File:

PDF, 722 KB

english, 2010

14

Computing the Local Consensus of Trees

Kannan, Sampath, Warnow, Tandy, Yooseph, Shibu

Journal:

SIAM Journal on Computing

Year:

1998

Language:

english

File:

PDF, 436 KB

english, 1998

15

Metagenomic investigation of microbes and viruses in patients with jaw osteonecrosis associated with bisphosphonate therapy

Parish P. Sedghizadeh, Shibu Yooseph, Douglas W. Fadrosh, Lisa Zeigler-Allen, Mathangi Thiagarajan, Hamid Salek, Farid Farahnik, Shannon J. Williamson

Journal:

Oral Surgery Oral Medicine Oral Pathology and Oral Radiology

Year:

2012

Language:

english

File:

PDF, 581 KB

english, 2012

16

Comparative genome analysis of 19Ureaplasma urealyticumandUreaplasma parvumstrains

Vanya Paralanov, Jin Lu, Lynn B Duffy, Donna M Crabb, Susmita Shrivastava, Barbara A Methé, Jason Inman, Shibu Yooseph, Li Xiao, Gail H Cassell, Ken B Waites, John I Glass

Journal:

BMC Microbiology

Year:

2012

Language:

english

File:

PDF, 1.56 MB

english, 2012

17

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

Dupont, Chris L, Rusch, Douglas B, Yooseph, Shibu, Lombardo, Mary-Jane, Alexander Richter, R, Valas, Ruben, Novotny, Mark, Yee-Greenbaum, Joyclyn, Selengut, Jeremy D, Haft, Dan H, Halpern, Aaron L, La

Journal:

The ISME Journal

Year:

2012

Language:

english

File:

PDF, 806 KB

english, 2012

18

Evolution of allostery in the cyclic nucleotide binding module

Natarajan Kannan, Jian Wu, Ganesh S Anand, Shibu Yooseph…

Journal:

Year:

2007

Language:

english

File:

PDF, 1.24 MB

english, 2007

19

Anin vitrobiofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome

Edlund, Anna, Yang, Youngik, Hall, Adam P, Guo, Lihong, Lux, Renate, He, Xuesong, Nelson, Karen E, Nealson, Kenneth H, Yooseph, Shibu, Shi, Wenyuan, McLean, Jeffrey S

Journal:

Year:

2013

Language:

english

File:

PDF, 1.33 MB

english, 2013

20

Haplotyping as Perfect Phylogeny: A Direct Approach

Bafna, Vineet, Gusfield, Dan, Lancia, Giuseppe, Yooseph, Shibu

Journal:

Journal of Computational Biology

Year:

2003

Language:

english

File:

PDF, 375 KB

english, 2003

21

Tu1905 Distinct Adherent Bacterial Communities in Colon Cancer Tumors and Their Matched Normal

Brim, Hassan, Yooseph, Shibu, Lee, Edward L., Torralba, Manolito, Nelson, Karen E., Ashktorab, Hassan

Journal:

Gastroenterology

Year:

2013

Language:

english

File:

PDF, 175 KB

english, 2013

22

[ACM Press the Conference - San Diego, California (2013.07.22-2013.07.25)] Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE '13 - Large memory high performance computing enables comparison across human gut microbiome of patients with autoimmune diseases and healthy subjects

Wu, Sitao, Li, Weizhong, Smarr, Larry, Nelson, Karen, Yooseph, Shibu, Torralba, Manolito

Year:

2013

Language:

english

File:

PDF, 341 KB

english, 2013

23

Zinc Finger Gene Clusters and Tandem Gene Duplication

Tang, Mengxiang, Waterman, Michael, Yooseph, Shibu

Journal:

Journal of Computational Biology

Year:

2002

Language:

english

File:

PDF, 369 KB

english, 2002

24

Constructing Evolutionary Trees in the Presence of Polymorphic Characters

Bonet, Maria, Phillips, Cynthia, Warnow, Tandy, Yooseph, Shibu

Journal:

SIAM Journal on Computing

Year:

1999

Language:

english

File:

PDF, 465 KB

english, 1999

25

A Note on Efficient Computation of Haplotypes via Perfect Phylogeny

Bafna, Vineet, Gusfield, Dan, Hannenhalli, Sridhar, Yooseph, Shibu

Journal:

Journal of Computational Biology

Year:

2004

Language:

english

File:

PDF, 90 KB

english, 2004

26

ThurGood: Evaluating Assembly-to-Assembly Mapping

Shatkay, Hagit, Miller, Jason, Mobarry, Clark, Flanigan, Michael, Yooseph, Shibu, Sutton, Granger

Journal:

Journal of Computational Biology

Year:

2004

Language:

english

File:

PDF, 189 KB

english, 2004

27

Better Methods for Solving Parsimony and Compatibility

BONET, MARIA, STEEL, MIKE, WARNOW, TANDY, YOOSEPH, SHIBU

Journal:

Journal of Computational Biology

Year:

1998

Language:

english

File:

PDF, 2.35 MB

english, 1998

28

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

Llorens-Marès, Tomàs, Yooseph, Shibu, Goll, Johannes, Hoffman, Jeff, Vila-Costa, Maria, Borrego, Carles M, Dupont, Chris L, Casamayor, Emilio O

Journal:

The ISME Journal

Year:

2015

Language:

english

File:

PDF, 1.26 MB

english, 2015

29

Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea

Larsson, John, Celepli, Narin, Ininbergs, Karolina, Dupont, Christopher L, Yooseph, Shibu, Bergman, Bigitta, Ekman, Martin

Journal:

The ISME Journal

Year:

2014

Language:

english

File:

PDF, 1.47 MB

english, 2014

30

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

He, Xuesong, McLean, Jeffrey S., Edlund, Anna, Yooseph, Shibu, Hall, Adam P., Liu, Su-Yang, Dorrestein, Pieter C., Esquenazi, Eduardo, Hunter, Ryan C., Cheng, Genhong, Nelson, Karen E., Lux, Renate, S

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.23 MB

english, 2015

31

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism

Edlund, Anna, Yang, Youngik, Yooseph, Shibu, Hall, Adam P, Nguyen, Don D, Dorrestein, Pieter C, Nelson, Karen E, He, Xuesong, Lux, Renate, Shi, Wenyuan, McLean, Jeffrey S

Journal:

The ISME Journal

Year:

2015

Language:

english

File:

PDF, 3.83 MB

english, 2015

32

[ACM Press the second annual international conference - New York, New York, United States (1998.03.22-1998.03.25)] Proceedings of the second annual international conference on Computational molecular biology - RECOMB '98 - Better methods for solving parsimony and compatibility

Bonet, Maria, Steel, Mike, Warnow, Tandy, Yooseph, Shibu

Year:

1998

Language:

english

File:

PDF, 1.36 MB

english, 1998

33

[ACM Press the fifth annual international conference - Montreal, Quebec, Canada (2001.04.22-2001.04.25)] Proceedings of the fifth annual international conference on Computational biology - RECOMB '01 - Zinc finger gene clusters and tandem gene duplication

Tang, Mengxiang, Waterman, Michael, Yooseph, Shibu

Year:

2001

Language:

english

File:

PDF, 238 KB

english, 2001

34

[ACM Press the twenty-eighth annual ACM symposium - Philadelphia, Pennsylvania, United States (1996.05.22-1996.05.24)] Proceedings of the twenty-eighth annual ACM symposium on Theory of computing - STOC '96 - Constructing evolutionary trees in the presence of polymorphic characters

Bonet, Maria, Phillips, Cynthia, Warnow, Tandy J., Yooseph, Shibu

Year:

1996

Language:

english

File:

PDF, 1.23 MB

english, 1996

35

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection

Yooseph, Shibu, Kirkness, Ewen F., Tran, Tuan M., Harkins, Derek M., Jones, Marcus B., Torralba, Manolito G., O’Connell, Elise, Nutman, Thomas B., Doumbo, Safiatou, Doumbo, Ogobara K., Traore, Boubaca

Journal:

Year:

2015

Language:

english

File:

PDF, 1.50 MB

english, 2015

36

Series on Advances in Bioinformatics and Computational Biololgy [Imperial College Press Computational Systems Bioinformatics - the Conference CSB 2006 - Stanford CA (2006.08.14-2006.08.18)] Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006 - EXPLORING THE OCEAN'S MICROBES: SEQUENCING THE SEVEN SEAS

Frazier, Marvin E., Rusch, Douglas B., Halpern, Aaron L., Heidelberg, Karla B., Sutton, Granger, Williamson, Shannon, Yooseph, Shibu, Wu, Dongying, Eisen, Jonathan A., Hoffman, Jeff, Howard, Charles H

Year:

2006

Language:

english

File:

PDF, 93 KB

english, 2006

37

Global biogeography of Prochlorococcus genome diversity in the surface ocean

Kent, Alyssa G, Dupont, Chris L, Yooseph, Shibu, Martiny, Adam C

Journal:

The ISME Journal

Year:

2016

Language:

english

File:

PDF, 890 KB

english, 2016

38

Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters

Brindefalk, Björn, Ekman, Martin, Ininbergs, Karolina, Dupont, Christopher L., Yooseph, Shibu, Pinhassi, Jarone, Bergman, Birgitta

Journal:

Environmental Microbiology

Year:

2016

Language:

english

File:

PDF, 1.88 MB

english, 2016

39

Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis

Rajagopala, Seesandra V., Yooseph, Shibu, Harkins, Derek M., Moncera, Kelvin J., Zabokrtsky, Keri B., Torralba, Manolito G., Tovchigrechko, Andrey, Highlander, Sarah K., Pieper, Rembert, Sender, Leona

Journal:

Year:

2016

Language:

english

File:

PDF, 715 KB

english, 2016

40

Effect of Macondo Prospect 252 Oil on Microbiota Associated with PelagicSargassumin the Northern Gulf of Mexico

Torralba, Manolito G., Franks, James S., Gomez, Andres, Yooseph, Shibu, Nelson, Karen E., Grimes, D. Jay

Journal:

Microbial Ecology

Year:

2017

Language:

english

File:

PDF, 1.57 MB

english, 2017

41

Meta-omic analyses of Baltic Sea cyanobacteria: Diversity, community structure and salt acclimation

Celepli, Narin, Sundh, John, Ekman, Martin, Dupont, Chris L., Yooseph, Shibu, Bergman, Birgitta, Ininbergs, Karolina

Journal:

Environmental Microbiology

Year:

2016

Language:

english

File:

PDF, 2.04 MB

english, 2016

42

GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly

Zhong, Cuncong, Yang, Youngik, Yooseph, Shibu

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 798 KB

english, 2016

43

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies

Greenwald, William W., Klitgord, Niels, Seguritan, Victor, Yooseph, Shibu, Venter, J. Craig, Garner, Chad, Nelson, Karen E., Li, Weizhong

Journal:

Year:

2017

Language:

english

File:

PDF, 1.25 MB

english, 2017

44

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease

Moustafa, Ahmed, Li, Weizhong, Anderson, Ericka L, Wong, Emily H M, Dulai, Parambir S, Sandborn, William J, Biggs, William, Yooseph, Shibu, Jones, Marcus B, Venter, J Craig, Nelson, Karen E, Chang, Jo

Journal:

Clinical and Translational Gastroenterology

Year:

2018

Language:

english

File:

PDF, 1.07 MB

english, 2018

45

[IEEE 2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Orlando, FL, USA (2017.10.19-2017.10.21)] 2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - GRASP2: Fast and memory-efficient gene-centric assembly and homolog search

Zhong, Cuncong, Yang, Youngik, Yooseph, Shibu

Year:

2017

Language:

english

File:

PDF, 263 KB

english, 2017

46

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific

Rusch, Douglas B, Halpern, Aaron L, Sutton, Granger, Heidelberg, Karla B, Williamson, Shannon, Yooseph, Shibu, Wu, Dongying, Eisen, Jonathan A, Hoffman, Jeff M, Remington, Karin, Beeson, Karen, Tran,

Journal:

Year:

2007

Language:

english

File:

PDF, 3.58 MB

english, 2007

47

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

Yooseph, Shibu, Sutton, Granger, Rusch, Douglas B, Halpern, Aaron L, Williamson, Shannon J, Remington, Karin, Eisen, Jonathan A, Heidelberg, Karla B, Manning, Gerard, Li, Weizhong, Jaroszewski, Lukasz

Journal:

Year:

2007

Language:

english

File:

PDF, 1.86 MB

english, 2007

48

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles

Zhong, Cuncong, Edlund, Anna, Yang, Youngik, McLean, Jeffrey S., Yooseph, Shibu, Elofsson, Arne

Journal:

PLoS Computational Biology

Year:

2016

Language:

english

File:

PDF, 3.13 MB

english, 2016

49

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

Wu, Dongying, Wu, Martin, Halpern, Aaron, Rusch, Douglas B., Yooseph, Shibu, Frazier, Marvin, Venter, J. Craig, Eisen, Jonathan A., Fleischer, Robert

Journal:

Year:

2011

Language:

english

File:

PDF, 775 KB

english, 2011

50

Going Deeper: Metagenome of a Hadopelagic Microbial Community

Eloe, Emiley A., Fadrosh, Douglas W., Novotny, Mark, Zeigler Allen, Lisa, Kim, Maria, Lombardo, Mary-Jane, Yee-Greenbaum, Joyclyn, Yooseph, Shibu, Allen, Eric E., Lasken, Roger, Williamson, Shannon J.

Journal:

Year:

2011

Language:

english

File:

PDF, 1.20 MB

english, 2011