Pierre Baldi

Pierre Baldi

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Pierre Baldi

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Training and Validation of Deep Neural Networks for the Prediction of 90-Day Post-Liver Transplant Mortality Using UNOS Registry Data.

Transplant Proc 2020 Jan 8. Epub 2020 Jan 8.

Department of Anesthesiology and Perioperative Medicine, University of California at Los Angeles, Los Angeles, California, United States.

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http://dx.doi.org/10.1016/j.transproceed.2019.10.019DOI Listing
January 2020

An automated machine learning-based model predicts postoperative mortality using readily-extractable preoperative electronic health record data.

Br J Anaesth 2019 12 15;123(6):877-886. Epub 2019 Oct 15.

Department of Computer Science, University of California, Los Angeles, CA, USA; Department of Anaesthesiology and Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, CA, USA; Department of Biomathematics, University of California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1016/j.bja.2019.07.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883494PMC
December 2019

Distinct metabolic adaptation of liver circadian pathways to acute and chronic patterns of alcohol intake.

Proc Natl Acad Sci U S A 2019 Dec 22;116(50):25250-25259. Epub 2019 Nov 22.

Center for Epigenetics and Metabolism-U1233 INSERM-Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697;

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http://dx.doi.org/10.1073/pnas.1911189116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6911183PMC
December 2019

Functional Conservation of LncRNA JPX Despite Sequence and Structural Divergence.

J Mol Biol 2019 Sep 10. Epub 2019 Sep 10.

Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.09.002DOI Listing
September 2019

The capacity of feedforward neural networks.

Neural Netw 2019 Aug 22;116:288-311. Epub 2019 Apr 22.

Department of Mathematics, University of California, Irvine, United States. Electronic address:

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http://dx.doi.org/10.1016/j.neunet.2019.04.009DOI Listing
August 2019

Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites.

Genome Res 2019 08 27;29(8):1298-1309. Epub 2019 Jun 27.

Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA.

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http://dx.doi.org/10.1101/gr.240861.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6673722PMC
August 2019

Time of Exercise Specifies the Impact on Muscle Metabolic Pathways and Systemic Energy Homeostasis.

Cell Metab 2019 Jul 18;30(1):92-110.e4. Epub 2019 Apr 18.

Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2019.03.013DOI Listing
July 2019

Mitochondrial Akt Signaling Modulated Reprogramming of Somatic Cells.

Sci Rep 2019 Jul 9;9(1):9919. Epub 2019 Jul 9.

UC Irvine Diabetes Center, University of California, Irvine, California, USA.

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http://dx.doi.org/10.1038/s41598-019-46359-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6616364PMC
July 2019

Hippocampal gene expression patterns linked to late-life physical activity oppose age and AD-related transcriptional decline.

Neurobiol Aging 2019 06 20;78:142-154. Epub 2019 Feb 20.

Institute for Memory Impairments and Neurological Disorders, University of California-Irvine, Irvine, CA, USA; Department of Neurology, University of California-Irvine, Irvine, CA, USA.

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http://dx.doi.org/10.1016/j.neurobiolaging.2019.02.012DOI Listing
June 2019

Gap Junction Channels of Innexins and Connexins: Relations and Computational Perspectives.

Int J Mol Sci 2019 May 19;20(10). Epub 2019 May 19.

Department of Computer Science, Institute for Genomics and Bioinformatics, and Center for Machine Learning and Intelligent Systems, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.3390/ijms20102476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6566657PMC
May 2019

Light Entrains Diurnal Changes in Insulin Sensitivity of Skeletal Muscle via Ventromedial Hypothalamic Neurons.

Cell Rep 2019 May;27(8):2385-2398.e3

Diabetes Center of the Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland; Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland; Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, CA 92607, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.04.093DOI Listing
May 2019

Defining the Independence of the Liver Circadian Clock.

Cell 2019 May;177(6):1448-1462.e14

Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.04.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6813833PMC
May 2019

Neural network gradient Hamiltonian Monte Carlo.

Comput Stat 2019 Mar 8;34(1):281-299. Epub 2019 Jan 8.

Donald Bren School of Information and Computer Sciences, University of California, Irvine, USA.

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http://dx.doi.org/10.1007/s00180-018-00861-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6833949PMC
March 2019

Population-wide analysis of differences in disease progression patterns in men and women.

Nat Commun 2019 02 8;10(1):666. Epub 2019 Feb 8.

Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41467-019-08475-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368599PMC
February 2019

Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle.

Cell Rep 2018 12;25(12):3299-3314.e6

Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.11.077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6433478PMC
December 2018

Development and Validation of a Deep Neural Network Model for Prediction of Postoperative In-hospital Mortality.

Anesthesiology 2018 10;129(4):649-662

From the Department of Anesthesiology and Perioperative Care (C.K.L., M.C.) Department of Computer Sciences (C.K.L., P.B.) Department of Bioengineering (M.C.), University of California Irvine, Irvine, California Department of Anesthesiology and Perioperative Medicine, University of California Los Angeles, Los Angeles, California (I.H., E.G., M.C.).

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http://dx.doi.org/10.1097/ALN.0000000000002186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6148401PMC
October 2018

Deep Learning Localizes and Identifies Polyps in Real Time With 96% Accuracy in Screening Colonoscopy.

Gastroenterology 2018 10 18;155(4):1069-1078.e8. Epub 2018 Jun 18.

Department of Computer Science, University of California, Irvine, California; Institute for Genomics and Bioinformatics, University of California, Irvine, California; Center for Machine Learning and Intelligent Systems, University of California, Irvine, California. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2018.06.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174102PMC
October 2018

Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming.

iScience 2018 Aug 8;6:232-246. Epub 2018 Aug 8.

Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2018.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137960PMC
August 2018

Learning in the Machine: Random Backpropagation and the Deep Learning Channel.

Artif Intell 2018 Jul 3;260:1-35. Epub 2018 Apr 3.

Department of Mathematics, University of California, Irvine.

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http://dx.doi.org/10.1016/j.artint.2018.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5931406PMC
July 2018

CircadiOmics: circadian omic web portal.

Nucleic Acids Res 2018 07;46(W1):W157-W162

Department of Computer Science, University of California, Irvine, CA 92617, USA.

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http://dx.doi.org/10.1093/nar/gky441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030824PMC
July 2018

Inner and Outer Recursive Neural Networks for Chemoinformatics Applications.

J Chem Inf Model 2018 02 26;58(2):207-211. Epub 2018 Jan 26.

Department of Computer Science, University of California, Irvine , Irvine, California 92697, United States.

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http://dx.doi.org/10.1021/acs.jcim.7b00384DOI Listing
February 2018

ClusterCAD: a computational platform for type I modular polyketide synthase design.

Nucleic Acids Res 2018 01;46(D1):D509-D515

Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gkx893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753242PMC
January 2018

Learning in the machine: The symmetries of the deep learning channel.

Neural Netw 2017 Nov 5;95:110-133. Epub 2017 Sep 5.

Department of Mathematics, University of California, Irvine, Irvine, CA 92617, United States.

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http://dx.doi.org/10.1016/j.neunet.2017.08.008DOI Listing
November 2017

Guidelines for Genome-Scale Analysis of Biological Rhythms.

J Biol Rhythms 2017 Oct 3;32(5):380-393. Epub 2017 Nov 3.

27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.

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http://dx.doi.org/10.1177/0748730417728663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5692188PMC
October 2017

Distinct Circadian Signatures in Liver and Gut Clocks Revealed by Ketogenic Diet.

Cell Metab 2017 Sep;26(3):523-538.e5

Center for Epigenetics and Metabolism, Department of Biological Chemistry, U1233 INSERM, University of California, Irvine, Irvine, CA, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15504131173050
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http://dx.doi.org/10.1016/j.cmet.2017.08.015DOI Listing
September 2017

Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity.

PLoS One 2016 7;11(9):e0162363. Epub 2016 Sep 7.

Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162363PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014426PMC
August 2017

MotifMap-RNA: a genome-wide map of RBP binding sites.

Bioinformatics 2017 Jul;33(13):2029-2031

Department of Computer Science and Institute for Genomics and Bioinformatics.

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http://dx.doi.org/10.1093/bioinformatics/btx087DOI Listing
July 2017

A multi-resolution approach for spinal metastasis detection using deep Siamese neural networks.

Comput Biol Med 2017 05 27;84:137-146. Epub 2017 Mar 27.

Institute for Genomics and Bioinformatics and Department of Computer Science, University of California, Irvine, CA 92697, USA. Electronic address:

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http://dx.doi.org/10.1016/j.compbiomed.2017.03.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6042511PMC
May 2017

SIRT6 Suppresses Cancer Stem-like Capacity in Tumors with PI3K Activation Independently of Its Deacetylase Activity.

Cell Rep 2017 02;18(8):1858-1868

Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland; Diabetes Center of the Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.01.065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5329120PMC
February 2017

A theory of local learning, the learning channel, and the optimality of backpropagation.

Neural Netw 2016 Nov 5;83:51-74. Epub 2016 Aug 5.

Department of Computer Science, University of California, Irvine, Irvine, CA 92697-3435, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neunet.2016.07.006DOI Listing
November 2016

Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction.

J Chem Inf Model 2016 11 25;56(11):2125-2128. Epub 2016 Oct 25.

University of California, Irvine , Department of Computer Science, Irvine, California 92697, United States.

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http://dx.doi.org/10.1021/acs.jcim.6b00351DOI Listing
November 2016

Gut microbiota directs PPARγ-driven reprogramming of the liver circadian clock by nutritional challenge.

EMBO Rep 2016 09 14;17(9):1292-303. Epub 2016 Jul 14.

Center for Epigenetics and Metabolism, Department of Biological Chemistry, U904 INSERM, University of California Irvine, Irvine, CA, USA

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http://dx.doi.org/10.15252/embr.201642463DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5007574PMC
September 2016

ISMB 2016 Proceedings.

Bioinformatics 2016 06;32(12):i1-i2

National Center of Biotechnology Information, NIH.

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http://dx.doi.org/10.1093/bioinformatics/btw326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908371PMC
June 2016

What time is it? Deep learning approaches for circadian rhythms.

Bioinformatics 2016 Jun;32(12):i8-i17

Department of Computer Science, Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908327PMC
June 2016

VIRALpro: a tool to identify viral capsid and tail sequences.

Bioinformatics 2016 05 5;32(9):1405-7. Epub 2016 Jan 5.

Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860506PMC
May 2016

Lung Adenocarcinoma Distally Rewires Hepatic Circadian Homeostasis.

Cell 2016 May;165(4):896-909

Center for Epigenetics and Metabolism, INSERM Unit 904, Department of Biological Chemistry, University of California, Irvine (UCI), Irvine, CA 92697, USA. Electronic address:

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https://www.researchgate.net/profile/Thales_Papagiannakopoul
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http://www.cell.com/cell/pdf/S0092-8674(16)30482-2.pdf
Web Search
http://dx.doi.org/10.1016/j.cell.2016.04.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373476PMC
May 2016

Mitochondrial mutations in subjects with psychiatric disorders.

PLoS One 2015 26;10(5):e0127280. Epub 2015 May 26.

Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127280PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4444211PMC
April 2016

Comparative Circadian Metabolomics Reveal Differential Effects of Nutritional Challenge in the Serum and Liver.

J Biol Chem 2016 Feb 7;291(6):2812-28. Epub 2015 Dec 7.

From the Center for Epigenetics and Metabolism, U904 INSERM, and the Department of Biological Chemistry, University of California, Irvine, California 92697-4625 and

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http://dx.doi.org/10.1074/jbc.M115.681130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742746PMC
February 2016

Accurate and efficient target prediction using a potency-sensitive influence-relevance voter.

J Cheminform 2015 29;7:63. Epub 2015 Dec 29.

School of Information and Computer Sciences, University of California, Irvine, Irvine, USA.

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http://dx.doi.org/10.1186/s13321-015-0110-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696267PMC
December 2015

Function and Regulation of Cph2 in Candida albicans.

Eukaryot Cell 2015 Nov 4;14(11):1114-26. Epub 2015 Sep 4.

Department of Biological Chemistry, University of California, Irvine, California, USA Institute for Genomics and Bioinformatics, University of California, Irvine, California, USA

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http://dx.doi.org/10.1128/EC.00102-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4621314PMC
November 2015

Atmospheric Oxidation of Squalene: Molecular Study Using COBRA Modeling and High-Resolution Mass Spectrometry.

Environ Sci Technol 2015 Nov 4;49(22):13304-13. Epub 2015 Nov 4.

School of Information and Computer Sciences, University of California , Irvine, California 92697, United States.

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http://dx.doi.org/10.1021/acs.est.5b03552DOI Listing
November 2015

The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework.

Bioinformatics 2015 Oct 6;31(19):3181-8. Epub 2015 Jun 6.

Department of Computer Science, Institute for Genomics and Bioinformatics, Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine (UCI), Irvine, CA - 92697, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv353DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4592335PMC
October 2015

Towards a systems view of IBS.

Nat Rev Gastroenterol Hepatol 2015 Oct 25;12(10):592-605. Epub 2015 Aug 25.

Institute for Genomics and Bioinformatics, University of California at Irvine, 4038 Bren Hall, Irvine, CA 92697-3435, USA.

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http://dx.doi.org/10.1038/nrgastro.2015.121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001844PMC
October 2015

The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition.

Nucleic Acids Res 2014 Dec 20;42(22):13615-32. Epub 2014 Nov 20.

Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA

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http://dx.doi.org/10.1093/nar/gku1186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267635PMC
December 2014

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity.

Bioinformatics 2014 Sep 24;30(18):2592-7. Epub 2014 May 24.

Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4215083PMC
September 2014

Partitioning circadian transcription by SIRT6 leads to segregated control of cellular metabolism.

Cell 2014 Jul;158(3):659-72

Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, CA 92697, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA; INSERM U904, Sprague Hall, University of California, Irvine, Irvine, CA 92697, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674140088
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http://dx.doi.org/10.1016/j.cell.2014.06.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5472354PMC
July 2014

Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures.

Bioinformatics 2014 Jun 25;30(12):1681-9. Epub 2014 Feb 25.

Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USADepartment of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058938PMC
June 2014

The Dropout Learning Algorithm.

Artif Intell 2014 May;210:78-122

Department of Computer Science University of California, Irvine Irvine, CA 92697-3435.

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http://dx.doi.org/10.1016/j.artint.2014.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3996711PMC
May 2014

A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins.

PLoS One 2013 25;8(7):e68934. Epub 2013 Jul 25.

Department Chemistry and Biochemistry, University of California San Diego, San Diego, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068934PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3723809PMC
March 2014

Combining docking site and phosphosite predictions to find new substrates: identification of smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal kinase (JNK) substrate.

Cell Signal 2013 Dec 24;25(12):2518-29. Epub 2013 Aug 24.

Department of Developmental and Cell Biology, University of California Irvine, United States; Center for Complex Biological Systems, University of California Irvine, United States.

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http://dx.doi.org/10.1016/j.cellsig.2013.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132694PMC
December 2013

Small-molecule 3D structure prediction using open crystallography data.

J Chem Inf Model 2013 Dec 10;53(12):3127-30. Epub 2013 Dec 10.

Institute for Genomics and Bioinformatics , University of California, Irvine , Irvine, California 92697, United States.

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http://dx.doi.org/10.1021/ci4005282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3918487PMC
December 2013

Reprogramming of the circadian clock by nutritional challenge.

Cell 2013 Dec;155(7):1464-78

Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2013.11.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573395PMC
December 2013

ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

J Chem Inf Model 2013 Nov 11;53(11):2812-9. Epub 2013 Nov 11.

Institute for Genomics and Bioinformatics and School of Information and Computer Sciences, University of California , Irvine, California 92697, United States.

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http://dx.doi.org/10.1021/ci400326pDOI Listing
November 2013

Cycles in spatial and temporal chromosomal organization driven by the circadian clock.

Nat Struct Mol Biol 2013 Oct 22;20(10):1206-13. Epub 2013 Sep 22.

Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California Irvine, Irvine, California, USA.

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http://dx.doi.org/10.1038/nsmb.2667DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885543PMC
October 2013

Leptin engages a hypothalamic neurocircuitry to permit survival in the absence of insulin.

Cell Metab 2013 Sep;18(3):431-44

Department of Internal Medicine, Division of Hypothalamic Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.1016/j.cmet.2013.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890693PMC
September 2013

Deep architectures and deep learning in chemoinformatics: the prediction of aqueous solubility for drug-like molecules.

J Chem Inf Model 2013 Jul 2;53(7):1563-75. Epub 2013 Jul 2.

School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1021/ci400187yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3739985PMC
July 2013

Circadian clock regulates the host response to Salmonella.

Proc Natl Acad Sci U S A 2013 Jun 28;110(24):9897-902. Epub 2013 May 28.

Center for Epigenetics and Metabolism, Department of Biological Chemistry, Institute for Immunology, School of Medicine, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1073/pnas.1120636110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683799PMC
June 2013

A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions.

Bioinformatics 2013 May 23;29(10):1299-307. Epub 2013 Apr 23.

Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732027PMC
May 2013

Circadian acetylome reveals regulation of mitochondrial metabolic pathways.

Proc Natl Acad Sci U S A 2013 Feb 22;110(9):3339-44. Epub 2013 Jan 22.

Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1073/pnas.1217632110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587221PMC
February 2013

GRHL3/GET1 and trithorax group members collaborate to activate the epidermal progenitor differentiation program.

PLoS Genet 2012 19;8(7):e1002829. Epub 2012 Jul 19.

Department of Biological Chemistry, University of California Irvine, Irvine, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1002829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400561PMC
January 2013

Deep architectures for protein contact map prediction.

Bioinformatics 2012 Oct 30;28(19):2449-57. Epub 2012 Jul 30.

Department of Computer Science, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463120PMC
October 2012

ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

J Chem Inf Model 2012 Oct 1;52(10):2526-40. Epub 2012 Oct 1.

Institute for Genomics and Bioinformatics and Department of Computer Science, University of California, Irvine, CA, USA.

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http://dx.doi.org/10.1021/ci3003039DOI Listing
October 2012

Complex-valued autoencoders.

Neural Netw 2012 Sep 4;33:136-47. Epub 2012 May 4.

Department of Computer Science, UCI, Irvine, CA 92697-3435, USA.

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http://dx.doi.org/10.1016/j.neunet.2012.04.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399055PMC
September 2012

A WNT/p21 circuit directed by the C-clamp, a sequence-specific DNA binding domain in TCFs.

Mol Cell Biol 2012 Sep 9;32(18):3648-62. Epub 2012 Jul 9.

Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA.

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http://dx.doi.org/10.1128/MCB.06769-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430198PMC
September 2012

Biomimetic Design of Protein Nanomaterials for Hydrophobic Molecular Transport.

Adv Funct Mater 2012 Aug 23;22(15):3170-3180. Epub 2012 Apr 23.

Department of Chemical Engineering and Materials Science, University of California, 916 Engineering Tower, Irvine, CA 92697-2575.

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http://dx.doi.org/10.1002/adfm.201200052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603581PMC
August 2012

Cyber-T web server: differential analysis of high-throughput data.

Nucleic Acids Res 2012 Jul 16;40(Web Server issue):W553-9. Epub 2012 May 16.

Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/nar/gks420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394347PMC
July 2012

Rationally selected single-site mutants of the Thermoascus aurantiacus endoglucanase increase hydrolytic activity on cellulosic substrates.

Biotechnol Bioeng 2012 Jun 2;109(6):1595-9. Epub 2012 Jan 2.

Department of Chemical Engineering and Materials Science, The Henry Samueli School of Engineering, University of California, Irvine, California, USA.

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http://dx.doi.org/10.1002/bit.24414DOI Listing
June 2012

COBRA: a computational brewing application for predicting the molecular composition of organic aerosols.

Environ Sci Technol 2012 Jun 18;46(11):6048-55. Epub 2012 May 18.

School of Information and Computer Sciences, University of California, Irvine, California 92697-3435, United States.

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http://pubs.acs.org/doi/10.1021/es3003734
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http://dx.doi.org/10.1021/es3003734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385869PMC
June 2012

Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy.

Mol Cell Proteomics 2012 May 3;11(5):138-47. Epub 2012 Apr 3.

Departments of Physiology & Biophysics and Developmental & Cell Biology, University of California, Irvine, California 92697, USA.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M111.016352
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http://dx.doi.org/10.1074/mcp.M111.016352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418852PMC
May 2012

Retrotransposon profiling of RNA polymerase III initiation sites.

Genome Res 2012 Apr 27;22(4):681-92. Epub 2012 Jan 27.

Department of Biological Chemistry, School of Medicine, University of California, Irvine, California 92697, USA.

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http://dx.doi.org/10.1101/gr.131219.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317150PMC
April 2012

Coordination of the transcriptome and metabolome by the circadian clock.

Proc Natl Acad Sci U S A 2012 Apr 19;109(14):5541-6. Epub 2012 Mar 19.

Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1073/pnas.1118726109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325727PMC
April 2012

Speeding up chemical searches using the inverted index: the convergence of chemoinformatics and text search methods.

J Chem Inf Model 2012 Apr 10;52(4):891-900. Epub 2012 Apr 10.

Departments of Computer Science, University of California, Irvine, Irvine, California 92697-3435, United States.

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http://dx.doi.org/10.1021/ci200552rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415597PMC
April 2012

Modeling of mitochondria bioenergetics using a composable chemiosmotic energy transduction rate law: theory and experimental validation.

PLoS One 2011 8;6(9):e14820. Epub 2011 Sep 8.

Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014820PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169640PMC
February 2012

SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations.

Proteins 2012 Jan 9;80(1):142-53. Epub 2011 Nov 9.

Department of Computer Science, University of California, Irvine, California, USA.

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http://dx.doi.org/10.1002/prot.23170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240718PMC
January 2012

Genome-wide identification of Bcl11b gene targets reveals role in brain-derived neurotrophic factor signaling.

PLoS One 2011 1;6(9):e23691. Epub 2011 Sep 1.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023691PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164671PMC
December 2011

MotifMap: integrative genome-wide maps of regulatory motif sites for model species.

BMC Bioinformatics 2011 Dec 30;12:495. Epub 2011 Dec 30.

Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1186/1471-2105-12-495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293935PMC
December 2011

Visual adaptation and novelty responses in the superior colliculus.

Eur J Neurosci 2011 Sep 22;34(5):766-79. Epub 2011 Aug 22.

Centre for Neuroscience Studies, Queen's University, Kingston, Ontario, Canada.

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http://dx.doi.org/10.1111/j.1460-9568.2011.07805.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3168683PMC
September 2011

Tree and Hashing Data Structures to Speed up Chemical Searches: Analysis and Experiments.

Mol Inform 2011 Sep 5;30(9):791-800. Epub 2011 Sep 5.

School of Information and Computer Sciences, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697-3435, USA.

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http://dx.doi.org/10.1002/minf.201100089DOI Listing
September 2011