David Knowles

David Knowles

UNVERIFIED PROFILE

Are you David Knowles?   Register this Author

Register author
David Knowles

David Knowles

Publications by authors named "David Knowles"

Are you David Knowles?   Register this Author

64Publications

1142Reads

5Profile Views

Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features.

PLoS Comput Biol 2019 May 28;15(5):e1006743. Epub 2019 May 28.

Department of Radiology, Stanford University School of Medicine, Stanford, California, USA.

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006743
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6555538PMC
May 2019

Annotation-free quantification of RNA splicing using LeafCutter.

Nat Genet 2018 01 11;50(1):151-158. Epub 2017 Dec 11.

Department of Genetics, Stanford University, Stanford, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-017-0004-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5742080PMC
January 2018

Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression.

Am J Hum Genet 2017 Nov 26;101(5):686-699. Epub 2017 Oct 26.

Department of Genetics, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ajhg.2017.09.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673624PMC
November 2017

Enhancing image quality in cleared tissue with adaptive optics.

J Biomed Opt 2016 12;21(12):121508

University of California Santa Cruz, W.M. Keck Center for Adaptive Optical Microscopy, Baskin Engineering, 1154 High Street, Santa Cruz, California 95064, United States.

View Article

Download full-text PDF

Source
http://biomedicaloptics.spiedigitallibrary.org/article.aspx?
Publisher Site
http://dx.doi.org/10.1117/1.JBO.21.12.121508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5997003PMC
December 2016

Impact of the X Chromosome and sex on regulatory variation.

Genome Res 2016 06 21;26(6):768-77. Epub 2016 Apr 21.

Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Computer Science, Stanford University, Stanford, California 94305, USA;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.197897.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889977PMC
June 2016

RNA splicing is a primary link between genetic variation and disease.

Science 2016 Apr 28;352(6285):600-4. Epub 2016 Apr 28.

Department of Genetics, Stanford University, Stanford, CA, USA. Department of Biology, Stanford University, Stanford, CA, USA. Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aad9417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5182069PMC
April 2016

An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants.

Am J Hum Genet 2016 Jan 31;98(1):216-24. Epub 2015 Dec 31.

Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ajhg.2015.11.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716687PMC
January 2016

Pitman Yor Diffusion Trees for Bayesian Hierarchical Clustering.

IEEE Trans Pattern Anal Mach Intell 2015 Feb;37(2):271-89

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1109/TPAMI.2014.2313115DOI Listing
February 2015

Relational Learning and Network Modelling Using Infinite Latent Attribute Models.

IEEE Trans Pattern Anal Mach Intell 2015 Feb;37(2):462-74

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1109/TPAMI.2014.2324586DOI Listing
February 2015

Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants.

Am J Hum Genet 2014 Sep;95(3):245-56

Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00029297140034
Publisher Site
http://dx.doi.org/10.1016/j.ajhg.2014.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157143PMC
September 2014

Assessment of accuracy of marker ball placement in pre-operative templating for total hip arthroplasty.

J Arthroplasty 2014 Aug 21;29(8):1658-60. Epub 2014 Mar 21.

Royal Lancaster Infirmary, Lancaster, United Kingdom.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S08835403140017
Publisher Site
http://dx.doi.org/10.1016/j.arth.2014.03.013DOI Listing
August 2014

Allelic expression of deleterious protein-coding variants across human tissues.

PLoS Genet 2014 May 1;10(5):e1004304. Epub 2014 May 1.

Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America; Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America; Department of Computer Science, Stanford University School of Medicine, Stanford, California, United States of America.

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pgen.1004304
Publisher Site
http://dx.doi.org/10.1371/journal.pgen.1004304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006732PMC
May 2014

Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution.

Wiley Interdiscip Rev Dev Biol 2013 Nov-Dec;2(6):767-79. Epub 2013 Feb 4.

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/wdev.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819199PMC
April 2014

Grape RNA-Seq analysis pipeline environment.

Bioinformatics 2013 Mar 17;29(5):614-21. Epub 2013 Jan 17.

Bioinformatics and Genomics Group, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain.

View Article

Download full-text PDF

Source
http://bioinformatics.oxfordjournals.org/content/early/2013/
Web Search
http://webext.pasteur.fr/tekaia/EMBO_GELC_NGS_IPT/TALKS/Djeb
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btt016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582270PMC
March 2013

Intron-centric estimation of alternative splicing from RNA-seq data.

Bioinformatics 2013 Jan 21;29(2):273-4. Epub 2012 Nov 21.

Centre de Regulació Genòmica, 08003 Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bts678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546801PMC
January 2013

A fractured and immovable ceramic liner in a screw-fixed acetabular shell during total hip arthroplasty: a case report.

J Orthop Surg (Hong Kong) 2012 Dec;20(3):395-7

Department of Orthopaedic Surgery, Royal Lancaster Infirmary, Lancaster, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1177/230949901202000328DOI Listing
December 2012

Fast computation and applications of genome mappability.

PLoS One 2012 19;7(1):e30377. Epub 2012 Jan 19.

Institut de Génétique et Développement (IGDR), Université Rennes 1, Rennes, France.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030377PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261895PMC
June 2012

Three-dimensional morphology and gene expression mapping for the Drosophila blastoderm.

Authors:
David W Knowles

Cold Spring Harb Protoc 2012 Feb 1;2012(2):150-61. Epub 2012 Feb 1.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/pdb.top067843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428898PMC
February 2012

Distinct epigenomic features in end-stage failing human hearts.

Circulation 2011 Nov 24;124(22):2411-22. Epub 2011 Oct 24.

Division of Cardiovascular Medicine, University of Cambridge, Addenbrooke's Centre for Clinical Investigation, Level 6, Hills Rd, Cambridge, CB2 0QQ UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1161/CIRCULATIONAHA.111.040071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634158PMC
November 2011

Dichotomous cellular properties of mouse orexin/hypocretin neurons.

J Physiol 2011 Jun 11;589(Pt 11):2767-79. Epub 2011 Apr 11.

Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1113/jphysiol.2011.208637DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112554PMC
June 2011

Nonparametric identification of regulatory interactions from spatial and temporal gene expression data.

BMC Bioinformatics 2010 Aug 4;11:413. Epub 2010 Aug 4.

Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-11-413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2933715PMC
August 2010

Recent de novo origin of human protein-coding genes.

Genome Res 2009 Oct 2;19(10):1752-9. Epub 2009 Sep 2.

Smurfit Institute of Genetics, University of Dublin, Trinity College, Ireland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.095026.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765279PMC
October 2009

Damage to the superior gluteal nerve during the direct lateral approach to the hip: a cadaveric study.

J Arthroplasty 2007 Dec;22(8):1198-200

Central Manchester and Manchester Children's University Hospital, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.arth.2006.11.013DOI Listing
December 2007

The control of tissue architecture over nuclear organization is crucial for epithelial cell fate.

J Cell Sci 2007 May 3;120(Pt 9):1596-606. Epub 2007 Apr 3.

Department of Basic Medical Sciences and Cancer Center, Purdue University, 625 Harrison Street, West Lafayette, IN 47907-2026, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1242/jcs.03439DOI Listing
May 2007

NuMA influences higher order chromatin organization in human mammary epithelium.

Mol Biol Cell 2007 Feb 15;18(2):348-61. Epub 2006 Nov 15.

Department of Basic Medical Sciences and Cancer Center, Purdue University, West Lafayette, IN 47907-2026, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1091/mbc.e06-06-0551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1783787PMC
February 2007

High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes.

Mol Biol Evol 2006 Aug 23;23(8):1548-57. Epub 2006 May 23.

Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msl017DOI Listing
August 2006

Automated local bright feature image analysis of nuclear protein distribution identifies changes in tissue phenotype.

Proc Natl Acad Sci U S A 2006 Mar 10;103(12):4445-50. Epub 2006 Mar 10.

Biophysics and Cancer Biology Departments, Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0509944102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450191PMC
March 2006

No effect of skin anesthesia on pain intensity ratings associated with elicitation of the H-reflex in the soleus muscle.

Int J Neurosci 2004 Dec;114(12):1549-60

Department of Exercise Science, University of Georgia, Athens, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/00207450490509276DOI Listing
December 2004

In situ analyses of genome instability in breast cancer.

Nat Genet 2004 Sep 8;36(9):984-8. Epub 2004 Aug 8.

Department of Laboratory Medicine and Comprehensive Cancer Center, University of California San Francisco, California, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ng1409DOI Listing
September 2004

Examination of pain ratings associated with elicitation of the maximal H-wave and maximal M-wave in the soleus and flexor carpi radialis muscles.

Int J Neurosci 2003 Nov;113(11):1477-86

Department of Exercise Science, University of Georgia, Athens, Georgia 30602-6554, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/00207450390231536DOI Listing
November 2003

Acute bouts of active and passive leg cycling attenuate the amplitude of the soleus H-reflex in humans.

Neurosci Lett 2003 Aug;347(2):69-72

Department of Exercise Science, The University of Georgia, Ramsey Student Center, 300 River Road, Athens, GA 30602-6554, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/s0304-3940(03)00652-9DOI Listing
August 2003

Evaluation of DD23 as a marker for detection of recurrent transitional cell carcinoma of the bladder in patients with a history of bladder cancer.

Urology 2003 Mar;61(3):539-43

Department of Urology, Columbia University College of Physicians and Surgeons, New York-Presbyterian Hospital, New York, New York, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/s0090-4295(02)02400-7DOI Listing
March 2003

The bacterial ribosome, a promising focus for structure-based drug design.

Curr Opin Pharmacol 2002 Oct;2(5):501-6

RiboTargets, Granta Park, Abington, Cambridge, UK.

View Article

Download full-text PDF

Source
October 2002

Inhibitors of protein farnesyltransferase as novel anticancer agents.

Curr Top Med Chem 2002 Mar;2(3):303-23

Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2174/1568026023394281DOI Listing
March 2002