Frederick P Roth

Frederick P Roth

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Frederick P Roth

Publications by authors named "Frederick P Roth"

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MaveQuest: a web resource for planning experimental tests of human variant effects.

Bioinformatics 2020 Apr 6. Epub 2020 Apr 6.

Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btaa228DOI Listing
April 2020

Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network.

Cell Syst 2020 Jan 23;10(1):25-38.e10. Epub 2019 Oct 23.

Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.09.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6989212PMC
January 2020

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect.

Genome Biol 2019 11 4;20(1):223. Epub 2019 Nov 4.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.

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http://dx.doi.org/10.1186/s13059-019-1845-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6827219PMC
November 2019

Quantifying immune-based counterselection of somatic mutations.

PLoS Genet 2019 07 25;15(7):e1008227. Epub 2019 Jul 25.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pgen.1008227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657826PMC
July 2019

Characterizing ABC-Transporter Substrate-Likeness Using a Clean-Slate Genetic Background.

Front Pharmacol 2019 25;10:448. Epub 2019 Apr 25.

Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, United States.

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http://dx.doi.org/10.3389/fphar.2019.00448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6494965PMC
April 2019

The Impact of Oncogenic EGFRvIII on the Proteome of Extracellular Vesicles Released from Glioblastoma Cells.

Mol Cell Proteomics 2018 10 13;17(10):1948-1964. Epub 2018 Jul 13.

From the ‡Research Institute of the McGill University Health Centre, Glen Site, McGill University, Montreal, Quebec, H4A 3J1, Canada;

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http://www.mcponline.org/lookup/doi/10.1074/mcp.RA118.000644
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http://dx.doi.org/10.1074/mcp.RA118.000644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6166673PMC
October 2018

Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas.

Hum Genet 2018 Sep 2;137(9):665-678. Epub 2018 Aug 2.

The Donnelly Centre, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1007/s00439-018-1916-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153521PMC
September 2018

Modeling the impact of drug interactions on therapeutic selectivity.

Nat Commun 2018 08 27;9(1):3452. Epub 2018 Aug 27.

Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey.

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http://dx.doi.org/10.1038/s41467-018-05954-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6110842PMC
August 2018

Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target.

Genome Res 2017 09 8;27(9):1487-1500. Epub 2017 Jun 8.

Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, Kyungpook National University School of Medicine, Daegu, 41944, Korea.

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http://dx.doi.org/10.1101/gr.211649.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5580709PMC
September 2017

Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I.

Hum Mutat 2017 09;38(9):1051-1063

Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas.

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http://dx.doi.org/10.1002/humu.23293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5746193PMC
September 2017

Variant Interpretation: Functional Assays to the Rescue.

Am J Hum Genet 2017 Sep;101(3):315-325

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.07.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590843PMC
September 2017

A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and -methyladenosine modification.

RNA 2017 03 19;23(3):270-283. Epub 2016 Dec 19.

Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto M5S 3E1, Ontario, Canada

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http://dx.doi.org/10.1261/rna.059105.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311483PMC
March 2017

Systematic identification of phosphorylation-mediated protein interaction switches.

PLoS Comput Biol 2017 03 27;13(3):e1005462. Epub 2017 Mar 27.

CellNetworks, Bioquant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1005462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386296PMC
March 2017

Taking Exception to Human Eugenics.

Genetics 2016 10;204(2):821-823

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138

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http://www.genetics.org/cgi/doi/10.1534/genetics.116.192096
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http://dx.doi.org/10.1534/genetics.116.192096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068865PMC
October 2016

An extended set of yeast-based functional assays accurately identifies human disease mutations.

Genome Res 2016 05 14;26(5):670-80. Epub 2016 Mar 14.

Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1Z8, Canada.

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http://dx.doi.org/10.1101/gr.192526.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864455PMC
May 2016

Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

Mol Syst Biol 2016 Apr 22;12(4):863. Epub 2016 Apr 22.

Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Canadian Institute for Advanced Research, Toronto, ON, Canada Department of Computer Science, University of Toronto, Toronto, Ontario, Canada

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848762PMC
http://dx.doi.org/10.15252/msb.20156660DOI Listing
April 2016

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

Cell 2016 Feb;164(4):805-17

Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.01.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882190PMC
February 2016

A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.

Cell 2016 Jan;164(1-2):310-323

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.11.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4715267PMC
January 2016

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.

Cell 2015 Dec 25;163(6):1515-26. Epub 2015 Nov 25.

Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G1Z8, Canada. Electronic address:

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http://www.cell.com/cell/pdf/S0092-8674(15)01495-6.pdf
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http://www.cell.com/cms/attachment/2042476803/2055463631/mmc
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http://linkinghub.elsevier.com/retrieve/pii/S009286741501495
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http://dx.doi.org/10.1016/j.cell.2015.11.015DOI Listing
December 2015

SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets.

Nucleic Acids Res 2015 Jul 6;43(W1):W276-82. Epub 2015 May 6.

Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X8, Canada.

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http://dx.doi.org/10.1093/nar/gkv459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489257PMC
July 2015

Protein domain-level landscape of cancer-type-specific somatic mutations.

PLoS Comput Biol 2015 Mar 20;11(3):e1004147. Epub 2015 Mar 20.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario, Canada; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America; Canadian Institute for Advanced Research, Toronto, Ontario, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1004147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368709PMC
March 2015

Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.

Nat Methods 2015 Feb 22;12(2):154-9. Epub 2014 Dec 22.

1] Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada. [4] Center for Cancer Systems Biology (CCSB), Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [5] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. [6] Canadian Institute for Advanced Research, Toronto, Ontario, Canada.

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http://www.nature.com/articles/nmeth.3215
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http://dx.doi.org/10.1038/nmeth.3215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480866PMC
February 2015

A proteome-scale map of the human interactome network.

Cell 2014 Nov;159(5):1212-1226

Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://llama.mshri.on.ca/publications/Rolland_Cell_2014.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S009286741401422
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http://dx.doi.org/10.1016/j.cell.2014.10.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266588PMC
November 2014

Target-independent prediction of drug synergies using only drug lipophilicity.

J Chem Inf Model 2014 Aug 1;54(8):2286-93. Epub 2014 Aug 1.

Faculty of Engineering and Natural Sciences, Biological Sciences and Bioengineering Program, ⊥Faculty of Engineering and Natural Sciences, Computer Science and Engineering Program, and ▽Nanotechnology Research and Application Center, Sabanci University , Istanbul 34956, Turkey.

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http://dx.doi.org/10.1021/ci500276xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4144720PMC
August 2014

Large-scale identification and analysis of suppressive drug interactions.

Chem Biol 2014 Apr 3;21(4):541-551. Epub 2014 Apr 3.

Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Center for Cancer Systems Biology, Dana-Farber Cancer Institute, One Jimmy Fund Way, Boston, MA 02215, USA; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada; Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2014.02.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4281482PMC
April 2014

The insertion Green Monster (iGM) method for expression of multiple exogenous genes in yeast.

G3 (Bethesda) 2014 Apr 28;4(7):1183-91. Epub 2014 Apr 28.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115

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http://dx.doi.org/10.1534/g3.114.010868DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455768PMC
April 2014

Systems biology and the analysis of genetic variation.

Curr Opin Genet Dev 2013 Dec 28;23(6):599-601. Epub 2013 Nov 28.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2013.11.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116483PMC
December 2013

ChromoZoom: a flexible, fluid, web-based genome browser.

Bioinformatics 2013 Feb 6;29(3):384-6. Epub 2012 Dec 6.

Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bts695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562068PMC
February 2013

Introns in UTRs: why we should stop ignoring them.

Bioessays 2012 Dec 26;34(12):1025-34. Epub 2012 Oct 26.

Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.

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http://dx.doi.org/10.1002/bies.201200073DOI Listing
December 2012

The green monster process for the generation of yeast strains carrying multiple gene deletions.

J Vis Exp 2012 Dec 15(70):e4072. Epub 2012 Dec 15.

Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute.

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http://dx.doi.org/10.3791/4072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575205PMC
December 2012

Genome rearrangements caused by depletion of essential DNA replication proteins in Saccharomyces cerevisiae.

Genetics 2012 Sep 5;192(1):147-60. Epub 2012 Jun 5.

Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.

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http://dx.doi.org/10.1534/genetics.112.141051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430531PMC
September 2012

Systematic exploration of synergistic drug pairs.

Mol Syst Biol 2011 Nov 8;7:544. Epub 2011 Nov 8.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/msb.2011.71DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261710PMC
November 2011

Discovering the targets of drugs via computational systems biology.

J Biol Chem 2011 Jul 12;286(27):23653-8. Epub 2011 May 12.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1074/jbc.R110.174797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129145PMC
July 2011

Reconstitution of human RNA interference in budding yeast.

Nucleic Acids Res 2011 Apr 19;39(7):e43. Epub 2011 Jan 19.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1093/nar/gkq1321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074155PMC
April 2011

Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes.

PLoS Genet 2011 Apr 14;7(4):e1001366. Epub 2011 Apr 14.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1001366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077370PMC
April 2011

Genome-wide functional analysis of human 5' untranslated region introns.

Genome Biol 2010 11;11(3):R29. Epub 2010 Mar 11.

Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, 250 Longwood Avenue, SGMB-322, Boston, MA 02115, USA.

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http://dx.doi.org/10.1186/gb-2010-11-3-r29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864569PMC
September 2010

A genome-wide gene function prediction resource for Drosophila melanogaster.

PLoS One 2010 Aug 12;5(8):e12139. Epub 2010 Aug 12.

Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012139PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2920829PMC
August 2010

FuncBase: a resource for quantitative gene function annotation.

Bioinformatics 2010 Jul 21;26(14):1806-7. Epub 2010 May 21.

Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894510PMC
July 2010

Numerous conserved and divergent microRNAs expressed by herpes simplex viruses 1 and 2.

J Virol 2010 May 24;84(9):4659-72. Epub 2010 Feb 24.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Ave., Boston, MA 02115, USA.

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http://dx.doi.org/10.1128/JVI.02725-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2863732PMC
May 2010

The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types.

Genetics 2010 May 9;185(1):65-80. Epub 2010 Mar 9.

Department of Microbiology, College of Biological Sciences, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1534/genetics.110.114074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2870977PMC
May 2010

Absence of evidence for MHC-dependent mate selection within HapMap populations.

PLoS Genet 2010 Apr 29;6(4):e1000925. Epub 2010 Apr 29.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2861700PMC
April 2010

Interpreting metabolomic profiles using unbiased pathway models.

PLoS Comput Biol 2010 Feb 26;6(2):e1000692. Epub 2010 Feb 26.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1000692
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http://dx.doi.org/10.1371/journal.pcbi.1000692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829050PMC
February 2010

Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome.

Genome Res 2009 Dec 2;19(12):2334-42. Epub 2009 Oct 2.

Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1101/gr.098640.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792173PMC
December 2009

Next generation software for functional trend analysis.

Bioinformatics 2009 Nov 28;25(22):3043-4. Epub 2009 Aug 28.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue and Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800365PMC
November 2009

Quantitative phenotyping via deep barcode sequencing.

Genome Res 2009 Oct 21;19(10):1836-42. Epub 2009 Jul 21.

Department of Molecular Genetics, University of Toronto, Ontario, Canada.

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http://dx.doi.org/10.1101/gr.093955.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765281PMC
October 2009

Pathways of the heart.

Circ Cardiovasc Genet 2009 Aug;2(4):303-5

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http://dx.doi.org/10.1161/CIRCGENETICS.109.892588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823807PMC
August 2009

Q&A: epistasis.

J Biol 2009 22;8(4):35. Epub 2009 May 22.

Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, 250 Longwood Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1186/jbiol144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688915PMC
July 2009

Literature-curated protein interaction datasets.

Nat Methods 2009 Jan;6(1):39-46

Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nmeth.1284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683745PMC
January 2009

Chemical substructures that enrich for biological activity.

Bioinformatics 2008 Nov 10;24(21):2518-25. Epub 2008 Sep 10.

Harvard University Graduate Biophysics Program, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732283PMC
November 2008

The Synergizer service for translating gene, protein and other biological identifiers.

Bioinformatics 2008 Oct 12;24(19):2272-3. Epub 2008 Aug 12.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553440PMC
October 2008

A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity.

Genes Dev 2008 Sep;22(18):2535-49

Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://dx.doi.org/10.1101/gad.1678608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2546694PMC
September 2008

A race through the maze of genomic evidence.

Genome Biol 2008 27;9 Suppl 1:S1. Epub 2008 Jun 27.

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http://dx.doi.org/10.1186/gb-2008-9-s1-s1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447543PMC
August 2008

Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function.

Genome Biol 2008 27;9 Suppl 1:S7. Epub 2008 Jun 27.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, Massachusetts 02115, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2008-9-s1-s7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447541PMC
August 2008

An en masse phenotype and function prediction system for Mus musculus.

Genome Biol 2008 27;9 Suppl 1:S8. Epub 2008 Jun 27.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1186/gb-2008-9-s1-s8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447542PMC
August 2008

Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing.

Nat Methods 2008 Jul 15;5(7):597-600. Epub 2008 Jun 15.

Center for Cancer Systems Biology, Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nmeth.1224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743938PMC
July 2008

Defining genetic interaction.

Proc Natl Acad Sci U S A 2008 Mar 27;105(9):3461-6. Epub 2008 Feb 27.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0712255105
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http://dx.doi.org/10.1073/pnas.0712255105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265146PMC
March 2008

Functional specificity among ribosomal proteins regulates gene expression.

Cell 2007 Nov;131(3):557-71

Department of Systems Biology, Harvard Medical School, Boston, MA 02119, USA.

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http://dx.doi.org/10.1016/j.cell.2007.08.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2443060PMC
November 2007

Genetic interaction screens advance in reverse.

Genes Dev 2007 Jan;21(2):137-42

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1101/gad.1512707DOI Listing
January 2007

Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants.

Nat Genet 2006 Oct 24;38(10):1216-20. Epub 2006 Sep 24.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ng1888DOI Listing
October 2006