Publications by authors named "Gustavo Stolovitzky"

100Publications

Deterministic Lateral Displacement: Challenges and Perspectives.

ACS Nano 2020 09 26;14(9):10784-10795. Epub 2020 Aug 26.

School of Engineering, Macquarie University, Macquarie Park, New South Wales 2109, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acsnano.0c05186DOI Listing
September 2020

Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.

Cell Syst 2020 Aug 24;11(2):186-195.e9. Epub 2020 Jul 24.

Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany; European Molecular Biology Laboratory-The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK; Institute for Computational Biomedicine, Heidelberg University Hospital and Heidelberg University, Faculty of Medicine, Bioquant Heidelberg, Hedelberg 69120, Germany. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2020.06.013DOI Listing
August 2020

R/PY-SUMMA: An R/Python Package for Unsupervised Ensemble Learning for Binary Classification Problems in Bioinformatics.

J Comput Biol 2020 Sep 3;27(9):1337-1340. Epub 2020 Jan 3.

IBM Translational Systems Biology Program, IBM Research, Yorktown Heights, New York.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/cmb.2019.0348DOI Listing
September 2020

NeTFactor, a framework for identifying transcriptional regulators of gene expression-based biomarkers.

Sci Rep 2019 09 10;9(1):12970. Epub 2019 Sep 10.

Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-49498-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6737052PMC
September 2019

Mitochondrial origins of fractional control in regulated cell death.

Nat Commun 2019 03 21;10(1):1313. Epub 2019 Mar 21.

IBM T.J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY, 10598, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-019-09275-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6428895PMC
March 2019

A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes.

Sci Rep 2017 12 18;7(1):17689. Epub 2017 Dec 18.

Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-017-16627-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5735158PMC
December 2017

Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology.

Pac Symp Biocomput 2018 ;23:8-19

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA.

View Article

Download full-text PDF

Source
August 2018

A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer.

JCO Clin Cancer Inform 2017 11;1:1-15

Fatemeh Seyednasrollah and Laura L. Elo, Turku Centre for Biotechnology; University of Turku; Åbo Akademi University, Turku, Finland; Devin C. Koestler, University of Kansas Medical Center, Kansas City, KS; Tao Wang, University of Texas Southwestern Medical Center, Dallas, TX; Stephen R. Piccolo, Brigham Young University, Provo; University of Utah, Salt Lake City, Utah, UT; Roberto Vega, Russell Greiner, and Luke Kumar, University of Alberta; Alberta Innovates Centre for Machine Learning, Edmonton, Alberta, Canada; Christiane Fuchs, Helmholtz Zentrum München, Neuherberg; Technische Universität München, Garching, Germany; Eyal Gofer, The Hebrew University, Jerusalem, Israel; Russell D. Wolfinger, SAS Institute, Cary, NC; Kimberly Kanigel Winner and James C. Costello, University of Colorado, Anschutz Medical Campus, Aurora, CO; Chris Bare, Elias Chaibub Neto, Thomas Yu, Thea Norman, and Justin Guinney, Sage Bionetworks, Seattle, WA; Liji Shen and Fang Liz Zhou, Sanofi, Bridgewater, NJ; Kald Abdallah, AstraZeneca, Gaithersburg, MD; Gustavo Stolovitzky, IBM Research, Yorktown Heights; Howard I. Scher, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Howard R. Soule, Prostate Cancer Foundation, Santa Monica; Charles J. Ryan, University of California, San Francisco, CA; Christopher J. Sweeney, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA; and Oliver Sartor, Tulane University, New Orleans, LA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1200/CCI.17.00018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874023PMC
November 2017

The inconvenience of data of convenience: computational research beyond post-mortem analyses.

Nat Methods 2017 09;14(10):937-938

Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.4457DOI Listing
September 2017

Broken flow symmetry explains the dynamics of small particles in deterministic lateral displacement arrays.

Proc Natl Acad Sci U S A 2017 06 12;114(26):E5034-E5041. Epub 2017 Jun 12.

IBM T. J. Watson Research Center, Yorktown Heights, NY 10598;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1706645114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495280PMC
June 2017

Nanoscale lateral displacement arrays for the separation of exosomes and colloids down to 20 nm.

Nat Nanotechnol 2016 11 1;11(11):936-940. Epub 2016 Aug 1.

IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nnano.2016.134DOI Listing
November 2016

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 10 10;7:13205. Epub 2016 Oct 10.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms13205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062501PMC
October 2016

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 08 23;7:12460. Epub 2016 Aug 23.

Sage Bionetworks, Seattle, Washington 98115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms12460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996969PMC
August 2016

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.

Authors:
Genevera I Allen Nicola Amoroso Catalina Anghel Venkat Balagurusamy Christopher J Bare Derek Beaton Roberto Bellotti David A Bennett Kevin L Boehme Paul C Boutros Laura Caberlotto Cristian Caloian Frederick Campbell Elias Chaibub Neto Yu-Chuan Chang Beibei Chen Chien-Yu Chen Ting-Ying Chien Tim Clark Sudeshna Das Christos Davatzikos Jieyao Deng Donna Dillenberger Richard J B Dobson Qilin Dong Jimit Doshi Denise Duma Rosangela Errico Guray Erus Evan Everett David W Fardo Stephen H Friend Holger Fröhlich Jessica Gan Peter St George-Hyslop Satrajit S Ghosh Enrico Glaab Robert C Green Yuanfang Guan Ming-Yi Hong Chao Huang Jinseub Hwang Joseph Ibrahim Paolo Inglese Anandhi Iyappan Qijia Jiang Yuriko Katsumata John S K Kauwe Arno Klein Dehan Kong Roland Krause Emilie Lalonde Mario Lauria Eunjee Lee Xihui Lin Zhandong Liu Julie Livingstone Benjamin A Logsdon Simon Lovestone Tsung-Wei Ma Ashutosh Malhotra Lara M Mangravite Taylor J Maxwell Emily Merrill John Nagorski Aishwarya Namasivayam Manjari Narayan Mufassra Naz Stephen J Newhouse Thea C Norman Ramil N Nurtdinov Yen-Jen Oyang Yudi Pawitan Shengwen Peng Mette A Peters Stephen R Piccolo Paurush Praveen Corrado Priami Veronica Y Sabelnykova Philipp Senger Xia Shen Andrew Simmons Aristeidis Sotiras Gustavo Stolovitzky Sabina Tangaro Andrea Tateo Yi-An Tung Nicholas J Tustison Erdem Varol George Vradenburg Michael W Weiner Guanghua Xiao Lei Xie Yang Xie Jia Xu Hojin Yang Xiaowei Zhan Yunyun Zhou Fan Zhu Hongtu Zhu Shanfeng Zhu

Alzheimers Dement 2016 06 11;12(6):645-53. Epub 2016 Apr 11.

School of Computer Science, Fudan University, Shanghai, Shanghai, China; Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, Shanghai, China; Centre for Computational Systems Biology, Fudan University, Shanghai, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jalz.2016.02.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474755PMC
June 2016

Noise-driven causal inference in biomolecular networks.

PLoS One 2015 1;10(6):e0125777. Epub 2015 Jun 1.

IBM T. J. Watson Research Center, 1101 Kitchawan Road, Route 134, Yorktown Heights, N.Y. 10598, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125777PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4452541PMC
March 2016

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

Nat Methods 2015 Jul 18;12(7):623-30. Epub 2015 May 18.

1] Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Pharmacology &Toxicology, University of Toronto, Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.3407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856034PMC
July 2015

The Prostate Cancer DREAM Challenge: A Community-Wide Effort to Use Open Clinical Trial Data for the Quantitative Prediction of Outcomes in Metastatic Prostate Cancer.

Oncologist 2015 May 16;20(5):459-60. Epub 2015 Mar 16.

Project Data Sphere, Raleigh, North Carolina, USA; Sanofi US, Bridgewater, New Jersey, USA; Sage Bionetworks, Seattle, Washington, USA; IBM T.J. Watson Research Center, Yorktown Heights, New York, USA; Icahn School of Medicine at Mount Sinai, New York, New York, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1634/theoncologist.2015-0054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425397PMC
May 2015

DREAMTools: a Python package for scoring collaborative challenges.

F1000Res 2015 9;4:1030. Epub 2015 Oct 9.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI),Wellcome Trust Genome Campus, Cambridge, UK; RWTH Aachen University Medical Hospital, Joint Research Centre for Computational Biomedicine (JRCCOMBINE), Aachen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.12688/f1000research.7118.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837986PMC
May 2016

A community computational challenge to predict the activity of pairs of compounds.

Nat Biotechnol 2014 Dec 17;32(12):1213-22. Epub 2014 Nov 17.

1] Department of Systems Biology, Columbia University, New York, New York, USA. [2] Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA. [3] Department of Biomedical Informatics, Columbia University, New York, New York, USA. [4] Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA. [5] Institute for Cancer Genetics, Columbia University, New York, New York, USA. [6] Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt.3052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4399794PMC
December 2014

Fixed-gap tunnel junction for reading DNA nucleotides.

ACS Nano 2014 Dec 12;8(12):11994-2003. Epub 2014 Nov 12.

Biodesign Institute, ‡Department of Physics, §Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/nn505356gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4278685PMC
December 2014

A crowd-sourcing approach for the construction of species-specific cell signaling networks.

Bioinformatics 2015 Feb 7;31(4):484-91. Epub 2014 Oct 7.

IBM Research, Computational Biology Center, Yorktown Heights, NY 10598, USA, ProtATonce Ltd, Scientific Park Lefkippos, Patriarchou Grigoriou & Neapoleos 15343 Ag. Paraskevi, Attiki, Greece, National Technical University of Athens, Heroon Polytechniou 9, Zografou, 15780, Greece and Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btu659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325542PMC
February 2015

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge.

Bioinformatics 2015 Feb 17;31(4):471-83. Epub 2014 Sep 17.

IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, USA, Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland, Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy, ProtATonce Ltd, Scientific Park Lefkippos, Patriarchou Grigoriou & Neapoleos 15343 Ag. Paraskevi, Attiki and National Technical University of Athens, Heroon Polytechniou 9, Zografou 15780, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btu611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325540PMC
February 2015

Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages.

Nanotechnology 2014 Jul 12;25(26):265101. Epub 2014 Jun 12.

IBM T J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, 10598, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1088/0957-4484/25/26/265101DOI Listing
July 2014

RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2013 special issue.

J Comput Biol 2014 May;21(5):371-2

1 Departments of Systems Biology, Biochemistry & Molecular Biophysics, Biomedical Informatics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center , New York, New York.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/cmb.2014.009pDOI Listing
May 2014

Regulating the transport of DNA through biofriendly nanochannels in a thin solid membrane.

Sci Rep 2014 Feb 5;4:3985. Epub 2014 Feb 5.

IBM T J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY, 10598, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep03985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914175PMC
February 2014

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge.

Bioinformatics 2013 Nov 20;29(22):2892-9. Epub 2013 Aug 20.

Department of Computer Science, Wayne State University, Perinatology Research Branch, NICHD/NIH, Detroit, MI 48201, USA, The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Rovereto 38068, Italy, ETH Zurich, Zurich 8092, Switzerland, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA and Philip Morris International, Research & Development, Neuchâtel CH-2000, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btt492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810846PMC
November 2013

An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation.

Nanotechnology 2013 May 12;24(19):195702. Epub 2013 Apr 12.

IBM Research, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1088/0957-4484/24/19/195702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681960PMC
May 2013

Dynamics of DNA translocation in a solid-state nanopore immersed in aqueous glycerol.

Nanotechnology 2012 Nov 12;23(45):455102. Epub 2012 Oct 12.

IBM T J Watson Research Center, Yorktown Heights, 10598, USA.

View Article

Download full-text PDF

Source
http://stacks.iop.org/0957-4484/23/i=45/a=455102?key=crossre
Publisher Site
http://dx.doi.org/10.1088/0957-4484/23/45/455102DOI Listing
November 2012

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 special issue.

J Comput Biol 2012 Feb;19(2):101

Columbia Initiative in Systems Biology, Columbia University, New York, New York, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/cmb.2012.010pDOI Listing
February 2012

Slowing and controlling the translocation of DNA in a solid-state nanopore.

Nanoscale 2012 Feb 14;4(4):1068-77. Epub 2011 Nov 14.

IBM Research, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c1nr11201eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543692PMC
February 2012

Characterizing and controlling the motion of ssDNA in a solid-state nanopore.

Biophys J 2011 Nov 1;101(9):2214-22. Epub 2011 Nov 1.

IBM T. J. Watson Research Center, Yorktown Heights, New York, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bpj.2011.08.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207162PMC
November 2011

Electrochemical protection of thin film electrodes in solid state nanopores.

Nanotechnology 2011 Jul 20;22(27):275304. Epub 2011 May 20.

IBM T J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1088/0957-4484/22/27/275304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174014PMC
July 2011

Setting the standards for signal transduction research.

Sci Signal 2011 Feb 15;4(160):pe10. Epub 2011 Feb 15.

European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://ginaetleo.com/failure-of-college-democracy-essay-on-6
Web Search
http://stke.sciencemag.org/cgi/doi/10.1126/scisignal.2001844
Publisher Site
http://dx.doi.org/10.1126/scisignal.2001844DOI Listing
February 2011

Tribological effects on DNA translocation in a nanochannel coated with a self-assembled monolayer.

J Phys Chem B 2010 Dec 3;114(51):17172-6. Epub 2010 Dec 3.

IBM T. J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/abs/10.1021/jp108865q
Publisher Site
http://dx.doi.org/10.1021/jp108865qDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013290PMC
December 2010

Electrochemical characterization of thin film electrodes toward developing a DNA transistor.

Langmuir 2010 Dec 22;26(24):19191-8. Epub 2010 Nov 22.

IBM T. J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/la102671gDOI Listing
December 2010

When the optimal is not the best: parameter estimation in complex biological models.

PLoS One 2010 Oct 25;5(10):e13283. Epub 2010 Oct 25.

Laboratorio de Sistemas Complejos, Depto de Computación, FCEyN, Buenos Aires University, Buenos Aires, Argentina.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013283PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2963600PMC
October 2010

Base-by-base ratcheting of single stranded DNA through a solid-state nanopore.

Phys Rev Lett 2010 Jun 10;104(23):238103. Epub 2010 Jun 10.

IBM T. J. Watson Research Center, PO Box 218, Yorktown Heights, New York 10598, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174011PMC
http://dx.doi.org/10.1103/PhysRevLett.104.238103DOI Listing
June 2010

Revealing strengths and weaknesses of methods for gene network inference.

Proc Natl Acad Sci U S A 2010 Apr 22;107(14):6286-91. Epub 2010 Mar 22.

Laboratory of Intelligent Systems, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0913357107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851985PMC
April 2010

Lessons from the DREAM2 Challenges.

Ann N Y Acad Sci 2009 Mar;1158:159-95

IBM Computational Biology Center, Yorktown Heights, New York, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1749-6632.2009.04497.xDOI Listing
March 2009

The challenges of systems biology. Preface.

Ann N Y Acad Sci 2009 Mar;1158:ix-xii

IBM Computational Biology Center Yorktown Heights, New York, USA.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1111/j.1749-6632.2009.04470.x
Publisher Site
http://dx.doi.org/10.1111/j.1749-6632.2009.04470.xDOI Listing
March 2009

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes.

Proc Natl Acad Sci U S A 2009 Jan 31;106(1):244-9. Epub 2008 Dec 31.

Department of Biomedical Informatics, Joint Centers for Systems Biology, Columbia University, New York, NY 10032, USA.

View Article

Download full-text PDF

Source
http://www.pnas.org/cgi/doi/10.1073/pnas.0806445106
Publisher Site
http://dx.doi.org/10.1073/pnas.0806445106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613038PMC
January 2009

Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks.

Proc Natl Acad Sci U S A 2008 Dec 25;105(49):19235-40. Epub 2008 Nov 25.

Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, 1 Gustave Levy Place, New York, NY 10029, USA.

View Article

Download full-text PDF

Source
http://www.pnas.org/cgi/doi/10.1073/pnas.0805344105
Publisher Site
http://dx.doi.org/10.1073/pnas.0805344105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614745PMC
December 2008

A noise model for mass spectrometry based proteomics.

Bioinformatics 2008 Apr 18;24(8):1070-7. Epub 2008 Mar 18.

IBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598, USA.

View Article

Download full-text PDF

Source
https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btn078DOI Listing
April 2008

Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference.

Ann N Y Acad Sci 2007 Dec 9;1115:1-22. Epub 2007 Oct 9.

IBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1196/annals.1407.021DOI Listing
December 2007

Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.

Bioinformatics 2007 Aug 31;23(16):2163-73. Epub 2007 May 31.

Department of Molecular Biophysics & Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btm291DOI Listing
August 2007

A single nucleotide polymorphism in the MDM2 gene disrupts the oscillation of p53 and MDM2 levels in cells.

Cancer Res 2007 Mar;67(6):2757-65

Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, New Jersey, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/0008-5472.CAN-06-2656DOI Listing
March 2007

Comparison of Amersham and Agilent microarray technologies through quantitative noise analysis.

OMICS 2006 ;10(4):532-44

IBM TJ Watson Research Center, Yorktown Heights, New York, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/omi.2006.10.532DOI Listing
March 2007

Can we identify cellular pathways implicated in cancer using gene expression data?

Proc IEEE Comput Soc Bioinform Conf 2003 ;2:94-103

Pennsylvania State University, University Park, 16802, USA.

View Article

Download full-text PDF

Source
August 2006

A robust meta-classification strategy for cancer diagnosis from gene expression data.

Proc IEEE Comput Syst Bioinform Conf 2005 :322-5

IBM Computational Biology Center, IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, USA.

View Article

Download full-text PDF

Source
http://conferences.computer.org/bioinformatics/CSB2005/PDF3/
Web Search
http://dx.doi.org/10.1109/csb.2005.7DOI Listing
May 2007