Publications by authors named "William S Noble"

88Publications

Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics.

J Proteome Res 2020 03 24;19(3):1147-1153. Epub 2020 Feb 24.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.9b00666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7175947PMC
March 2020

Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments.

J Proteome Res 2020 03 17;19(3):1267-1274. Epub 2020 Feb 17.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.9b00780DOI Listing
March 2020

Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells.

Methods 2020 01 16;170:61-68. Epub 2019 Sep 16.

Division of Hematology, University of Washington School of Medicine, Seattle, WA, United States; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymeth.2019.09.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6949367PMC
January 2020

High-Throughput Single-Cell Sequencing with Linear Amplification.

Mol Cell 2019 11 5;76(4):676-690.e10. Epub 2019 Sep 5.

Department of Genome Sciences, University of Washington, Seattle, WA, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2019.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874760PMC
November 2019

Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes.

ISME J 2020 01 6;14(1):39-52. Epub 2019 Sep 6.

Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Ave NE, Seattle, WA, 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41396-019-0503-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908719PMC
January 2020

Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression.

J Biol Chem 2019 05 22;294(22):8760-8772. Epub 2019 Apr 22.

From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057,

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.RA119.007832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6552432PMC
May 2019

Detecting Modifications in Proteomics Experiments with Param-Medic.

J Proteome Res 2019 04 5;18(4):1902-1906. Epub 2019 Mar 5.

Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.8b00954DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450762PMC
April 2019

Submodular Maximization via Gradient Ascent: The Case of Deep Submodular Functions.

Adv Neural Inf Process Syst 2018 Dec;2018:7989-7999

Depts. of Electrical & Computer Engineering, Seattle, WA 98195.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351064PMC
December 2018

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.

Cell 2019 01 3;176(1-2):377-390.e19. Epub 2019 Jan 3.

Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98105, USA; Howard Hughes Medical Institute, Seattle, WA 98105, USA. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00928674183155
Publisher Site
http://dx.doi.org/10.1016/j.cell.2018.11.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690346PMC
January 2019

MoMo: discovery of statistically significant post-translational modification motifs.

Bioinformatics 2019 08;35(16):2774-2782

Department of Pharmacology, University of Nevada, Reno, NV, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty1058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691336PMC
August 2019

Computational methods for analyzing and modeling genome structure and organization.

Wiley Interdiscip Rev Syst Biol Med 2019 01 18;11(1):e1435. Epub 2018 Jul 18.

Department of Genome Sciences, University of Washington, Seattle, Washington.

View Article

Download full-text PDF

Source
https://onlinelibrary.wiley.com/doi/abs/10.1002/wsbm.1435
Publisher Site
http://dx.doi.org/10.1002/wsbm.1435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294685PMC
January 2019

Submodular Generalized Matching for Peptide Identification in Tandem Mass Spectrometry.

IEEE/ACM Trans Comput Biol Bioinform 2019 Jul-Aug;16(4):1168-1181. Epub 2018 Apr 2.

View Article

Download full-text PDF

Source
https://ieeexplore.ieee.org/document/8329526/
Publisher Site
http://dx.doi.org/10.1109/TCBB.2018.2822280DOI Listing
February 2020

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.

Methods 2018 06 31;142:59-73. Epub 2018 Jan 31.

Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Division of Hematology, Department of Medicine, University of Washington, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymeth.2018.01.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993575PMC
June 2018

Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein.

J Comp Neurol 2017 Oct 24;525(15):3341-3359. Epub 2017 Jul 24.

Department of Biomedical Sciences, Florida State University, Tallahassee, Florida.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/cne.24281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5564178PMC
October 2017

The dynamic three-dimensional organization of the diploid yeast genome.

Elife 2017 05 24;6. Epub 2017 May 24.

Department of Genome Sciences, University of Washington, Seattle, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.23623DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5476426PMC
May 2017

Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings.

J Proteome Res 2017 04 13;16(4):1817-1824. Epub 2017 Mar 13.

Department of Genome Sciences, University of Washington , Seattle, Washington 98195, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.7b00028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738039PMC
April 2017

Massively multiplex single-cell Hi-C.

Nat Methods 2017 03 30;14(3):263-266. Epub 2017 Jan 30.

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.4155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330809PMC
March 2017

Mapping 3D genome architecture through in situ DNase Hi-C.

Nat Protoc 2016 11 29;11(11):2104-21. Epub 2016 Sep 29.

Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nprot.2016.126
Publisher Site
http://dx.doi.org/10.1038/nprot.2016.126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5547819PMC
November 2016

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0.

J Am Soc Mass Spectrom 2016 11 29;27(11):1719-1727. Epub 2016 Aug 29.

Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Box 1031, 17121, Solna, Sweden.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s13361-016-1460-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5059416PMC
November 2016

Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.

J Proteome Res 2016 08 22;15(8):2749-59. Epub 2016 Jul 22.

Department of Genome Sciences, University of Washington , Seattle 98195, Washington, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.6b00290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5116375PMC
August 2016

An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing.

J Proteome Res 2016 08 19;15(8):2697-705. Epub 2016 Jul 19.

Department of Genome Sciences and ‡Department of Computer Science and Engineering, University of Washington , Seattle, Washington 98195-5065, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.6b00239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5116374PMC
August 2016

Faster and more accurate graphical model identification of tandem mass spectra using trellises.

Bioinformatics 2016 06;32(12):i322-i331

Department of Computer Science and Engineering Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btw269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908353PMC
June 2016

Distinct epigenetic features of differentiation-regulated replication origins.

Epigenetics Chromatin 2016 10;9:18. Epub 2016 May 10.

DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13072-016-0067-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862150PMC
May 2016

Technical advances in proteomics: new developments in data-independent acquisition.

F1000Res 2016 31;5. Epub 2016 Mar 31.

Department of Genome Sciences, University of Washington, Seattle, WA, 98109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.12688/f1000research.7042.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4821292PMC
April 2016

Analysis methods for studying the 3D architecture of the genome.

Genome Biol 2015 Sep 2;16:183. Epub 2015 Sep 2.

Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-015-0745-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556012PMC
September 2015

A deeper look into Comet--implementation and features.

J Am Soc Mass Spectrom 2015 Nov 27;26(11):1865-74. Epub 2015 Jun 27.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s13361-015-1179-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4607604PMC
November 2015

Comprehensive identification and analysis of human accelerated regulatory DNA.

Genome Res 2015 Sep 23;25(9):1245-55. Epub 2015 Jun 23.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.192591.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561485PMC
September 2015

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program.

Genome Res 2015 Aug 20;25(8):1104-13. Epub 2015 May 20.

Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA; Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.183699.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509995PMC
August 2015

The MEME Suite.

Nucleic Acids Res 2015 Jul 7;43(W1):W39-49. Epub 2015 May 7.

Department of Genome Sciences, Department of Computer Science and Engineering, University of Washington, Seattle, WA 98109, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489269PMC
July 2015

Accurate identification of centromere locations in yeast genomes using Hi-C.

Nucleic Acids Res 2015 Jun 4;43(11):5331-9. Epub 2015 May 4.

Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA Department of Computer Science and Engineering, University of Washington, 185 Stevens Way, Seattle, WA 98195, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477656PMC
June 2015

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C.

BMC Genomics 2015 Feb 25;16:121. Epub 2015 Feb 25.

Department of Genome Sciences, University of Washington, Seattle, 98195, WA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-015-1236-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369351PMC
February 2015

Escape from X inactivation varies in mouse tissues.

PLoS Genet 2015 Mar 18;11(3):e1005079. Epub 2015 Mar 18.

Department of Pathology, University of Washington, Seattle, Washington, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1005079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364777PMC
March 2015

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.

Nat Methods 2015 Jan 1;12(1):71-8. Epub 2014 Dec 1.

1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Division of Hematology, University of Washington, Seattle, Washington, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.3205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4281301PMC
January 2015

Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry.

Uncertain Artif Intell 2014 ;30:320-329

Department of Genome Sciences University of Washington Seattle, WA 98195.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4185971PMC
January 2014

Comparative analysis of metazoan chromatin organization.

Nature 2014 Aug;512(7515):449-52

1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature13415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227084PMC
August 2014

Motif-based analysis of large nucleotide data sets using MEME-ChIP.

Nat Protoc 2014 22;9(6):1428-50. Epub 2014 May 22.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nprot.2014.083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175909PMC
December 2014

Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome.

Nucleus 2013 Nov-Dec;4(6):487-93. Epub 2013 Dec 5.

Veterans Affairs Palo Alto Health Care System; Stanford University Medical School; Palo Alto, CA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/nucl.27364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3925693PMC
October 2014

Genomic interaction profiles in breast cancer reveal altered chromatin architecture.

PLoS One 2013 3;8(9):e73974. Epub 2013 Sep 3.

Department of Medicine, Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, California, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073974PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760796PMC
May 2014

A statistical approach to peptide identification from clustered tandem mass spectrometry data.

Proceedings (IEEE Int Conf Bioinformatics Biomed) 2012 Oct:648-653

Department of Statistics, University of Washington, Seattle, WA, USA,

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1109/BIBMW.2012.6470214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698614PMC
October 2012

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.

Genome Res 2012 Sep;22(9):1798-812

Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.139105.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431495PMC
September 2012

Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra.

Uncertain Artif Intell 2012 Aug;28:775-785

Department of Genome Sciences, University of Washington, Seattle, WA 98195.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221238PMC
August 2012

A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes.

Methods 2012 Nov 6;58(3):277-88. Epub 2012 Jul 6.

Institute for Stem Cell and Regenerative Medicine, University of Washington, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymeth.2012.06.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477625PMC
November 2012

Maintaining replication origins in the face of genomic change.

Genome Res 2012 Oct 4;22(10):1940-52. Epub 2012 Jun 4.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.138248.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460189PMC
October 2012

Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure.

BMC Bioinformatics 2011 May 13;12:154. Epub 2011 May 13.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

View Article

Download full-text PDF

Source
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
Publisher Site
http://dx.doi.org/10.1186/1471-2105-12-154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118164PMC
May 2011

Precursor charge state prediction for electron transfer dissociation tandem mass spectra.

J Proteome Res 2010 Oct;9(10):5438-44

Department of Biochemistry, University of Washington, Seattle, Washington, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/pr1006685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2966942PMC
October 2010

A three-dimensional model of the yeast genome.

Nature 2010 May 2;465(7296):363-7. Epub 2010 May 2.

Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98195-8056, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nature08973
Publisher Site
http://dx.doi.org/10.1038/nature08973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874121PMC
May 2010

Large-scale prediction of protein-protein interactions from structures.

BMC Bioinformatics 2010 Mar 18;11:144. Epub 2010 Mar 18.

Department of Genome Sciences University of Washington, Seattle, WA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-11-144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845582PMC
March 2010

How does multiple testing correction work?

Authors:
William S Noble

Nat Biotechnol 2009 Dec;27(12):1135-7

Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt1209-1135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907892PMC
December 2009

MEME SUITE: tools for motif discovery and searching.

Nucleic Acids Res 2009 Jul 20;37(Web Server issue):W202-8. Epub 2009 May 20.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.

View Article

Download full-text PDF

Source
http://nar.oxfordjournals.org/content/37/suppl_2/W202.full.p
Web Search
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkp335
Publisher Site
http://dx.doi.org/10.1093/nar/gkp335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703892PMC
July 2009

Combining classifiers for improved classification of proteins from sequence or structure.

BMC Bioinformatics 2008 Sep 22;9:389. Epub 2008 Sep 22.

NEC Laboratories of America, Princeton, NJ, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-9-389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561051PMC
September 2008

Rapid and accurate peptide identification from tandem mass spectra.

J Proteome Res 2008 Jul 28;7(7):3022-7. Epub 2008 May 28.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/pr800127yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667385PMC
July 2008

A new pairwise kernel for biological network inference with support vector machines.

BMC Bioinformatics 2007 ;8 Suppl 10:S8

Centre for Computational Biology, Ecole des Mines de Paris, 35 rue Saint-Honoré, 77300 Fontainebleau, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-8-S10-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2230501PMC
April 2008

Widely distributed noncoding purifying selection in the human genome.

Proc Natl Acad Sci U S A 2007 Jul 17;104(30):12410-5. Epub 2007 Jul 17.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0705140104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1941483PMC
July 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Identification of higher-order functional domains in the human ENCODE regions.

Genome Res 2007 Jun;17(6):917-27

Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.6081407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891350PMC
June 2007

Unsupervised segmentation of continuous genomic data.

Bioinformatics 2007 Jun 23;23(11):1424-6. Epub 2007 Mar 23.

Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btm096DOI Listing
June 2007

What is a support vector machine?

Authors:
William S Noble

Nat Biotechnol 2006 Dec;24(12):1565-7

Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt1206-1565DOI Listing
December 2006

Identifying remote protein homologs by network propagation.

FEBS J 2005 Oct;272(20):5119-28

Department of Genome Sciences Department of Computer Science and Engineering University of Washington Seattle, WA, USA.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1111/j.1742-4658.2005.04947.x
Publisher Site
http://dx.doi.org/10.1111/j.1742-4658.2005.04947.xDOI Listing
October 2005

Genomic data visualization on the Web.

Bioinformatics 2004 Jul 26;20(11):1804-5. Epub 2004 Feb 26.

Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bth154DOI Listing
July 2004

Classification and subtype prediction of adult soft tissue sarcoma by functional genomics.

Am J Pathol 2003 Aug;163(2):691-700

Swim Across America Laboratory, Department of Surgery, Memorial-Sloan Kettering Cancer Center, New York and Columbia Genome Center, Columbia University, New York, New York 10021, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868218PMC
http://dx.doi.org/10.1016/S0002-9440(10)63696-6DOI Listing
August 2003