Ziv Bar-Joseph

Ziv Bar-Joseph

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Ziv Bar-Joseph

Publications by authors named "Ziv Bar-Joseph"

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Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors.

Cell Stem Cell 2020 Apr 30;26(4):593-608.e8. Epub 2020 Jan 30.

Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2019.12.009DOI Listing
April 2020

Inferring TF activation order in time series scRNA-Seq studies.

PLoS Comput Biol 2020 Feb 18;16(2):e1007644. Epub 2020 Feb 18.

Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048296PMC
February 2020

Deep learning for inferring gene relationships from single-cell expression data.

Proc Natl Acad Sci U S A 2019 Dec 10. Epub 2019 Dec 10.

Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213;

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http://dx.doi.org/10.1073/pnas.1911536116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936704PMC
December 2019

Continuous-state HMMs for modeling time-series single-cell RNA-Seq data.

Bioinformatics 2019 Nov;35(22):4707-4715

Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, US.

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http://dx.doi.org/10.1093/bioinformatics/btz296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853676PMC
November 2019

Integrating multiomics longitudinal data to reconstruct networks underlying lung development.

Am J Physiol Lung Cell Mol Physiol 2019 11 21;317(5):L556-L568. Epub 2019 Aug 21.

Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama.

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http://dx.doi.org/10.1152/ajplung.00554.2018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879899PMC
November 2019

Cell lineage inference from SNP and scRNA-Seq data.

Nucleic Acids Res 2019 06;47(10):e56

Computational Biology Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/nar/gkz146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547431PMC
June 2019

Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains.

Proc Natl Acad Sci U S A 2019 06 24;116(24):11770-11775. Epub 2019 May 24.

Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213;

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http://dx.doi.org/10.1073/pnas.1816315116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6575235PMC
June 2019

Dynamic interaction network inference from longitudinal microbiome data.

Microbiome 2019 04 2;7(1):54. Epub 2019 Apr 2.

Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, 15213, Pennsylvania, USA.

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http://dx.doi.org/10.1186/s40168-019-0660-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446388PMC
April 2019

Protein interaction disruption in cancer.

BMC Cancer 2019 Apr 23;19(1):370. Epub 2019 Apr 23.

Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.

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http://dx.doi.org/10.1186/s12885-019-5532-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6823625PMC
April 2019

Network-guided prediction of aromatase inhibitor response in breast cancer.

PLoS Comput Biol 2019 02 11;15(2):e1006730. Epub 2019 Feb 11.

Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386390PMC
February 2019

Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data.

Bioinformatics 2019 Feb 15. Epub 2019 Feb 15.

Microsoft Research, Redmond, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz095DOI Listing
February 2019

Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer.

Genes Chromosomes Cancer 2019 01 18;58(1):34-42. Epub 2018 Nov 18.

Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania.

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http://dx.doi.org/10.1002/gcc.22688DOI Listing
January 2019

Predicting protein targets for drug-like compounds using transcriptomics.

PLoS Comput Biol 2018 12 7;14(12):e1006651. Epub 2018 Dec 7.

Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300300PMC
December 2018

Hercules: a profile HMM-based hybrid error correction algorithm for long reads.

Nucleic Acids Res 2018 11;46(21):e125

Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey.

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http://dx.doi.org/10.1093/nar/gky724DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265270PMC
November 2018

A web server for comparative analysis of single-cell RNA-seq data.

Nat Commun 2018 11 13;9(1):4768. Epub 2018 Nov 13.

Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.

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http://www.nature.com/articles/s41467-018-07165-2
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http://dx.doi.org/10.1038/s41467-018-07165-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6233170PMC
November 2018

Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.

Cell Stem Cell 2018 10;23(4):586-598.e8

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Centre for Cardiac and Vascular Biology, The University of Queensland, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S19345909183044
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http://dx.doi.org/10.1016/j.stem.2018.09.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6220122PMC
October 2018

iDREM: Interactive visualization of dynamic regulatory networks.

PLoS Comput Biol 2018 03 14;14(3):e1006019. Epub 2018 Mar 14.

Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5868853PMC
March 2018

Network Design and the Brain.

Trends Cogn Sci 2018 01 17;22(1):64-78. Epub 2017 Oct 17.

Carnegie Mellon University, Center for the Neural Basis of Cognition, Department of Biological Sciences, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1016/j.tics.2017.09.012DOI Listing
January 2018

Reconstructing differentiation networks and their regulation from time series single-cell expression data.

Genome Res 2018 Jan 9. Epub 2018 Jan 9.

Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

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http://dx.doi.org/10.1101/gr.225979.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5848617PMC
January 2018

MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor.

Bioinformatics 2017 Nov;33(21):3477-3479

Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860172PMC
November 2017

Reconstructing cancer drug response networks using multitask learning.

BMC Syst Biol 2017 Oct 10;11(1):96. Epub 2017 Oct 10.

Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1186/s12918-017-0471-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635550PMC
October 2017

Using neural networks for reducing the dimensions of single-cell RNA-Seq data.

Nucleic Acids Res 2017 Sep;45(17):e156

Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/nar/gkx681DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737331PMC
September 2017

TASIC: determining branching models from time series single cell data.

Bioinformatics 2017 Aug;33(16):2504-2512

Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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https://academic.oup.com/bioinformatics/article/33/16/2504/3
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http://dx.doi.org/10.1093/bioinformatics/btx173DOI Listing
August 2017

Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men.

AIDS 2017 03;31(5):623-633

aDepartment of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh bComputer Science Department, School of Computer Science, Carnegie Mellon University cMolecular Biology Information Service, University of Pittsburgh dComputational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, Pennsylvania eDepartment of Radiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois fDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland gDepartment of Neurology, David Geffen School of Medicine, University of California Los Angeles, California hDepartment of Psychiatry, Rush University Medical Center, Chicago, Illinois iDepartment of Neurology, Johns Hopkins Bayview Medical Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1097/QAD.0000000000001379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389669PMC
March 2017

Selecting the most appropriate time points to profile in high-throughput studies.

Elife 2017 01 26;6. Epub 2017 Jan 26.

Machine Learning and Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, United States.

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http://dx.doi.org/10.7554/eLife.18541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319842PMC
January 2017

Genome wide predictions of miRNA regulation by transcription factors.

Bioinformatics 2016 09;32(17):i746-i754

Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA 15213.

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http://dx.doi.org/10.1093/bioinformatics/btw452DOI Listing
September 2016

Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments.

Cell Syst 2016 07 21;3(1):35-42. Epub 2016 Jul 21.

Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4966908PMC
July 2016

Reconstructing the temporal progression of HIV-1 immune response pathways.

Bioinformatics 2016 06;32(12):i253-i261

Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908338PMC
June 2016

The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease Progression.

Methods Mol Biol 2016 ;1303:493-506

Microsoft Research, Cambridge, MA, 02142, USA,

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http://dx.doi.org/10.1007/978-1-4939-2627-5_30DOI Listing
April 2016

Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch.

Retrovirology 2015 Oct 6;12:85. Epub 2015 Oct 6.

Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh/GSPH, Room A435, Crabtree Hall, 130 DeSoto Street, Pittsburgh, PA, 15261, USA.

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http://www.retrovirology.com/content/12/1/85
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http://dx.doi.org/10.1186/s12977-015-0211-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594640PMC
October 2015

De novo ChIP-seq analysis.

Genome Biol 2015 Sep 23;16:205. Epub 2015 Sep 23.

Computational Biology Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, 15213, USA.

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http://dx.doi.org/10.1186/s13059-015-0756-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579611PMC
September 2015

Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks.

PLoS Comput Biol 2015 Jul 28;11(7):e1004347. Epub 2015 Jul 28.

Lane Center for Computational Biology, Machine Learning Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517947PMC
July 2015

SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data.

Bioinformatics 2015 Apr 4;31(8):1250-7. Epub 2014 Dec 4.

Lane Center for Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA Lane Center for Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu800DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393515PMC
April 2015

cDREM: inferring dynamic combinatorial gene regulation.

J Comput Biol 2015 Apr;22(4):324-33

Lane Center for Computational Biology, Carnegie Mellon University , Pittsburgh, Pennsylvania.

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http://dx.doi.org/10.1089/cmb.2015.0010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394168PMC
April 2015

ModuleBlast: identifying activated sub-networks within and across species.

Nucleic Acids Res 2015 Feb 26;43(3):e20. Epub 2014 Nov 26.

Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA

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http://dx.doi.org/10.1093/nar/gku1224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330341PMC
February 2015

Gene expression in relation to exhaled nitric oxide identifies novel asthma phenotypes with unique biomolecular pathways.

Am J Respir Crit Care Med 2014 Dec;190(12):1363-72

1 Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Asthma Institute at UPMC, Pittsburgh, Pennsylvania.

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http://dx.doi.org/10.1164/rccm.201406-1099OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4294630PMC
December 2014

Multitask learning of signaling and regulatory networks with application to studying human response to flu.

PLoS Comput Biol 2014 Dec 18;10(12):e1003943. Epub 2014 Dec 18.

Lane Center for Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270428PMC
December 2014

Topological properties of robust biological and computational networks.

J R Soc Interface 2014 Jul 30;11(96):20140283. Epub 2014 Apr 30.

Machine Learning Department, Carnegie Mellon University, , Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1098/rsif.2014.0283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032542PMC
July 2014

Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells.

BMC Syst Biol 2013 Dec 12;7:138. Epub 2013 Dec 12.

Department of Pathology, University of Pittsburgh, School of Medicine, S701 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1186/1752-0509-7-138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3924228PMC
December 2013

Predicting tissue specific transcription factor binding sites.

BMC Genomics 2013 Nov 15;14:796. Epub 2013 Nov 15.

Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.

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http://dx.doi.org/10.1186/1471-2164-14-796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898213PMC
November 2013

ExpressionBlast: mining large, unstructured expression databases.

Nat Methods 2013 Oct;10(10):925-6

1] Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA. [2].

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http://dx.doi.org/10.1038/nmeth.2630DOI Listing
October 2013

Reconstructing dynamic microRNA-regulated interaction networks.

Proc Natl Acad Sci U S A 2013 Sep 28;110(39):15686-91. Epub 2013 Aug 28.

Ray and Stephanie Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213.

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http://dx.doi.org/10.1073/pnas.1303236110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785769PMC
September 2013

Identifying proteins controlling key disease signaling pathways.

Bioinformatics 2013 Jul;29(13):i227-36

Computer Science Department and Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694658PMC
July 2013

Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation.

Bioinformatics 2013 Jul;29(13):i89-97

Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694655PMC
July 2013

A high-throughput framework to detect synapses in electron microscopy images.

Bioinformatics 2013 Jul;29(13):i9-17

Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694654PMC
July 2013

Probabilistic error correction for RNA sequencing.

Nucleic Acids Res 2013 May 4;41(10):e109. Epub 2013 Apr 4.

Machine Learning Department, Carnegie Mellon University, 5000 Forbes Avenue Pittsburgh, PA 15217, USA.

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http://dx.doi.org/10.1093/nar/gkt215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664804PMC
May 2013

MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts.

BMC Infect Dis 2013 May 30;13:250. Epub 2013 May 30.

Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 425 Parran Hall, 130 Desoto Street, Pittsburgh, PA 15261, USA.

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http://dx.doi.org/10.1186/1471-2334-13-250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3680326PMC
May 2013

Linking the signaling cascades and dynamic regulatory networks controlling stress responses.

Genome Res 2013 Feb 11;23(2):365-76. Epub 2012 Oct 11.

Computer Science Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

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http://dx.doi.org/10.1101/gr.138628.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561877PMC
February 2013

A network-based approach for predicting missing pathway interactions.

PLoS Comput Biol 2012 16;8(8):e1002640. Epub 2012 Aug 16.

School of Computer Science and Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002640DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3420932PMC
December 2012

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.

BMC Syst Biol 2012 Aug 16;6:104. Epub 2012 Aug 16.

Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1186/1752-0509-6-104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464930PMC
August 2012

Studying and modelling dynamic biological processes using time-series gene expression data.

Nat Rev Genet 2012 Jul 18;13(8):552-64. Epub 2012 Jul 18.

Lane Center for Computational Biology and Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.1038/nrg3244DOI Listing
July 2012

Matching experiments across species using expression values and textual information.

Bioinformatics 2012 Jun;28(12):i258-64

Lane Center for Computational Biology, Carnegie Mellon University Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371837PMC
June 2012

The sirtuin SIRT6 regulates lifespan in male mice.

Nature 2012 Feb 22;483(7388):218-21. Epub 2012 Feb 22.

The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.

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http://www.nature.com/articles/nature10815
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http://dx.doi.org/10.1038/nature10815DOI Listing
February 2012

Comparative expression profile of miRNA and mRNA in primary peripheral blood mononuclear cells infected with human immunodeficiency virus (HIV-1).

PLoS One 2011 28;6(7):e22730. Epub 2011 Jul 28.

Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022730PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145673PMC
December 2011

Learning cellular sorting pathways using protein interactions and sequence motifs.

J Comput Biol 2011 Nov 14;18(11):1709-22. Epub 2011 Oct 14.

Language Technology Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.1089/cmb.2011.0193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216107PMC
November 2011

Algorithms in nature: the convergence of systems biology and computational thinking.

Mol Syst Biol 2011 Nov 8;7:546. Epub 2011 Nov 8.

Lane Center for Computational Biology and Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1038/msb.2011.78DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261700PMC
November 2011

DECOD: fast and accurate discriminative DNA motif finding.

Bioinformatics 2011 Sep 12;27(17):2361-7. Epub 2011 Jul 12.

Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157928PMC
September 2011

Biological interaction networks are conserved at the module level.

BMC Syst Biol 2011 Aug 23;5:134. Epub 2011 Aug 23.

Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1186/1752-0509-5-134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212960PMC
August 2011

Discriminative motif finding for predicting protein subcellular localization.

IEEE/ACM Trans Comput Biol Bioinform 2011 Mar-Apr;8(2):441-51

Carnegie Mellon University, Pittsburgh, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1109/TCBB.2009.82DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3050600PMC
June 2011

Discovering pathways by orienting edges in protein interaction networks.

Nucleic Acids Res 2011 Mar 24;39(4):e22. Epub 2010 Nov 24.

Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1093/nar/gkq1207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045580PMC
March 2011

A biological solution to a fundamental distributed computing problem.

Science 2011 Jan;331(6014):183-5

Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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January 2011

Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering.

Genome Biol 2010 23;11(7):R77. Epub 2010 Jul 23.

Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926788PMC
December 2010

Computational methods for analyzing dynamic regulatory networks.

Methods Mol Biol 2010 ;674:419-41

Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1007/978-1-60761-854-6_24DOI Listing
December 2010

Cross-species queries of large gene expression databases.

Bioinformatics 2010 Oct 11;26(19):2416-23. Epub 2010 Aug 11.

Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944203PMC
October 2010

Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes.

BMC Genomics 2010 Aug 17;11:478. Epub 2010 Aug 17.

Department of Microbiology and Molecular Genetics, The Institute for Medical Research-Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.

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http://dx.doi.org/10.1186/1471-2164-11-478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091674PMC
August 2010

Integrating multiple evidence sources to predict transcription factor binding in the human genome.

Genome Res 2010 Apr 10;20(4):526-36. Epub 2010 Mar 10.

Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1101/gr.096305.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847756PMC
April 2010

Cross species expression analysis of innate immune response.

J Comput Biol 2010 Mar;17(3):253-68

School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

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http://dx.doi.org/10.1089/cmb.2009.0147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198893PMC
March 2010

IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability.

PLoS One 2009 Oct 15;4(10):e7469. Epub 2009 Oct 15.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Boston, Massachusetts, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758590PMC
October 2009

Backup in gene regulatory networks explains differences between binding and knockout results.

Mol Syst Biol 2009 16;5:276. Epub 2009 Jun 16.

Computer Science Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1038/msb.2009.33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2710864PMC
September 2009

Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells.

Mol Biol Cell 2009 Sep 1;20(17):3851-64. Epub 2009 Jul 1.

Fred Hutchinson Cancer Research Center, Basic Sciences Division, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1091/mbc.e09-04-0347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735484PMC
September 2009

Cross species analysis of microarray expression data.

Bioinformatics 2009 Jun 8;25(12):1476-83. Epub 2009 Apr 8.

School of Computer Science and Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732912PMC
June 2009

Schools anxiously await NRC program rankings.

Authors:
Ziv Bar-Joseph

Science 2009 May;324(5931):1140-1

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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May 2009

A probabilistic generative model for GO enrichment analysis.

Nucleic Acids Res 2008 Oct 1;36(17):e109. Epub 2008 Aug 1.

Computer Science Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, 15213 USA.

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http://dx.doi.org/10.1093/nar/gkn434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553574PMC
October 2008

Extracting dynamics from static cancer expression data.

IEEE/ACM Trans Comput Biol Bioinform 2008 Apr-Jun;5(2):172-82

Department of Computer Science, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1109/TCBB.2007.70233DOI Listing
July 2008

Alignment and classification of time series gene expression in clinical studies.

Bioinformatics 2008 Jul;24(13):i147-55

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718630PMC
July 2008

Protein complex identification by supervised graph local clustering.

Bioinformatics 2008 Jul;24(13):i250-8

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718642PMC
July 2008

A mixture of feature experts approach for protein-protein interaction prediction.

BMC Bioinformatics 2007 ;8 Suppl 10:S6

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1186/1471-2105-8-S10-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2230507PMC
April 2008

A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli.

PLoS Comput Biol 2008 Mar 28;4(3):e1000044. Epub 2008 Mar 28.

Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266799PMC
March 2008

Combined analysis reveals a core set of cycling genes.

Genome Biol 2007 ;8(7):R146

Department of Computer Science, Carnegie Mellon University, Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323241PMC
February 2008

Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells.

Proc Natl Acad Sci U S A 2008 Jan 14;105(3):955-60. Epub 2008 Jan 14.

Department of Computer Science, School of Computer Science and Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0704723105
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242708PMC
January 2008

Impact of the solvent capacity constraint on E. coli metabolism.

BMC Syst Biol 2008 Jan 23;2. Epub 2008 Jan 23.

The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA.

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http://dx.doi.org/10.1186/1752-0509-2-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2270259PMC
January 2008

Continuous hidden process model for time series expression experiments.

Bioinformatics 2007 Jul;23(13):i459-67

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm218DOI Listing
July 2007

A patient-gene model for temporal expression profiles in clinical studies.

J Comput Biol 2007 Apr;14(3):324-38

Simmons Center for Interstitial Lung Disease, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.1089/cmb.2007.0001DOI Listing
April 2007

Inferring pairwise regulatory relationships from multiple time series datasets.

Bioinformatics 2007 Mar 19;23(6):755-63. Epub 2007 Jan 19.

Machine Learning Department, Language Technologies Institute, Computer Science Department and Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl676DOI Listing
March 2007

Reconstructing dynamic regulatory maps.

Mol Syst Biol 2007 16;3:74. Epub 2007 Jan 16.

Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1038/msb4100115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800355PMC
February 2007

Identifying cycling genes by combining sequence homology and expression data.

Bioinformatics 2006 Jul;22(14):e314-22

School of Computer Science, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl229DOI Listing
July 2006

STEM: a tool for the analysis of short time series gene expression data.

BMC Bioinformatics 2006 Apr 5;7:191. Epub 2006 Apr 5.

Center for Automated and Learning and Discovery, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1186/1471-2105-7-191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456994PMC
April 2006