Works matching AU Berger, Bonnie

Results: 134

Struct2Net: a web service to predict protein–protein interactions using a structure-based approach.

Published in:

Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W508, doi. 10.1093/nar/gkq481

By:

Singh, Rohit;
Park, Daniel;
Xu, Jinbo;
Hosur, Raghavendra;
Berger, Bonnie

Publication type:

Article

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_2, p. W281

By:

Waldispühl, Jerome;
Devadas, Srinivas;
Berger, Bonnie;
Clote, Peter

Publication type:

Article

transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 11, p. w189, doi. 10.1093/nar/gkl205

By:

Waldispühl, J.;
Berger, Bonnie;
Clote, Peter;
Steyaert, Jean-Marc

Publication type:

Article

Proteomic and Functional Genomic Landscape of Receptor Tyrosine Kinase and Ras to Extracellular Signal-Regulated Kinase Signaling.

Published in:

Science Signaling, 2011, v. 4, n. 196, p. 1, doi. 10.1126/scisignal.2002029

By:

Friedman, Adam A.;
Tucker, George;
Singh, Rohit;
Yan, Dong;
Vinayagam, Arunachalam;
Yanhui Hu;
Binari, Richard;
Hong, Pengyu;
Sun, Xiaoyun;
Porto, Maura;
Pacifico, Svetlana;
Murali, Thilakam;
Jr., Russell L. Finley;
Asara, John M.;
Berger, Bonnie;
Perrimon, Norbert

Publication type:

Article

A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.

Published in:

Genome Biology, 2012, v. 13, n. 8, p. 1, doi. 10.1186/gb-2012-13-8-r76

By:

Hosur, Raghavendra;
Peng, Jian;
Vinayagam, Arunachalam;
Stelzl, Ulrich;
Xu, Jinbo;
Perrimon, Norbert;
Bienkowska, Jadwiga;
Berger, Bonnie

Publication type:

Article

A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers.

Published in:

Genome Biology, 2012, v. 13, n. 8, p. 1, doi. 10.1186/gb-2012-13-8-r71

By:

Palmer, Nathan P.;
Schmid, Patrick R.;
Berger, Bonnie;
Kohane, Isaac S.

Publication type:

Article

MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis.

Published in:

Genome Biology, 2012, v. 13, n. 1, p. 1, doi. 10.1186/gb-2012-13-1-r6

By:

Chindelevitch, Leonid;
Stanley, Sarah;
Hung, Deborah;
Regev, Aviv;
Berger, Bonnie

Publication type:

Article

Scanorama: integrating large and diverse single-cell transcriptomic datasets.

Published in:

Nature Protocols, 2024, v. 19, n. 8, p. 2283, doi. 10.1038/s41596-024-00991-3

By:

Hie, Brian L.;
Kim, Soochi;
Rando, Thomas A.;
Bryson, Bryan;
Berger, Bonnie

Publication type:

Article

Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN.

Published in:

Nature Protocols, 2023, v. 18, n. 2, p. 319, doi. 10.1038/s41596-022-00763-x

By:

Kinman, Laurel F.;
Powell, Barrett M.;
Zhong, Ellen D.;
Berger, Bonnie;
Davis, Joseph H.

Publication type:

Article

Reply to "Do genome-scale models need exact solvers or clearer standards?".

Published in:

2015

By:

Chindelevitch, Leonid;
Trigg, Jason;
Regev, Aviv;
Berger, Bonnie

Publication type:

Letter to the Editor

Large-scale identification of genetic design strategies using local search.

Published in:

Molecular Systems Biology, 2009, v. 5, n. 1, p. 296, doi. 10.1038/msb.2009.57

By:

Lun, Desmond S;
Rockwell, Graham;
Guido, Nicholas J;
Baym, Michael;
Kelner, Jonathan A;
Berger, Bonnie;
Galagan, James E;
Church, George M

Publication type:

Article

2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 6, p. 1, doi. 10.1371/journal.pcbi.1005561

By:

Fogg, Christiana N.;
Kovats, Diane E.;
Berger, Bonnie

Publication type:

Article

2017 ISCB Innovator Award: Aviv Regev.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 6, p. 1, doi. 10.1371/journal.pcbi.1005558

By:

Fogg, Christiana N.;
Kovats, Diane E.;
Berger, Bonnie

Publication type:

Article

2017 ISCB Overton Prize awarded to Christoph Bock.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 6, p. 1, doi. 10.1371/journal.pcbi.1005559

By:

Fogg, Christiana N.;
Kovats, Diane E.;
Berger, Bonnie

Publication type:

Article

2017 Outstanding Contributions to ISCB Award: Fran Lewitter.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 6, p. 1, doi. 10.1371/journal.pcbi.1005560

By:

Fogg, Christiana N.;
Kovats, Diane E.;
Berger, Bonnie

Publication type:

Article

HIV specific CD8<sup>+</sup> T<sub>RM</sub>-like cells in tonsils express exhaustive signatures in the absence of natural HIV control.

Published in:

Frontiers in Immunology, 2022, v. 13, p. 01, doi. 10.3389/fimmu.2022.912038

By:

Fardoos, Rabiah;
Nyquist, Sarah K.;
Asowata, Osaretin E.;
Kazer, Samuel W.;
Singh, Alveera;
Ngoepe, Abigail;
Giandhari, Jennifer;
Mthabela, Ntombifuthi;
Ramjit, Dirhona;
Singh, Samita;
Karim, Farina;
Buus, Søren;
Anderson, Frank;
Porterfield, J. Zachary;
Sibiya, Andile L.;
Bipath, Rishan;
Moodley, Kumeshan;
Kuhn, Warren;
Berger, Bonnie;
Son Nguyen

Publication type:

Article

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.

Published in:

BMC Systems Biology, 2014, v. 8, n. 1, p. 1, doi. 10.1186/1752-0509-8-13

By:

Meyer, Pablo;
Cokelaer, Thomas;
Chandran, Deepak;
Kyung Hyuk Kim;
Po-Ru Loh;
Tucker, George;
Lipson, Mark;
Berger, Bonnie;
Kreutz, Clemens;
Raue, Andreas;
Steiert, Bernhard;
Timmer, Jens;
Bilal, Erhan;
Sauro, Herbert M.;
Stolovitzky, Gustavo;
Saez-Rodriguez, Julio

Publication type:

Article

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 1, p. 1, doi. 10.1371/journal.pcbi.1004087

By:

Karp, Peter D.;
Berger, Bonnie;
Kovats, Diane;
Lengauer, Thomas;
Linial, Michal;
Sabeti, Pardis;
Hide, Winston;
Rost, Burkhard

Publication type:

Article

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003502

By:

Berger, Emily;
Yorukoglu, Deniz;
Peng, Jian;
Berger, Bonnie

Publication type:

Article

BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 3, p. 1, doi. 10.1371/journal.pcbi.1000333

By:

Bryan Jr., Allen W.;
Menke, Matthew;
Cowen, Lenore J.;
Lindquist, Susan L.;
Berger, Bonnie

Publication type:

Article

Efficient Algorithms for Probing the RNA Mutation Landscape.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 8, p. 1, doi. 10.1371/journal.pcbi.1000124

By:

Waldispühl, Jérôme;
Devadas, Srinivas;
Berger, Bonnie;
Clote, Peter

Publication type:

Article

Matt: Local Flexibility Aids Protein Multiple Structure Alignment.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 1, p. e10, doi. 10.1371/journal.pcbi.0040010

By:

Menke, Matthew;
Berger, Bonnie;
Cowen, Lenore

Publication type:

Article

Reasons for Exercise Behavior Among American and Chinese College Women.

Published in:

Women in Sport & Physical Activity Journal, 2014, v. 22, n. 1, p. 18, doi. 10.1123/wspaj.2014-0005

By:

Zi Yan;
Berger, Bonnie;
Tobar, David;
Cardinal, Bradley J.

Publication type:

Article

Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-57148-3

By:

Kshirsagar, Meghana;
Meller, Artur;
Humphreys, Ian R.;
Sledzieski, Samuel;
Xu, Yixi;
Dodhia, Rahul;
Horvitz, Eric;
Berger, Bonnie;
Bowman, Gregory R.;
Ferres, Juan Lavista;
Baker, David;
Baek, Minkyung

Publication type:

Article

Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities.

Published in:

Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-1084-z

By:

Nazeen, Sumaiya;
Palmer, Nathan P.;
Berger, Bonnie;
Kohane, Isaac S.

Publication type:

Article

Reconstructing Causal Biological Networks through Active Learning.

Published in:

PLoS ONE, 2016, v. 11, n. 3, p. 1, doi. 10.1371/journal.pone.0150611

By:

Cho, Hyunghoon;
Berger, Bonnie;
Peng, Jian

Publication type:

Article

Low-diameter graph decomposition is in NC.

Published in:

Random Structures & Algorithms, 1994, v. 5, n. 3, p. 441, doi. 10.1002/rsa.3240050305

By:

Awerbuch, Baruch;
Berger, Bonnie;
Cowen, Lenore;
Peleg, David

Publication type:

Article

Finding RNA structure in the unstructured RBPome.

Published in:

BMC Genomics, 2018, v. 19, p. 1, doi. 10.1186/s12864-018-4540-1

By:

Orenstein, Yaron;
Ohler, Uwe;
Berger, Bonnie

Publication type:

Article

Functional Movement Testing of Female Track and Field Athletes: Before and After an Indoor Season.

Published in:

Journal of Exercise Physiology Online, 2021, v. 24, n. 1, p. 54

By:

Gustafson, Aliyah M.;
Darby, Lynn A.;
Berger, Bonnie G.

Publication type:

Article

Athletic Identity, Career Maturity, and Subjective Well-being of NCAA Division I and III Football Players.

Published in:

Journal of Sport Behavior, 2021, v. 44, n. 3, p. 321

By:

Mathews, Alyssa. M.;
Berger, Bonnie G.;
Darby, Lynn A.;
Owen, David R.;
Tobar, David A.

Publication type:

Article

Mood Alteration After 15 Minutes of Preferred Intensity Exercise: Examining Heart Rate, Perceived Exertion, and Enjoyment.

Published in:

Journal of Sport Behavior, 2016, v. 39, n. 1, p. 3

By:

Berger, Bonnie G.;
Darby, Lynn A.;
Yu Zhang;
Owen, David R.;
Tobar, David A.

Publication type:

Article

Exercise makes you feel good, but does feeling good make you exercise?: an examination of obese dieters.

Published in:

2007

By:

Carels, Robert A.;
Coit, Carissa;
Young, Kathleen;
Berger, Bonnie

Publication type:

journal article

Improving the Power of GWAS and Avoiding Confounding from Population Stratification with PC-Select.

Published in:

Genetics, 2014, v. 197, n. 3, p. 1045, doi. 10.1534/genetics.114.164285

By:

Tucker, George;
Price, Alkes L.;
Berger, Bonnie

Publication type:

Article

Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium.

Published in:

Genetics, 2013, v. 193, n. 4, p. 1233, doi. 10.1534/genetics.112.147330

By:

Loh, Po-Ru;
Lipson, Mark;
Patterson, Nick;
Moorjani, Priya;
Pickrell, Joseph K.;
Reich, David;
Berger, Bonnie

Publication type:

Article

The Importance of Motor Coordination for Children's Motivational Orientations in Sport.

Published in:

Adapted Physical Activity Quarterly, 1998, v. 15, n. 4, p. 316, doi. 10.1123/apaq.15.4.316

By:

Rose, Betty;
Larkin, Dawne;
Berger, Bonnie G.

Publication type:

Article

Coordination and gender influences on the perceived competence of children.

Published in:

Adapted Physical Activity Quarterly, 1997, v. 14, n. 3, p. 210, doi. 10.1123/apaq.14.3.210

By:

Rose, Betty;
Larkin, Dawne;
Berger, Bonnie G.

Publication type:

Article

Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis).

Published in:

BMC Genomics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12864-022-08867-0

By:

Jaiswal, Swati;
Nyquist, Sarah K.;
Boyce, Shayla;
Jivanjee, Tasneem;
Ibrahim, Samira;
Bromley, Joshua D.;
Gatter, G. James;
Gideon, Hannah;
Patel, Kush;
Ganchua, Sharie Keanne;
Berger, Bonnie;
Fortune, Sarah M.;
Flynn, JoAnne L.;
Shalek, Alex K.;
Behar, Samuel M.

Publication type:

Article

ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing.

Published in:

PLoS Computational Biology, 2016, v. 12, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004816

By:

Berger, Bonnie;
Gaasterland, Terry;
Lengauer, Thomas;
Orengo, Christine;
Gaeta, Bruno;
Markel, Scott;
Valencia, Alfonso

Publication type:

Article

Water Resources: Agricultural and Environmental Issues.

Published in:

BioScience, 2004, v. 54, n. 10, p. 909, doi. 10.1641/0006-3568(2004)054[0909:WRAAEI]2.0.CO;2

By:

Pimentel, David;
Berger, Bonnie;
Filiberto, David;
Newton, Michelle;
Wolfe, Benjamin;
Karabinakis, Elizabeth;
Clark, Steven;
Poon, Elaine;
Abbett, Elizabeth;
Nandagopal, Sudha

Publication type:

Article

Predicting the mutational drivers of future SARS-CoV-2 variants of concern.

Published in:

Science Translational Medicine, 2022, v. 14, n. 633, p. 1, doi. 10.1126/scitranslmed.abk3445

By:

Maher, M. Cyrus;
Bartha, Istvan;
Weaver, Steven;
di Iulio, Julia;
Ferri, Elena;
Soriaga, Leah;
Lempp, Florian A.;
Hie, Brian L.;
Bryson, Bryan;
Berger, Bonnie;
Robertson, David L.;
Snell, Gyorgy;
Corti, Davide;
Virgin, Herbert W.;
Kosakovsky Pond, Sergei L.;
Telenti, Amalio

Publication type:

Article

SCA: recovering single-cell heterogeneity through information-based dimensionality reduction.

Published in:

Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-02998-7

By:

DeMeo, Benjamin;
Berger, Bonnie

Publication type:

Article

Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing.

Published in:

Genome Biology, 2023, p. 1, doi. 10.1186/s13059-022-02841-5

By:

Smajlović, Haris;
Shajii, Ariya;
Berger, Bonnie;
Cho, Hyunghoon;
Numanagić, Ibrahim

Publication type:

Article

Optimizing a global alignment of protein interaction networks.

Published in:

Bioinformatics, 2013, v. 29, n. 21, p. 2765, doi. 10.1093/bioinformatics/btt486

By:

Chindelevitch, Leonid;
Ma, Cheng-Yu;
Liao, Chung-Shou;
Berger, Bonnie

Publication type:

Article

Compressive genomics for protein databases.

Published in:

Bioinformatics, 2013, v. 29, n. 13, p. i283, doi. 10.1093/bioinformatics/btt214

By:

Daniels, Noah M.;
Gallant, Andrew;
Peng, Jian;
Cowen, Lenore J.;
Baym, Michael;
Berger, Bonnie

Publication type:

Article

Editorial.

Published in:

Bioinformatics, 2012, v. 28, n. 12, p. i1, doi. 10.1093/bioinformatics/bts281

By:

Berger, Bonnie

Publication type:

Article

SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone.

Published in:

Bioinformatics, 2012, v. 28, n. 9, p. 1216, doi. 10.1093/bioinformatics/bts110

By:

Daniels, Noah M.;
Hosur, Raghavendra;
Berger, Bonnie;
Cowen, Lenore J.

Publication type:

Article

A method for probing the mutational landscape of amyloid structure.

Published in:

Bioinformatics, 2011, v. 27, n. 13, p. i34, doi. 10.1093/bioinformatics/btr238

By:

O'Donnell, Charles W.;
Waldispühl, Jérôme;
Lis, Mieszko;
Halfmann, Randal;
Devadas, Srinivas;
Lindquist, Susan;
Berger, Bonnie

Publication type:

Article

IsoRankN: spectral methods for global alignment of multiple protein networks.

Published in:

Bioinformatics, 2009, v. 25, n. 12, p. i253, doi. 10.1093/bioinformatics/btp203

By:

Chung-Shou Liao;
Kanghao Lu;
Michael Baym;
Rohit Singh;
Bonnie Berger

Publication type:

Article

Optimal contact map alignment of protein-protein interfaces.

Published in:

Bioinformatics, 2008, v. 24, n. 20, p. 2324, doi. 10.1093/bioinformatics/btn432

By:

Vinay Pulim;
Bonnie Berger;
Jadwiga Bienkowska

Publication type:

Article

Computational solutions for omics data.

Published in:

Nature Reviews Genetics, 2013, v. 14, n. 5, p. 333, doi. 10.1038/nrg3433

By:

Berger, Bonnie;
Peng, Jian;
Singh, Mona

Publication type:

Article