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1

A Primer on Metagenomics

Wooley, John C., Godzik, Adam, Friedberg, Iddo, Bourne, Philip E.

Journal:

PLoS Computational Biology

Année:

2010

Langue:

english

Fichier:

PDF, 362 KB

english, 2010

2

Complete Genome Sequence of a Rodent Torque Teno Virus in Hainan Island, China

Wu, Yue, Wang, Shanshan, Chen, Yunchun, Li, Lihua, Wang, Wenqi, Zhou, Huanhuan, Zhang, You, Zhang, Lei, Cui, Xiuji, Lv, Gang, Yin, Feifei, Friedberg, Iddo

Journal:

Microbiology Resource Announcements

Année:

2018

Langue:

english

Fichier:

PDF, 112 KB

english, 2018

3

Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon

Nett, Ryan S., Nguyen, Huy, Nagel, Raimund, Marcassa, Ariana, Charles, Trevor C., Friedberg, Iddo, Peters, Reuben J., Kent, Angela D.

Journal:

Année:

2020

Fichier:

PDF, 692 KB

2020

4

Protist diversity in a permanently ice-covered Antarctic Lake during the polar night transition

Bielewicz, Scott, Bell, Elanor, Kong, Weidong, Friedberg, Iddo, Priscu, John C, Morgan-Kiss, Rachael M

Journal:

The ISME Journal

Année:

2011

Langue:

english

Fichier:

PDF, 363 KB

english, 2011

5

New avenues in protein function prediction

Iddo Friedberg, Martin Jambon, Adam Godzik

Journal:

Protein Science

Année:

2006

Langue:

english

Fichier:

PDF, 56 KB

english, 2006

6

Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function

Iddo Friedberg, Hanah Margalit

Journal:

Protein Science

Année:

2002

Langue:

english

Fichier:

PDF, 302 KB

english, 2002

7

Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments

Iddo Friedberg, Tommy Kaplan, Hanah Margalit

Journal:

Protein Science

Année:

2000

Langue:

english

Fichier:

PDF, 308 KB

english, 2000

8

Identification and characterization of DUSP27, a novel dual-specific protein phosphatase

Ilan Friedberg, Konstantina Nika, Lutz Tautz, Kan Saito, Fabio Cerignoli, Iddo Friedberg, Adam Godzik, Tomas Mustelin

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 2.08 MB

english, 2007

9

The interplay of fold recognition and experimental structure determination in structural genomics

Iddo Friedberg, Lukasz Jaroszewski, Yuzhen Ye, Adam Godzik

Journal:

Current Opinion in Structural Biology

Année:

2004

Langue:

english

Fichier:

PDF, 205 KB

english, 2004

10

Connecting the Protein Structure Universe by Using Sparse Recurring Fragments

Iddo Friedberg, Adam Godzik

Journal:

Année:

2005

Langue:

english

Fichier:

PDF, 503 KB

english, 2005

11

Functional Differentiation of Proteins: Implications for Structural Genomics

Iddo Friedberg, Adam Godzik

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 573 KB

english, 2007

12

IPRStats: visualization of the functional potential of an InterProScan run

Ryan J Kelly, David E Vincent, Iddo Friedberg

Journal:

BMC Bioinformatics

Année:

2010

Langue:

english

Fichier:

PDF, 597 KB

english, 2010

13

The 2006 Automated Function Prediction Meeting

Ana PC Rodrigues, Barry J Grant, Adam Godzik, Iddo Friedberg

Journal:

BMC Bioinformatics

Année:

2007

Langue:

english

Fichier:

PDF, 218 KB

english, 2007

14

Protein Tyrosine Phosphatases in the Human Genome

Andres Alonso, Joanna Sasin, Nunzio Bottini, Ilan Friedberg, Iddo Friedberg, Andrei Osterman, Adam Godzik, Tony Hunter, Jack Dixon, Tomas Mustelin

Journal:

Année:

2004

Langue:

english

Fichier:

PDF, 432 KB

english, 2004

15

A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response

Scott Schwartz, Iddo Friedberg, Ivan V Ivanov, Laurie A Davidson, Jennifer S Goldsby, David B Dahl, Damir Herman, Mei Wang, Sharon M Donovan, Robert S Chapkin

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 978 KB

english, 2012

16

Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes

Ream, David C., Murakami, Samuel T., Schmidt, Emily E., Huang, Guo-Hua, Liang, Chun, Friedberg, Iddo, Cheng, Xiao-Wen

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 919 KB

english, 2013

17

Ten Simple Rules for a Community Computational Challenge

Friedberg, Iddo, Wass, Mark N., Mooney, Sean D., Radivojac, Predrag

Journal:

PLoS Computational Biology

Année:

2015

Langue:

english

Fichier:

PDF, 90 KB

english, 2015

18

Ten Simple Rules for Selecting a Postdoctoral Position

Bourne, Philip E., Friedberg, Iddo

Journal:

PLoS Computational Biology

Année:

2006

Fichier:

PDF, 26 KB

2006

19

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

Schnoes, Alexandra M., Ream, David C., Thorman, Alexander W., Babbitt, Patricia C., Friedberg, Iddo, Orengo, Christine A.

Journal:

PLoS Computational Biology

Année:

2013

Langue:

english

Fichier:

PDF, 2.43 MB

english, 2013

20

Meeting Report: BioSharing at ISMB 2010

Field, Dawn, Sansone, Susanna, DeLong, Edward F., Sterk, Peter, Friedberg, Iddo, Gaudet, Pascale, Lewis, Susanna, Kottmann, Renzo, Hirschman, Lynette, Garrity, George, Cochrane, Guy, Wooley, John, Mey

Journal:

Standards in Genomic Sciences

Année:

2010

Langue:

english

Fichier:

PDF, 184 KB

english, 2010

21

Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Special Interest Group at ISMB 2009

Field, Dawn, Friedberg, Iddo, Sterk, Peter, Kottmann, Renzo, Glöckner, Frank Oliver, Hirschman, Lynette, Garrity, George M., Cochrane, Guy, Wooley, John, Gilbert, Jack

Journal:

Standards in Genomic Sciences

Année:

2009

Langue:

english

Fichier:

PDF, 200 KB

english, 2009

22

A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins

Morton, James T., Freed, Stefan D., Lee, Shaun W., Friedberg, Iddo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.94 MB

english, 2015

23

Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010

Field, Dawn, Sansone, Susanna, DeLong, Edward F., Sterk, Peter, Friedberg, Iddo, Kottmann, Renzo, Hirschman, Lynette, Garrity, George, Cochrane, Guy, Wooley, John, Meyer, Folker, Hunter, Sarah, White,

Journal:

Standards in Genomic Sciences

Année:

2010

Langue:

english

Fichier:

PDF, 154 KB

english, 2010

24

Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

Wimalanathan, Kokulapalan, Friedberg, Iddo, Andorf, Carson M., Lawrence-Dill, Carolyn J.

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 3.14 MB

english, 2018

25

Correction: Ten Simple Rules for Selecting a Postdoctoral Position

Bourne, Philip E., Friedberg, Iddo

Journal:

PLoS Computational Biology

Année:

2006

Fichier:

PDF, 24 KB

2006

26

Gene Order Phylogeny and the Evolution of Methanogens

Luo, Haiwei, Sun, Zhiyi, Arndt, William, Shi, Jian, Friedman, Robert, Tang, Jijun, Friedberg, Iddo

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 167 KB

english, 2009

27

Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data

Kourmpetis, Yiannis A. I., van Dijk, Aalt D. J., Bink, Marco C. A. M., van Ham, Roeland C. H. J., ter Braak, Cajo J. F., Friedberg, Iddo

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 1.14 MB

english, 2010

28

Re-Annotation Is an Essential Step in Systems Biology Modeling of Functional Genomics Data

van den Berg, Bart H. J., McCarthy, Fiona M., Lamont, Susan J., Burgess, Shane C., Friedberg, Iddo

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 425 KB

english, 2010

29

Occupancy Modeling, Maximum Contig Size Probabilities and Designing Metagenomics Experiments

Stanhope, Stephen A., Friedberg, Iddo

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 609 KB

english, 2010

30

Novel Analysis of Oceanic Surface Water Metagenomes Suggests Importance of Polyphosphate Metabolism in Oligotrophic Environments

Temperton, Ben, Gilbert, Jack A., Quinn, John P., McGrath, John W., Friedberg, Iddo

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 1.97 MB

english, 2011

31

A Collaborative Filtering Approach for Protein-Protein Docking Scoring Functions

Bourquard, Thomas, Bernauer, Julie, Azé, Jérôme, Poupon, Anne, Friedberg, Iddo

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 700 KB

english, 2011

32

Ecogenomic Perspectives on Domains of Unknown Function: Correlation-Based Exploration of Marine Metagenomes

Buttigieg, Pier Luigi, Hankeln, Wolfgang, Kostadinov, Ivaylo, Kottmann, Renzo, Yilmaz, Pelin, Duhaime, Melissa Beth, Glöckner, Frank Oliver, Friedberg, Iddo

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 609 KB

english, 2013

33

High Precision Prediction of Functional Sites in Protein Structures

Buturovic, Ljubomir, Wong, Mike, Tang, Grace W., Altman, Russ B., Petkovic, Dragutin, Friedberg, Iddo

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 622 KB

english, 2014

34

Metagenomic Identification of a Novel Salt Tolerance Gene from the Human Gut Microbiome Which Encodes a Membrane Protein with Homology to a brp/blh-Family β-Carotene 15,15′-Monooxygenase

Culligan, Eamonn P., Sleator, Roy D., Marchesi, Julian R., Hill, Colin, Friedberg, Iddo

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 4.64 MB

english, 2014

35

Genome Sequences of Five Brucella canis Strains Isolated from Different Countries throughout the World

Girault, Guillaume, Ferreira Vicente, Acácia, Corde, Yannick, Souza Ribeiro Mioni, Mateus, Borges Keid, Lara, Jay, Maryne, Megid, Jane, Mick, Virginie, Friedberg, Iddo

Journal:

Microbiology Resource Announcements

Année:

2018

Langue:

english

Fichier:

PDF, 117 KB

english, 2018

36

Complete Genome Sequence of the Arcobacter halophilus Type Strain CCUG 53805

Miller, William G., Yee, Emma, Bono, James L., Friedberg, Iddo

Journal:

Microbiology Resource Announcements

Année:

2018

Langue:

english

Fichier:

PDF, 136 KB

english, 2018

37

Identifying Antimicrobial Peptides using Word Embedding with Deep Recurrent Neural Networks

Hamid, Md-Nafiz, Friedberg, Iddo, Hancock, John

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 1.72 MB

english, 2018

38

Chikungunya Virus in Febrile Humans and Aedes aegypti Mosquitoes, Yucatan, Mexico

Cigarroa-Toledo, Nohemi, Blitvich, Bradley J., Cetina-Trejo, Rosa C., Talavera-Aguilar, Lourdes G., Baak-Baak, Carlos M., Torres-Chablé, Oswaldo M., Hamid, Md-Nafiz, Friedberg, Iddo, González-Martinez

Journal:

Emerging Infectious Diseases

Année:

2016

Langue:

english

Fichier:

PDF, 659 KB

english, 2016

39

New Drosophila Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods

Kacsoh, Balint Z., Barton, Stephen, Jiang, Yuxiang, Zhou, Naihui, Mooney, Sean D., Friedberg, Iddo, Radivojac, Predrag, Greene, Casey S., Bosco, Giovanni

Journal:

G3 Genes|Genome|Genetics

Année:

2018

Langue:

english

Fichier:

PDF, 3.49 MB

english, 2018

40

Tracing the Ancestry of Operons in Bacteria

Nguyen, Huy, Jain, Ashish, Eulenstein, Oliver, Friedberg, Iddo, Schwartz, Russell

Journal:

Année:

2019

Fichier:

PDF, 4.18 MB

2019

41

Complete Genome Sequence of Salmonella enterica subsp. enterica Serotype Derby, Associated with the Pork Sector in France

Sévellec, Yann, Granier, Sophie A., Randomski, Nicolas, Felten, Arnaud, Le Hello, Simon, Feurer, Carole, Mistou, Michel-Yves, Cadel-Six, Sabrina, Friedberg, Iddo

Journal:

Microbiology Resource Announcements

Année:

2018

Langue:

english

Fichier:

PDF, 206 KB

english, 2018

42

Genome Sequence of the Probiotic Strain Bacillus velezensis Variant polyfermenticus GF423

Jeong, Haeyoung, Kim, JungAe, Choi, Soo-Keun, Pan, Jae-Gu, Friedberg, Iddo

Journal:

Microbiology Resource Announcements

Année:

2018

Fichier:

PDF, 117 KB

2018

43

Genome Sequence of the Probiotic Strain Bacillus velezensis Variant polyfermenticus GF423

Jeong, Haeyoung, Kim, JungAe, Choi, Soo-Keun, Pan, Jae-Gu, Friedberg, Iddo

Journal:

Microbiology Resource Announcements

Année:

2018

Langue:

english

Fichier:

PDF, 117 KB

english, 2018

44

Complete Genome Sequence of Ferriphaselus amnicola Strain OYT1, a Neutrophilic, Stalk-Forming, Iron-Oxidizing Bacterium

Kato, Shingo, Yuki, Masahiro, Itoh, Takashi, Ohkuma, Moriya, Friedberg, Iddo

Journal:

Microbiology Resource Announcements

Année:

2018

Fichier:

PDF, 188 KB

2018

45

SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier

Hu, Xiao, Friedberg, Iddo

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 740 KB

english, 2019

46

SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier

Hu, Xiao, Friedberg, Iddo

Journal:

Année:

2019

Fichier:

PDF, 740 KB

2019

47

Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells

Wierson, Wesley A., Simone, Brandon W., WareJoncas, Zachary, Mann, Carla, Welker, Jordan M., Kar, Bibekananda, Emch, Michael J., Friedberg, Iddo, Gendron, William A.C., Barry, Michael A., Clark, Karl

Journal:

The CRISPR Journal

Année:

2019

Langue:

english

Fichier:

PDF, 1.28 MB

english, 2019

48

Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells

Wierson, Wesley A., Simone, Brandon W., WareJoncas, Zachary, Mann, Carla, Welker, Jordan M., Kar, Bibekananda, Emch, Michael J., Friedberg, Iddo, Gendron, William A.C., Barry, Michael A., Clark, Karl

Journal:

The CRISPR Journal

Année:

2019

Fichier:

PDF, 1.28 MB

2019