James Zou

James Zou

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James Zou

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RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing.

RNA 2020 Jul 27;26(7):851-865. Epub 2020 Mar 27.

Department of Computer Science, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1261/rna.074161.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297119PMC
July 2020

Clinical Genetics Lacks Standard Definitions and Protocols for the Collection and Use of Diversity Measures.

Am J Hum Genet 2020 Jul 6;107(1):72-82. Epub 2020 Jun 6.

Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.ajhg.2020.05.005DOI Listing
July 2020

Integrating spatial gene expression and breast tumour morphology via deep learning.

Nat Biomed Eng 2020 Jun 22. Epub 2020 Jun 22.

Department of Computer Science, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1038/s41551-020-0578-xDOI Listing
June 2020

PB-Net: Automatic peak integration by sequential deep learning for multiple reaction monitoring.

J Proteomics 2020 May 13;223:103820. Epub 2020 May 13.

InterVenn Biosciences, United States of America; Department of Biomedical Data Science, Stanford University, United States of America. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2020.103820DOI Listing
May 2020

Video-based AI for beat-to-beat assessment of cardiac function.

Nature 2020 04 25;580(7802):252-256. Epub 2020 Mar 25.

Department of Computer Science, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1038/s41586-020-2145-8DOI Listing
April 2020

Predicting target genes of noncoding regulatory variants with ICE.

Bioinformatics 2020 Apr 24. Epub 2020 Apr 24.

Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1093/bioinformatics/btaa254DOI Listing
April 2020

RNA-GPS Predicts SARS-CoV-2 RNA Localization to Host Mitochondria and Nucleolus.

bioRxiv 2020 Apr 28. Epub 2020 Apr 28.

Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1101/2020.04.28.065201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7263502PMC
April 2020

A benchmark of algorithms for the analysis of pooled CRISPR screens.

Genome Biol 2020 03 9;21(1):62. Epub 2020 Mar 9.

Department of Bioengineering, Stanford University, 450 Serra Mall, Stanford, 94305, USA.

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http://dx.doi.org/10.1186/s13059-020-01972-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7063732PMC
March 2020

LitGen: Genetic Literature Recommendation Guided by Human Explanations.

Pac Symp Biocomput 2020 ;25:67-78

Department of Biomedical Data Science, Stanford University School of Medicine, USA.

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January 2020

Deep learning interpretation of echocardiograms.

NPJ Digit Med 2020 24;3:10. Epub 2020 Jan 24.

1Department of Electrical Engineering, Stanford University, Stanford, CA USA.

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http://dx.doi.org/10.1038/s41746-019-0216-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981156PMC
January 2020

Sex and gender analysis improves science and engineering.

Nature 2019 11 6;575(7781):137-146. Epub 2019 Nov 6.

History of Science, Gendered Innovations in Science, Health & Medicine, Engineering and Environment, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1038/s41586-019-1657-6DOI Listing
November 2019

Fast and covariate-adaptive method amplifies detection power in large-scale multiple hypothesis testing.

Nat Commun 2019 07 31;10(1):3433. Epub 2019 Jul 31.

Department of Electrical Engineering, Stanford University, Palo Alto, 94304, USA.

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http://dx.doi.org/10.1038/s41467-019-11247-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668431PMC
July 2019

VetTag: improving automated veterinary diagnosis coding via large-scale language modeling.

NPJ Digit Med 2019 8;2:35. Epub 2019 May 8.

2Department of Biomedical Data Science, Stanford University, Stanford, CA 94305 USA.

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http://dx.doi.org/10.1038/s41746-019-0113-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6550141PMC
May 2019

Modeling Spatial Correlation of Transcripts with Application to Developing Pancreas.

Sci Rep 2019 04 3;9(1):5592. Epub 2019 Apr 3.

Department of Biomedical Data Science, Stanford University, 450 Serra Mall, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1038/s41598-019-41951-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6447534PMC
April 2019

A primer on deep learning in genomics.

Nat Genet 2019 01 26;51(1):12-18. Epub 2018 Nov 26.

Scripps Research Translational Institute, La Jolla, CA, USA.

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http://www.nature.com/articles/s41588-018-0295-5
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http://dx.doi.org/10.1038/s41588-018-0295-5DOI Listing
January 2019

A novel FADS2 isoform identified in human milk fat globule suppresses FADS2 mediated Δ6-desaturation of omega-3 fatty acids.

Prostaglandins Leukot Essent Fatty Acids 2018 11 28;138:52-59. Epub 2018 Jun 28.

Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States; Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX, United States. Electronic address:

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http://dx.doi.org/10.1016/j.plefa.2018.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218299PMC
November 2018

DeepTag: inferring diagnoses from veterinary clinical notes.

NPJ Digit Med 2018 24;1:60. Epub 2018 Oct 24.

1Department of Biomedical Data Science, Stanford University, Stanford, CA 94305 USA.

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http://dx.doi.org/10.1038/s41746-018-0067-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6550285PMC
October 2018

Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites.

PLoS Biol 2018 09 13;16(9):e2005895. Epub 2018 Sep 13.

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.2005895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6155542PMC
September 2018

AI can be sexist and racist - it's time to make it fair.

Nature 2018 07;559(7714):324-326

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http://dx.doi.org/10.1038/d41586-018-05707-8DOI Listing
July 2018

Exploring patterns enriched in a dataset with contrastive principal component analysis.

Nat Commun 2018 05 30;9(1):2134. Epub 2018 May 30.

Department of Biomedical Data Science, Stanford University, 450 Serra Mall, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1038/s41467-018-04608-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5976774PMC
May 2018

Word embeddings quantify 100 years of gender and ethnic stereotypes.

Proc Natl Acad Sci U S A 2018 04 3;115(16):E3635-E3644. Epub 2018 Apr 3.

Department of Biomedical Data Science, Stanford University, Stanford, CA 94305;

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http://dx.doi.org/10.1073/pnas.1720347115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5910851PMC
April 2018

Correcting for Sample Heterogeneity in Methylome-Wide Association Studies.

Authors:
James Y Zou

Methods Mol Biol 2017 ;1589:107-114

School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/7651_2015_266DOI Listing
October 2017

Correcting for cell-type heterogeneity in DNA methylation: a comprehensive evaluation.

Nat Methods 2017 02;14(3):218-219

Department of Computer Science, University of California, Los Angeles, Los Angeles, California, USA.

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http://dx.doi.org/10.1038/nmeth.4190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5548185PMC
February 2017

Analysis of protein-coding genetic variation in 60,706 humans.

Nature 2016 08;536(7616):285-91

Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

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http://www.nature.com/articles/nature19057
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http://dx.doi.org/10.1038/nature19057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018207PMC
August 2016

Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns.

Proc Natl Acad Sci U S A 2015 Nov 19;112(44):13621-6. Epub 2015 Oct 19.

Department of Medicine, University of California, San Francisco, CA 94143;

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http://dx.doi.org/10.1073/pnas.1501741112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640764PMC
November 2015

Inferring parental genomic ancestries using pooled semi-Markov processes.

Bioinformatics 2015 Jun;31(12):i190-6

Microsoft Research, One Memorial Drive, Cambridge, MA 02142, USA, Blavatnik School of Computer Science, Tel Aviv University, Tel-Aviv 69978, Israel, Department of Bioengineering and Therapeutic Sciences and Department of Medicine, University of California, San Francisco, CA 94158 and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765873PMC
June 2015

Extended fertility and longevity: the genetic and epigenetic link.

Fertil Steril 2015 May 18;103(5):1117-24. Epub 2015 Mar 18.

Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00150282150013
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http://dx.doi.org/10.1016/j.fertnstert.2015.02.008DOI Listing
May 2015

Undesired usage and the robust self-assembly of heterogeneous structures.

Nat Commun 2015 Feb 11;6:6203. Epub 2015 Feb 11.

School of Engineering and Applied Sciences and Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1038/ncomms7203DOI Listing
February 2015

Epigenome-wide association studies without the need for cell-type composition.

Nat Methods 2014 Mar 26;11(3):309-11. Epub 2014 Jan 26.

eScience Research Group, Microsoft Research, Los Angeles, California, USA.

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http://dx.doi.org/10.1038/nmeth.2815DOI Listing
March 2014

Locus-specific editing of histone modifications at endogenous enhancers.

Nat Biotechnol 2013 Dec 8;31(12):1133-6. Epub 2013 Sep 8.

1] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA. [2] Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. [3] Broad Institute of Harvard and MIT, Cambridge Massachusetts, USA. [4] Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, USA. [5].

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http://dx.doi.org/10.1038/nbt.2701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858395PMC
December 2013

Getting the biggest birch for the bang: restoring and expanding upland birchwoods in the Scottish Highlands by managing red deer.

Ecol Evol 2013 Jul 22;3(7):1890-901. Epub 2013 May 22.

Forest Ecology and Conservation Group, Department of Plant Sciences, Downing Street, University of Cambridge Cambridge, CB2 3EA, UK.

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http://dx.doi.org/10.1002/ece3.548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728932PMC
July 2013

Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation.

J Virol 2011 Jul 4;85(13):6764-73. Epub 2011 May 4.

Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1128/JVI.00422-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3126495PMC
July 2011

Epstein-Barr virus nuclear antigens 3C and 3A maintain lymphoblastoid cell growth by repressing p16INK4A and p14ARF expression.

Proc Natl Acad Sci U S A 2011 Feb 18;108(5):1919-24. Epub 2011 Jan 18.

Department of Tumor Virology, Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan.

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http://dx.doi.org/10.1073/pnas.1019599108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033265PMC
February 2011

Religion and HIV in Tanzania: influence of religious beliefs on HIV stigma, disclosure, and treatment attitudes.

BMC Public Health 2009 Mar 4;9:75. Epub 2009 Mar 4.

School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.

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http://dx.doi.org/10.1186/1471-2458-9-75DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656538PMC
March 2009