Publications by authors named "Yuanfang Guan"

88Publications

Detecting Asymmetric Patterns and Localizing Cancers on Mammograms.

Patterns (N Y) 2020 Oct 21;1(7). Epub 2020 Sep 21.

Translational Research Lab of Arkansas State University and St. Bernard's Medical Center, Jonesboro, AR 72467, USA.

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http://dx.doi.org/10.1016/j.patter.2020.100106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7566852PMC
October 2020

FastClone is a probabilistic tool for deconvoluting tumor heterogeneity in bulk-sequencing samples.

Nat Commun 2020 09 8;11(1):4469. Epub 2020 Sep 8.

Department of Computational Medicine and Bioinformatics, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1038/s41467-020-18169-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7478963PMC
September 2020

COVID-19 drug repurposing: A review of computational screening methods, clinical trials, and protein interaction assays.

Med Res Rev 2020 Aug 30. Epub 2020 Aug 30.

Department of Computational Medicine and Bioinformatics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA.

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http://dx.doi.org/10.1002/med.21728DOI Listing
August 2020

Challenge-Enabled Machine Learning to Drug-Response Prediction.

AAPS J 2020 08 10;22(5):106. Epub 2020 Aug 10.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.

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http://dx.doi.org/10.1208/s12248-020-00494-5DOI Listing
August 2020

Graph2GO: a multi-modal attributed network embedding method for inferring protein functions.

Gigascience 2020 Aug;9(8)

Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.

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http://dx.doi.org/10.1093/gigascience/giaa081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7414417PMC
August 2020

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

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

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

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

Deep Learning Identifies Digital Biomarkers for Self-Reported Parkinson's Disease.

Patterns (N Y) 2020 Jun 28;1(3). Epub 2020 May 28.

Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1016/j.patter.2020.100042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7375444PMC
June 2020

Three-Plane-assembled Deep Learning Segmentation of Gliomas.

Radiol Artif Intell 2020 Mar 11;2(2):e190011. Epub 2020 Mar 11.

Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave, Ann Arbor, MI 48109.

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http://dx.doi.org/10.1148/ryai.2020190011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104789PMC
March 2020

Cellular, transcriptomic and isoform heterogeneity of breast cancer cell line revealed by full-length single-cell RNA sequencing.

Comput Struct Biotechnol J 2020 19;18:676-685. Epub 2020 Mar 19.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor 48109, MI, United States.

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http://dx.doi.org/10.1016/j.csbj.2020.03.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114460PMC
March 2020

Machine Learning for Cancer Drug Combination.

Clin Pharmacol Ther 2020 04 11;107(4):749-752. Epub 2020 Feb 11.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.

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http://dx.doi.org/10.1002/cpt.1773DOI Listing
April 2020

Treatment Stratification of Patients with Metastatic Castration-Resistant Prostate Cancer by Machine Learning.

iScience 2020 Feb 26;23(2):100804. Epub 2019 Dec 26.

Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2019.100804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976944PMC
February 2020

Prognostic model for multiple myeloma progression integrating gene expression and clinical features.

Gigascience 2019 12;8(12)

Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1093/gigascience/giz153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936209PMC
December 2019

Joint learning improves protein abundance prediction in cancers.

BMC Biol 2019 12 23;17(1):107. Epub 2019 Dec 23.

Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA.

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http://dx.doi.org/10.1186/s12915-019-0730-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6929375PMC
December 2019

Deep Residual Neural Networks Resolve Quartet Molecular Phylogenies.

Mol Biol Evol 2020 05;37(5):1495-1507

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI.

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http://dx.doi.org/10.1093/molbev/msz307DOI Listing
May 2020

Machine learning empowers phosphoproteome prediction in cancers.

Bioinformatics 2020 02;36(3):859-864

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz639DOI Listing
February 2020

Transcriptional regulation of microalgae for concurrent lipid overproduction and secretion.

Sci Adv 2019 01 30;5(1):eaau3795. Epub 2019 Jan 30.

Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.

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http://dx.doi.org/10.1126/sciadv.aau3795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6353619PMC
January 2019

Anchor: trans-cell type prediction of transcription factor binding sites.

Genome Res 2019 02 19;29(2):281-292. Epub 2018 Dec 19.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.237156.118
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http://dx.doi.org/10.1101/gr.237156.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360811PMC
February 2019

TAIJI: approaching experimental replicates-level accuracy for drug synergy prediction.

Bioinformatics 2019 07;35(13):2338-2339

Department of Computational Medicine and Bioinformatics.

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http://dx.doi.org/10.1093/bioinformatics/bty955DOI Listing
July 2019

Model-Based and Model-Free Techniques for Amyotrophic Lateral Sclerosis Diagnostic Prediction and Patient Clustering.

Neuroinformatics 2019 07;17(3):407-421

Statistics Online Computational Resource, Department of Health Behavior and Biological Sciences, University of Michigan, Ann Arbor, MI, 48109, USA.

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http://dx.doi.org/10.1007/s12021-018-9406-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6527505PMC
July 2019

High-Throughput Single-Cell Sequencing of both Alleles.

J Immunol 2018 12 31;201(11):3465-3470. Epub 2018 Oct 31.

Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109; and

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http://dx.doi.org/10.4049/jimmunol.1800774DOI Listing
December 2018

Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the neXt-MP50 Challenge.

J Proteome Res 2018 12 23;17(12):4061-4071. Epub 2018 Oct 23.

Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , Michigan 48109 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.8b00442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465108PMC
December 2018

Network Propagation Predicts Drug Synergy in Cancers.

Cancer Res 2018 09 27;78(18):5446-5457. Epub 2018 Jul 27.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.

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http://dx.doi.org/10.1158/0008-5472.CAN-18-0740DOI Listing
September 2018

A similarity-based approach to leverage multi-cohort medical data on the diagnosis and prognosis of Alzheimer's disease.

Gigascience 2018 07;7(7)

Department of Computational Medicine and Bioinformatics, University of Michigan, 2017G Palmer Commons, 100 Washtenaw Avenue, Ann Arbor, MI, USA 48109.

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http://dx.doi.org/10.1093/gigascience/giy085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054197PMC
July 2018

Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile.

Bioinformatics 2018 12;34(23):3975-3982

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247930PMC
December 2018

YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU.

Bioinformatics 2018 10;34(20):3578-3580

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6184538PMC
October 2018

DNAp: A Pipeline for DNA-seq Data Analysis.

Sci Rep 2018 05 1;8(1):6793. Epub 2018 May 1.

Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, 72467, United States of America.

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http://dx.doi.org/10.1038/s41598-018-25022-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5931599PMC
May 2018

Brain-specific functional relationship networks inform autism spectrum disorder gene prediction.

Transl Psychiatry 2018 03 6;8(1):56. Epub 2018 Mar 6.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1038/s41398-018-0098-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838237PMC
March 2018

Accurate prediction of personalized olfactory perception from large-scale chemoinformatic features.

Gigascience 2018 02;7(2)

Department of Computational Medicine and Bioinformatics and Departments of Internal Medicine and Human Genetics and School of Public Health, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.

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https://academic.oup.com/gigascience/article/doi/10.1093/gig
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http://dx.doi.org/10.1093/gigascience/gix127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5824779PMC
February 2018

Complete hazard ranking to analyze right-censored data: An ALS survival study.

PLoS Comput Biol 2017 12 18;13(12):e1005887. Epub 2017 Dec 18.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005887DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749893PMC
December 2017

GATA3 Abundance Is a Critical Determinant of T Cell Receptor β Allelic Exclusion.

Mol Cell Biol 2017 06 31;37(12). Epub 2017 May 31.

Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA

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http://dx.doi.org/10.1128/MCB.00052-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5452726PMC
June 2017

miRmine: a database of human miRNA expression profiles.

Bioinformatics 2017 May;33(10):1554-1560

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6044334PMC
May 2017

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

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

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

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

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

Sage Bionetworks, Seattle, Washington 98115, USA.

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

Genome-Wide Functional Annotation of Human Protein-Coding Splice Variants Using Multiple Instance Learning.

J Proteome Res 2016 06 9;15(6):1747-53. Epub 2016 May 9.

Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, and ∥Department of Electrical Engineering and Computer Science, University of Michigan , Ann Arbor, Michigan 48109, United States.

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http://pubs.acs.org/doi/10.1021/acs.jproteome.5b00883
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http://dx.doi.org/10.1021/acs.jproteome.5b00883DOI Listing
June 2016

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

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

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

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

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

A Network of Splice Isoforms for the Mouse.

Sci Rep 2016 Apr 15;6:24507. Epub 2016 Apr 15.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States.

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http://dx.doi.org/10.1038/srep24507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832266PMC
April 2016

Effects of Antioxidants in Human Cancers: Differential Effects on Non-Coding Intronic RNA Expression.

Antioxidants (Basel) 2016 Jan 4;5(1). Epub 2016 Jan 4.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI-48109, USA.

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http://dx.doi.org/10.3390/antiox5010001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4808750PMC
January 2016

Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.

J Proteome Res 2015 Sep 11;14(9):3484-91. Epub 2015 Aug 11.

Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science University of Michigan , Ann Arbor, Michigan 48109, United States.

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http://pubs.acs.org/doi/10.1021/acs.jproteome.5b00494
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http://dx.doi.org/10.1021/acs.jproteome.5b00494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4993635PMC
September 2015

Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes.

Semin Nephrol 2015 May;35(3):237-44

Department of Internal Medicine, University of Michigan, Ann Arbor, MI.

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http://dx.doi.org/10.1016/j.semnephrol.2015.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518206PMC
May 2015

MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome.

J Proteome Res 2015 Sep 3;14(9):3762-7. Epub 2015 Aug 3.

Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science, University of Michigan , Ann Arbor, Michigan 48109, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798783PMC
September 2015

Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study.

J Proteome Res 2015 Sep 23;14(9):3519-29. Epub 2015 Jul 23.

University of Michigan , 100 Washtenaw Avenue, Room 2044B, Palmer Commons, Ann Arbor, Michigan 48109, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760104PMC
September 2015

MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse.

Database (Oxford) 2015 7;2015:bav045. Epub 2015 May 7.

Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA

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http://dx.doi.org/10.1093/database/bav045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423410PMC
December 2015

Regulatory network inferred using expression data of small sample size: application and validation in erythroid system.

Bioinformatics 2015 Aug 2;31(15):2537-44. Epub 2015 Apr 2.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA, Department of Internal Medicine, and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514931PMC
August 2015

Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence.

Proteomics 2014 Dec 17;14(23-24):2709-18. Epub 2014 Nov 17.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1002/pmic.201400170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4372202PMC
December 2014

Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation.

Bioinformatics 2014 Dec 12;30(23):3325-33. Epub 2014 Aug 12.

Department of Computational Medicine and Bioinformatics, Department of Cell and Developmental Biology, Department of Internal Medicine and Department of Computer Science and Engineering, University of Michigan, MI48109, USA Department of Computational Medicine and Bioinformatics, Department of Cell and Developmental Biology, Department of Internal Medicine and Department of Computer Science and Engineering, University of Michigan, MI48109, USA Department of Computational Medicine and Bioinformatics, Department of Cell and Developmental Biology, Department of Internal Medicine and Department of Computer Science and Engineering, University of Michigan, MI48109, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296147PMC
December 2014

The emerging era of genomic data integration for analyzing splice isoform function.

Trends Genet 2014 Aug 17;30(8):340-7. Epub 2014 Jun 17.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, MI, USA; Department of Electrical Engineering and Computer Science, Ann Arbor, MI, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2014.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112133PMC
August 2014

Predicting dynamic signaling network response under unseen perturbations.

Bioinformatics 2014 Oct 11;30(19):2772-8. Epub 2014 Jun 11.

Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, Department of Internal Medicine and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173019PMC
October 2014

Biased, non-equivalent gene-proximal and -distal binding motifs of orphan nuclear receptor TR4 in primary human erythroid cells.

PLoS Genet 2014 May 8;10(5):e1004339. Epub 2014 May 8.

Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014424PMC
May 2014

A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines.

J Proteomics 2014 Jul 5;107:103-12. Epub 2014 May 5.

Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.

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http://dx.doi.org/10.1016/j.jprot.2014.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4123867PMC
July 2014

Identification of stage-specific genes associated with lupus nephritis and response to remission induction in (NZB × NZW)F1 and NZM2410 mice.

Arthritis Rheumatol 2014 Aug;66(8):2246-2258

Center for Autoimmunity and Musculoskeletal Diseases, Feinstein Institute for Medical Research, Manhasset, New York, NY 11030.

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http://dx.doi.org/10.1002/art.38679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4554534PMC
August 2014

Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.

PLoS Comput Biol 2013 7;9(11):e1003314. Epub 2013 Nov 7.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820534PMC
July 2014

A new system for comparative functional genomics of Saccharomyces yeasts.

Genetics 2013 Sep 12;195(1):275-87. Epub 2013 Jul 12.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

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http://dunham.gs.washington.edu/Caudy.pdf
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http://www.genetics.org/cgi/doi/10.1534/genetics.113.152918
Publisher Site
http://dx.doi.org/10.1534/genetics.113.152918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3761308PMC
September 2013

Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation.

Biotechnol Biofuels 2013 May 4;6(1):67. Epub 2013 May 4.

Key Laboratory of Eutrophication and Prevention of Red Tide of Guangdong Higher Education Institute, College of Life Science, Jinan University, Guangzhou, 510632, China.

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http://dx.doi.org/10.1186/1754-6834-6-67DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3662598PMC
May 2013

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

PLoS Comput Biol 2013 14;9(3):e1002957. Epub 2013 Mar 14.

Department of Computer Science, Princeton University, Princeton, New Jersey, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1002957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597527PMC
November 2013

Comparative gene expression between two yeast species.

BMC Genomics 2013 Jan 16;14:33. Epub 2013 Jan 16.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1186/1471-2164-14-33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556494PMC
January 2013

Tissue-specific functional networks for prioritizing phenotype and disease genes.

PLoS Comput Biol 2012 27;8(9):e1002694. Epub 2012 Sep 27.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.

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https://dx.plos.org/10.1371/journal.pcbi.1002694
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http://dx.doi.org/10.1371/journal.pcbi.1002694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459891PMC
January 2013

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.

Nucleic Acids Res 2012 Jul 7;40(Web Server issue):W484-90. Epub 2012 Jun 7.

Department of Computer Science, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA.

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http://dx.doi.org/10.1093/nar/gks458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394282PMC
July 2012

Nucleosome-coupled expression differences in closely-related species.

BMC Genomics 2011 Sep 26;12:466. Epub 2011 Sep 26.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1186/1471-2164-12-466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3209474PMC
September 2011

Functional genomics complements quantitative genetics in identifying disease-gene associations.

PLoS Comput Biol 2010 Nov 11;6(11):e1000991. Epub 2010 Nov 11.

Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978695PMC
November 2010

Systematic planning of genome-scale experiments in poorly studied species.

PLoS Comput Biol 2010 Mar 5;6(3):e1000698. Epub 2010 Mar 5.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832676PMC
March 2010

A genomewide functional network for the laboratory mouse.

PLoS Comput Biol 2008 Sep 26;4(9):e1000165. Epub 2008 Sep 26.

Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Princeton, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527685PMC
September 2008

Brassica juncea chitinase BjCHI1 inhibits growth of fungal phytopathogens and agglutinates Gram-negative bacteria.

J Exp Bot 2008 31;59(12):3475-84. Epub 2008 Jul 31.

School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.

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http://dx.doi.org/10.1093/jxb/ern197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2529242PMC
October 2008

Predicting gene function in a hierarchical context with an ensemble of classifiers.

Genome Biol 2008 27;9 Suppl 1:S3. Epub 2008 Jun 27.

Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447537PMC
August 2008

Functional analysis of gene duplications in Saccharomyces cerevisiae.

Genetics 2007 Feb 6;175(2):933-43. Epub 2006 Dec 6.

Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, New Jersey, USA.

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http://www.genetics.org/cgi/doi/10.1534/genetics.106.064329
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800624PMC
February 2007