Terence P Speed

Terence P Speed

UNVERIFIED PROFILE

Are you Terence P Speed?   Register this Author

Register author
Terence P Speed

Terence P Speed

Publications by authors named "Terence P Speed"

Are you Terence P Speed?   Register this Author

100Publications

1986Reads

49Profile Views

A new normalization for Nanostring nCounter gene expression data.

Nucleic Acids Res 2019 07;47(12):6073-6083

Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkz433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6614807PMC
July 2019

DECENT: Differential Expression with Capture Efficiency adjustmeNT for single-cell RNA-seq data.

Bioinformatics 2019 Jun 14. Epub 2019 Jun 14.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz453DOI Listing
June 2019

Using long-read sequencing to detect imprinted DNA methylation.

Nucleic Acids Res 2019 05;47(8):e46

The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkz107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486641PMC
May 2019

Maps of variability in cell lineage trees.

PLoS Comput Biol 2019 02 12;15(2):e1006745. Epub 2019 Feb 12.

Centre for Micro-Photonics, Department of Physics and Astronomy, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388934PMC
February 2019

Dysregulated IL-1β-GM-CSF Axis in Acute Rheumatic Fever That Is Limited by Hydroxychloroquine.

Circulation 2018 12;138(23):2648-2661

Divisions of Inflammation (M.L.K., W.J.M., J.L.K., I.P.W.), Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.

View Article

Download full-text PDF

Source
https://www.ahajournals.org/doi/10.1161/CIRCULATIONAHA.118.0
Publisher Site
http://dx.doi.org/10.1161/CIRCULATIONAHA.118.033891DOI Listing
December 2018

The healthy ageing gene expression signature for Alzheimer's disease diagnosis: a random sampling perspective.

Genome Biol 2018 07 25;19(1):97. Epub 2018 Jul 25.

Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, and Department of Mathematics and Statistics, University of Melbourne, Melbourne, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-018-1481-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060554PMC
July 2018

RLE plots: Visualizing unwanted variation in high dimensional data.

PLoS One 2018 5;13(2):e0191629. Epub 2018 Feb 5.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0191629PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798764PMC
March 2018

Correction to: A statistical framework for analyzing deep mutational scanning data.

Genome Biol 2018 02 7;19(1):17. Epub 2018 Feb 7.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-018-1391-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5803959PMC
February 2018

Joint Modeling of Mixed Species Infections Using a Bivariate Poisson Lognormal Model.

Am J Trop Med Hyg 2018 01;98(1):71-76

Department of Statistics, University of California, Berkeley, Berkeley, California.

View Article

Download full-text PDF

Source
http://www.ajtmh.org/content/journals/10.4269/ajtmh.17-0523
Publisher Site
http://dx.doi.org/10.4269/ajtmh.17-0523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5928727PMC
January 2018

Accurate RNA Sequencing From Formalin-Fixed Cancer Tissue To Represent High-Quality Transcriptome From Frozen Tissue.

JCO Precis Oncol 2018 26;2018. Epub 2018 Jan 26.

Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5976456PMC
http://dx.doi.org/10.1200/PO.17.00091DOI Listing
January 2018

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.

Genome Res 2017 12 2;27(12):2050-2060. Epub 2017 Nov 2.

Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.222109.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741059PMC
December 2017

A statistical framework for analyzing deep mutational scanning data.

Genome Biol 2017 Aug 7;18(1):150. Epub 2017 Aug 7.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-017-1272-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5547491PMC
August 2017

Deficiency of microRNA expands cell fate potential in pluripotent stem cells.

Science 2017 02 12;355(6325). Epub 2017 Jan 12.

Division of Cellular and Developmental Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94705, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aag1927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6138252PMC
February 2017

Contextual fear conditioning induces differential alternative splicing.

Neurobiol Learn Mem 2016 10 20;134 Pt B:221-35. Epub 2016 Jul 20.

Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.nlm.2016.07.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5028328PMC
October 2016

Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex.

BMC Genomics 2016 10 25;17(Suppl 8):727. Epub 2016 Oct 25.

Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-016-3065-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5088519PMC
October 2016

Corrigendum to 'MicroRNAs in CD4 T cell subsets are markers of disease risk and T cell dysfunction in individuals at risk for type 1 diabetes' [J. Autoimmun. 68C (2016) 52-61].

J Autoimmun 2016 Sep 25;73:130. Epub 2016 Apr 25.

The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jaut.2016.04.002DOI Listing
September 2016

MicroRNAs in CD4(+) T cell subsets are markers of disease risk and T cell dysfunction in individuals at risk for type 1 diabetes.

J Autoimmun 2016 Apr 11;68:52-61. Epub 2016 Jan 11.

The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S08968411153006
Publisher Site
http://dx.doi.org/10.1016/j.jaut.2015.12.006DOI Listing
April 2016

Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed.

Biostatistics 2016 Jan 17;17(1):16-28. Epub 2015 Aug 17.

Department of Statistics, University of California, Berkeley, CA 974720, USA and Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/biostatistics/kxv026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679071PMC
January 2016

Signatures of tumour immunity distinguish Asian and non-Asian gastric adenocarcinomas.

Gut 2015 Nov 10;64(11):1721-31. Epub 2014 Nov 10.

Department of Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore, Singapore Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore Cellular and Molecular Research, National Cancer Centre, Singapore, Singapore.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1136/gutjnl-2014-308252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4680172PMC
November 2015

Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data.

Nucleic Acids Res 2015 Sep 18;43(16):e106. Epub 2015 May 18.

Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia Department of Genetics, The University of Melbourne, VIC 3010, Australia

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652745PMC
September 2015

How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets.

Nucleic Acids Res 2015 Sep 21;43(16):7664-74. Epub 2015 Jul 21.

Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv736DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652761PMC
September 2015

Systematic noise degrades gene co-expression signals but can be corrected.

BMC Bioinformatics 2015 Sep 24;16:309. Epub 2015 Sep 24.

Bioinformatics Division, Walter + Eliza Hall Institute, 1G Royal Parade, Melbourne, 3050, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-015-0745-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583191PMC
September 2015

Statistical methods for handling unwanted variation in metabolomics data.

Anal Chem 2015 Apr 6;87(7):3606-15. Epub 2015 Mar 6.

∥Department of Statistics, University of California, Berkeley, California United States, 94720.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ac502439yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4544854PMC
April 2015

Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery.

PLoS One 2014 29;9(1):e86993. Epub 2014 Jan 29.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia ; Department of Mathematics and Statistics, University of Melbourne, Melbourne, Australia.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086993PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906086PMC
September 2014

Normalization of RNA-seq data using factor analysis of control genes or samples.

Nat Biotechnol 2014 Sep 24;32(9):896-902. Epub 2014 Aug 24.

1] Department of Statistics, University of California, Berkeley, Berkeley, California, USA. [2] Division of Biostatistics, University of California, Berkeley, Berkeley, California, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt.2931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404308PMC
September 2014

Dating rare mutations from small samples with dense marker data.

Genetics 2014 Aug 30;197(4):1315-27. Epub 2014 May 30.

Department of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, 3010 Australia Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052 Australia Department of Statistics, University of California, Berkeley, California 94720-3860.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.114.164616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125402PMC
August 2014

Combining calls from multiple somatic mutation-callers.

BMC Bioinformatics 2014 May 21;15:154. Epub 2014 May 21.

Department of Statistics, University of California at Berkeley, Berkeley CA 94720, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-15-154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035752PMC
May 2014

Statistical analysis of metabolomics data.

Methods Mol Biol 2013 ;1055:291-307

Metabolomics Australia, Bio21 Institute (Molecular Science and Biotechnology Institute), The University of Melbourne, Melbourne, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-62703-577-4_20DOI Listing
March 2014

A high force of plasmodium vivax blood-stage infection drives the rapid acquisition of immunity in papua new guinean children.

PLoS Negl Trop Dis 2013 5;7(9):e2403. Epub 2013 Sep 5.

Swiss Tropical and Public Health Institute, Basel, Switzerland ; University of Basel, Basel, Switzerland ; Walter and Eliza Hall Institute, Parkville, Victoria, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pntd.0002403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764149PMC
March 2014

Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron.

Neuron 2014 Feb;81(4):847-59

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Functional Genomics Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.neuron.2014.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412037PMC
February 2014

Comparing somatic mutation-callers: beyond Venn diagrams.

BMC Bioinformatics 2013 Jun 10;14:189. Epub 2013 Jun 10.

Department of Statistics, University of California at Berkeley, 367 Evans Hall, Berkeley, CA 94720, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-14-189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3702398PMC
June 2013

Id2-mediated inhibition of E2A represses memory CD8+ T cell differentiation.

J Immunol 2013 May 27;190(9):4585-94. Epub 2013 Mar 27.

Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4049/jimmunol.1300099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631715PMC
May 2013

Effect of vascular endothelial growth factor upregulation on retinal gene expression in the Kimba mouse.

Clin Exp Ophthalmol 2013 Apr 17;41(3):251-62. Epub 2012 Oct 17.

Department of Molecular Ophthalmology, Lions Eye Institute, Nedlands Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1442-9071.2012.02845.xDOI Listing
April 2013

Divergent lymphocyte signalling revealed by a powerful new tool for analysis of time-lapse microscopy.

Immunol Cell Biol 2013 Jan 2;91(1):70-81. Epub 2012 Oct 2.

Centre for Micro-Photonics, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, Hawthorn, Adelaide, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/icb.2012.49DOI Listing
January 2013

Copy-number-aware differential analysis of quantitative DNA sequencing data.

Genome Res 2012 Dec 9;22(12):2489-96. Epub 2012 Aug 9.

Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.139055.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514678PMC
December 2012

Normalizing and integrating metabolomics data.

Anal Chem 2012 Dec 29;84(24):10768-76. Epub 2012 Nov 29.

Metabolomics Australia at The University of Melbourne, Melbourne, Victoria, Australia.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/ac302748b
Publisher Site
http://dx.doi.org/10.1021/ac302748bDOI Listing
December 2012

Bayesian inference of signaling network topology in a cancer cell line.

Bioinformatics 2012 Nov 24;28(21):2804-10. Epub 2012 Aug 24.

Department of Biochemistry, The Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bts514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3476330PMC
November 2012

A Tetrahymena Piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus.

Mol Cell 2012 Nov 18;48(4):509-20. Epub 2012 Oct 18.

Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720-3200, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2012.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3513674PMC
November 2012

Using control genes to correct for unwanted variation in microarray data.

Biostatistics 2012 Jul 17;13(3):539-52. Epub 2011 Nov 17.

Department of Statistics, University of California at Berkeley, Berkeley, CA 94720-3860, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/biostatistics/kxr034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577104PMC
July 2012

SRMA: an R package for resequencing array data analysis.

Bioinformatics 2012 Jul 10;28(14):1928-30. Epub 2012 May 10.

Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bts286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389772PMC
July 2012

Genome-wide analysis of glucocorticoid receptor-binding sites in myotubes identifies gene networks modulating insulin signaling.

Proc Natl Acad Sci U S A 2012 Jul 25;109(28):11160-5. Epub 2012 Jun 25.

Endocrinology Graduate Program, Department of Nutritional Science and Toxicology, University of California, Berkeley, CA 94720, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1111334109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396543PMC
July 2012

Summarizing and correcting the GC content bias in high-throughput sequencing.

Nucleic Acids Res 2012 May 9;40(10):e72. Epub 2012 Feb 9.

Department of Statistics, University of California, Berkeley, CA 94720, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gks001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378858PMC
May 2012

The N-terminal domains of SOCS proteins: a conserved region in the disordered N-termini of SOCS4 and 5.

Proteins 2012 Mar;80(3):946-57

The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.23252DOI Listing
March 2012

Tissue-specific regulation of genes by estrogen receptors.

Semin Reprod Med 2012 Jan 23;30(1):14-22. Epub 2012 Jan 23.

Department of Nutritional Science and Toxicology, University of California, Berkeley, California 94720, USA.

View Article

Download full-text PDF

Source
https://www.thieme-connect.com/products/ejournals/pdf/10.105
Web Search
http://www.thieme-connect.de/DOI/DOI?10.1055/s-0031-1299593
Publisher Site
http://dx.doi.org/10.1055/s-0031-1299593DOI Listing
January 2012

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

Authors:
Marilyn B Renfree Anthony T Papenfuss Janine E Deakin James Lindsay Thomas Heider Katherine Belov Willem Rens Paul D Waters Elizabeth A Pharo Geoff Shaw Emily S W Wong Christophe M Lefèvre Kevin R Nicholas Yoko Kuroki Matthew J Wakefield Kyall R Zenger Chenwei Wang Malcolm Ferguson-Smith Frank W Nicholas Danielle Hickford Hongshi Yu Kirsty R Short Hannah V Siddle Stephen R Frankenberg Keng Yih Chew Brandon R Menzies Jessica M Stringer Shunsuke Suzuki Timothy A Hore Margaret L Delbridge Hardip R Patel Amir Mohammadi Nanette Y Schneider Yanqiu Hu William O'Hara Shafagh Al Nadaf Chen Wu Zhi-Ping Feng Benjamin G Cocks Jianghui Wang Paul Flicek Stephen M J Searle Susan Fairley Kathryn Beal Javier Herrero Dawn M Carone Yutaka Suzuki Sumio Sugano Atsushi Toyoda Yoshiyuki Sakaki Shinji Kondo Yuichiro Nishida Shoji Tatsumoto Ion Mandiou Arthur Hsu Kaighin A McColl Benjamin Lansdell George Weinstock Elizabeth Kuczek Annette McGrath Peter Wilson Artem Men Mehlika Hazar-Rethinam Allison Hall John Davis David Wood Sarah Williams Yogi Sundaravadanam Donna M Muzny Shalini N Jhangiani Lora R Lewis Margaret B Morgan Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Lynne Nazareth Andrew Cree Gerald Fowler Christie L Kovar Huyen H Dinh Vandita Joshi Chyn Jing Fremiet Lara Rebecca Thornton Lei Chen Jixin Deng Yue Liu Joshua Y Shen Xing-Zhi Song Janette Edson Carmen Troon Daniel Thomas Amber Stephens Lankesha Yapa Tanya Levchenko Richard A Gibbs Desmond W Cooper Terence P Speed Asao Fujiyama Jennifer A M Graves Rachel J O'Neill Andrew J Pask Susan M Forrest Kim C Worley

Genome Biol 2011 Aug 29;12(8):R81. Epub 2011 Aug 29.

The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2011-12-8-r81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277949PMC
August 2011

Discovery and molecular characterization of a Bcl-2-regulated cell death pathway in schistosomes.

Proc Natl Acad Sci U S A 2011 Apr 28;108(17):6999-7003. Epub 2011 Mar 28.

The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1100652108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3084110PMC
April 2011

High-quality DNA sequence capture of 524 disease candidate genes.

Proc Natl Acad Sci U S A 2011 Apr 5;108(16):6549-54. Epub 2011 Apr 5.

Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1018981108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080966PMC
April 2011

Unifying gene expression measures from multiple platforms using factor analysis.

PLoS One 2011 Mar 11;6(3):e17691. Epub 2011 Mar 11.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017691PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059153PMC
March 2011

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation.

Genome Res 2010 Dec 2;20(12):1719-29. Epub 2010 Nov 2.

Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.110601.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989998PMC
December 2010

Genome-wide analysis of glucocorticoid receptor binding regions in adipocytes reveal gene network involved in triglyceride homeostasis.

PLoS One 2010 Dec 20;5(12):e15188. Epub 2010 Dec 20.

Department of Nutritional Science & Toxicology, University of California, Berkeley, California, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015188PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004788PMC
December 2010

Conserved role of unc-79 in ethanol responses in lightweight mutant mice.

PLoS Genet 2010 Aug 12;6(8). Epub 2010 Aug 12.

Department of Neurology and the Ernest Gallo Clinic and Research Center, University of California San Francisco, Emeryville, California, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1001057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2920847PMC
August 2010

Protocol matters: which methylome are you actually studying?

Epigenomics 2010 Aug;2(4):587-98

Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2217/epi.10.36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090160PMC
August 2010

Estrogen receptor beta binds to and regulates three distinct classes of target genes.

J Biol Chem 2010 Jul 19;285(29):22059-66. Epub 2010 Apr 19.

Department of Nutritional Science and Toxicology, University of California, Berkeley, California 94720, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.M110.114116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903369PMC
July 2010

International network of cancer genome projects.

Authors:
Thomas J Hudson Warwick Anderson Axel Artez Anna D Barker Cindy Bell Rosa R Bernabé M K Bhan Fabien Calvo Iiro Eerola Daniela S Gerhard Alan Guttmacher Mark Guyer Fiona M Hemsley Jennifer L Jennings David Kerr Peter Klatt Patrik Kolar Jun Kusada David P Lane Frank Laplace Lu Youyong Gerd Nettekoven Brad Ozenberger Jane Peterson T S Rao Jacques Remacle Alan J Schafer Tatsuhiro Shibata Michael R Stratton Joseph G Vockley Koichi Watanabe Huanming Yang Matthew M F Yuen Bartha M Knoppers Martin Bobrow Anne Cambon-Thomsen Lynn G Dressler Stephanie O M Dyke Yann Joly Kazuto Kato Karen L Kennedy Pilar Nicolás Michael J Parker Emmanuelle Rial-Sebbag Carlos M Romeo-Casabona Kenna M Shaw Susan Wallace Georgia L Wiesner Nikolajs Zeps Peter Lichter Andrew V Biankin Christian Chabannon Lynda Chin Bruno Clément Enrique de Alava Françoise Degos Martin L Ferguson Peter Geary D Neil Hayes Thomas J Hudson Amber L Johns Arek Kasprzyk Hidewaki Nakagawa Robert Penny Miguel A Piris Rajiv Sarin Aldo Scarpa Tatsuhiro Shibata Marc van de Vijver P Andrew Futreal Hiroyuki Aburatani Mónica Bayés David D L Botwell Peter J Campbell Xavier Estivill Daniela S Gerhard Sean M Grimmond Ivo Gut Martin Hirst Carlos López-Otín Partha Majumder Marco Marra John D McPherson Hidewaki Nakagawa Zemin Ning Xose S Puente Yijun Ruan Tatsuhiro Shibata Michael R Stratton Hendrik G Stunnenberg Harold Swerdlow Victor E Velculescu Richard K Wilson Hong H Xue Liu Yang Paul T Spellman Gary D Bader Paul C Boutros Peter J Campbell Paul Flicek Gad Getz Roderic Guigó Guangwu Guo David Haussler Simon Heath Tim J Hubbard Tao Jiang Steven M Jones Qibin Li Nuria López-Bigas Ruibang Luo Lakshmi Muthuswamy B F Francis Ouellette John V Pearson Xose S Puente Victor Quesada Benjamin J Raphael Chris Sander Tatsuhiro Shibata Terence P Speed Lincoln D Stein Joshua M Stuart Jon W Teague Yasushi Totoki Tatsuhiko Tsunoda Alfonso Valencia David A Wheeler Honglong Wu Shancen Zhao Guangyu Zhou Lincoln D Stein Roderic Guigó Tim J Hubbard Yann Joly Steven M Jones Arek Kasprzyk Mark Lathrop Nuria López-Bigas B F Francis Ouellette Paul T Spellman Jon W Teague Gilles Thomas Alfonso Valencia Teruhiko Yoshida Karen L Kennedy Myles Axton Stephanie O M Dyke P Andrew Futreal Daniela S Gerhard Chris Gunter Mark Guyer Thomas J Hudson John D McPherson Linda J Miller Brad Ozenberger Kenna M Shaw Arek Kasprzyk Lincoln D Stein Junjun Zhang Syed A Haider Jianxin Wang Christina K Yung Anthony Cros Anthony Cross Yong Liang Saravanamuttu Gnaneshan Jonathan Guberman Jack Hsu Martin Bobrow Don R C Chalmers Karl W Hasel Yann Joly Terry S H Kaan Karen L Kennedy Bartha M Knoppers William W Lowrance Tohru Masui Pilar Nicolás Emmanuelle Rial-Sebbag Laura Lyman Rodriguez Catherine Vergely Teruhiko Yoshida Sean M Grimmond Andrew V Biankin David D L Bowtell Nicole Cloonan Anna deFazio James R Eshleman Dariush Etemadmoghadam Brooke B Gardiner Brooke A Gardiner James G Kench Aldo Scarpa Robert L Sutherland Margaret A Tempero Nicola J Waddell Peter J Wilson John D McPherson Steve Gallinger Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Debabrata Mukhopadhyay Lynda Chin Ronald A DePinho Sarah Thayer Lakshmi Muthuswamy Kamran Shazand Timothy Beck Michelle Sam Lee Timms Vanessa Ballin Youyong Lu Jiafu Ji Xiuqing Zhang Feng Chen Xueda Hu Guangyu Zhou Qi Yang Geng Tian Lianhai Zhang Xiaofang Xing Xianghong Li Zhenggang Zhu Yingyan Yu Jun Yu Huanming Yang Mark Lathrop Jörg Tost Paul Brennan Ivana Holcatova David Zaridze Alvis Brazma Lars Egevard Egor Prokhortchouk Rosamonde Elizabeth Banks Mathias Uhlén Anne Cambon-Thomsen Juris Viksna Fredrik Ponten Konstantin Skryabin Michael R Stratton P Andrew Futreal Ewan Birney Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Sancha Martin Jorge S Reis-Filho Andrea L Richardson Christos Sotiriou Hendrik G Stunnenberg Giles Thoms Marc van de Vijver Laura van't Veer Fabien Calvo Daniel Birnbaum Hélène Blanche Pascal Boucher Sandrine Boyault Christian Chabannon Ivo Gut Jocelyne D Masson-Jacquemier Mark Lathrop Iris Pauporté Xavier Pivot Anne Vincent-Salomon Eric Tabone Charles Theillet Gilles Thomas Jörg Tost Isabelle Treilleux Fabien Calvo Paulette Bioulac-Sage Bruno Clément Thomas Decaens Françoise Degos Dominique Franco Ivo Gut Marta Gut Simon Heath Mark Lathrop Didier Samuel Gilles Thomas Jessica Zucman-Rossi Peter Lichter Roland Eils Benedikt Brors Jan O Korbel Andrey Korshunov Pablo Landgraf Hans Lehrach Stefan Pfister Bernhard Radlwimmer Guido Reifenberger Michael D Taylor Christof von Kalle Partha P Majumder Rajiv Sarin T S Rao M K Bhan Aldo Scarpa Paolo Pederzoli Rita A Lawlor Massimo Delledonne Alberto Bardelli Andrew V Biankin Sean M Grimmond Thomas Gress David Klimstra Giuseppe Zamboni Tatsuhiro Shibata Yusuke Nakamura Hidewaki Nakagawa Jun Kusada Tatsuhiko Tsunoda Satoru Miyano Hiroyuki Aburatani Kazuto Kato Akihiro Fujimoto Teruhiko Yoshida Elias Campo Carlos López-Otín Xavier Estivill Roderic Guigó Silvia de Sanjosé Miguel A Piris Emili Montserrat Marcos González-Díaz Xose S Puente Pedro Jares Alfonso Valencia Heinz Himmelbauer Heinz Himmelbaue Victor Quesada Silvia Bea Michael R Stratton P Andrew Futreal Peter J Campbell Anne Vincent-Salomon Andrea L Richardson Jorge S Reis-Filho Marc van de Vijver Gilles Thomas Jocelyne D Masson-Jacquemier Samuel Aparicio Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Hendrik G Stunnenberg Laura van't Veer Douglas F Easton Paul T Spellman Sancha Martin Anna D Barker Lynda Chin Francis S Collins Carolyn C Compton Martin L Ferguson Daniela S Gerhard Gad Getz Chris Gunter Alan Guttmacher Mark Guyer D Neil Hayes Eric S Lander Brad Ozenberger Robert Penny Jane Peterson Chris Sander Kenna M Shaw Terence P Speed Paul T Spellman Joseph G Vockley David A Wheeler Richard K Wilson Thomas J Hudson Lynda Chin Bartha M Knoppers Eric S Lander Peter Lichter Lincoln D Stein Michael R Stratton Warwick Anderson Anna D Barker Cindy Bell Martin Bobrow Wylie Burke Francis S Collins Carolyn C Compton Ronald A DePinho Douglas F Easton P Andrew Futreal Daniela S Gerhard Anthony R Green Mark Guyer Stanley R Hamilton Tim J Hubbard Olli P Kallioniemi Karen L Kennedy Timothy J Ley Edison T Liu Youyong Lu Partha Majumder Marco Marra Brad Ozenberger Jane Peterson Alan J Schafer Paul T Spellman Hendrik G Stunnenberg Brandon J Wainwright Richard K Wilson Huanming Yang

Nature 2010 Apr;464(7291):993-8

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature08987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
April 2010

Unliganded estrogen receptor-beta regulation of genes is inhibited by tamoxifen.

Mol Cell Endocrinol 2010 Feb 8;315(1-2):201-7. Epub 2009 Sep 8.

Department of Obstetrics, Gynecology and Reproductive , University of California, San Francisco, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mce.2009.08.030DOI Listing
February 2010

Multiple testing and its applications to microarrays.

Stat Methods Med Res 2009 Dec;18(6):543-63

Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, NY 10029, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1177/0962280209351899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131454PMC
December 2009

Gene set enrichment analysis made simple.

Stat Methods Med Res 2009 Dec;18(6):565-75

Department of Biostatistics, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1177/0962280209351908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134237PMC
December 2009

Background adjustment for DNA microarrays using a database of microarray experiments.

J Comput Biol 2009 Nov;16(11):1501-15

Department of Community Health, Brown University, Providence, Rhode Island 02912, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/cmb.2009.0063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154459PMC
November 2009

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6.

Bioinformatics 2009 Sep 17;25(17):2149-56. Epub 2009 Jun 17.

Department of Statistics, University of California, Berkeley, California, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btp371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734319PMC
September 2009

Differential splicing using whole-transcript microarrays.

BMC Bioinformatics 2009 May 22;10:156. Epub 2009 May 22.

Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-10-156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703633PMC
May 2009

A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods.

Bioinformatics 2009 Apr 4;25(7):861-7. Epub 2009 Feb 4.

Department of Statistics, Life Sciences Division, University of California, Lawrence Berkeley National Laboratory, Berkeley, 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/btp074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660872PMC
April 2009

On gene ranking using replicated microarray time course data.

Biometrics 2009 Mar 5;65(1):40-51. Epub 2008 Jun 5.

Institute for Human Genetics, 513 Parnassus Avenue S965, University of California, San Francisco, California 94143-0794, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1541-0420.2008.01057.xDOI Listing
March 2009

Cell type- and estrogen receptor-subtype specific regulation of selective estrogen receptor modulator regulatory elements.

Mol Cell Endocrinol 2009 Feb 18;299(2):204-11. Epub 2008 Nov 18.

Departments of Obstetrics, Gynecology and Reproductive Sciences, Cellular and Molecular Pharmacology, Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S03037207080051
Publisher Site
http://dx.doi.org/10.1016/j.mce.2008.10.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3420066PMC
February 2009

Sparse combinatorial inference with an application in cancer biology.

Bioinformatics 2009 Jan 27;25(2):265-71. Epub 2008 Nov 27.

Department of Statistics, University of Warwick, Coventry, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btn611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639004PMC
January 2009

Network inference using informative priors.

Proc Natl Acad Sci U S A 2008 Sep 17;105(38):14313-8. Epub 2008 Sep 17.

Department of Statistics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0802272105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567188PMC
September 2008