Sridhar Hannenhalli

Sridhar Hannenhalli

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Sridhar Hannenhalli

Publications by authors named "Sridhar Hannenhalli"

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96Publications

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Allele-specific enhancers mediate associations between LCAT and ABCA1 polymorphisms and HDL metabolism.

PLoS One 2019 30;14(4):e0215911. Epub 2019 Apr 30.

Division of Endocrinology, Nutrition, and Diabetes, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215911PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6490890PMC
January 2020

Ligand dependent gene regulation by transient ERα clustered enhancers.

PLoS Genet 2020 Jan 6;16(1):e1008516. Epub 2020 Jan 6.

Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.

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http://dx.doi.org/10.1371/journal.pgen.1008516DOI Listing
January 2020

Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4 T Cells.

Cell Rep 2019 Dec;29(10):3019-3032.e6

Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.10.131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6934378PMC
December 2019

Beyond Synthetic Lethality: Charting the Landscape of Pairwise Gene Expression States Associated with Survival in Cancer.

Cell Rep 2019 Jul;28(4):938-948.e6

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.06.067DOI Listing
July 2019

ChIPulate: A comprehensive ChIP-seq simulation pipeline.

PLoS Comput Biol 2019 03 21;15(3):e1006921. Epub 2019 Mar 21.

The Institute of Mathematical Sciences/HBNI, Taramani, Chennai, India.

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http://dx.plos.org/10.1371/journal.pcbi.1006921
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http://dx.doi.org/10.1371/journal.pcbi.1006921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445533PMC
March 2019

Orphan CpG islands as alternative promoters.

Transcription 2018 28;9(3):171-176. Epub 2017 Nov 28.

a Center for Bioinformatics and Computational Biology , University of Maryland , College Park , MD , USA.

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http://dx.doi.org/10.1080/21541264.2017.1373209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5927659PMC
November 2018

Analysis and correction of compositional bias in sparse sequencing count data.

BMC Genomics 2018 Nov 6;19(1):799. Epub 2018 Nov 6.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.

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http://dx.doi.org/10.1186/s12864-018-5160-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219007PMC
November 2018

Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases.

Sci Rep 2018 Jul 19;8(1):10929. Epub 2018 Jul 19.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA.

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http://dx.doi.org/10.1038/s41598-018-29086-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053367PMC
July 2018

Genetic Reduction in Left Ventricular Protein Kinase C-α and Adverse Ventricular Remodeling in Human Subjects.

Circ Genom Precis Med 2018 03;11(3):e001901

From the Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia (R.H., M.P.M., J.B., K.B.M., T.P.C.); Cardiovascular Research Center (N.R.T., V.A.P., P.T.E.) and Center for Human Genetic Research and Cardiovascular Research Center (C.N.-C.), Massachusetts General Hospital, Boston; Department of Statistics, University of Illinois at Urbana-Champaign (S.D.Z.); Heidelberg University Hospital, Germany (B.M., H.A.K.); Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, Germany (F.R., M.S.); INSERM UMRS1166-IACN, Hôpital Pitié-Salpêtrière, Paris, France (E.V., F.C.); Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, MA (H.L.); Department of Epidemiology, University of Washington, Seattle (N.L.S.); Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands (J.F.F.); Boston University School of Medicine, MA (R.S.V.); Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands (P.v.d.H.); Medical and Population Genetics Program, Broad Institute, Cambridge, MA (C.N.-C.); Center for Applied Genomics, Children's Hospital of Philadelphia, PA (J.L., C.E.K., H.H.); Center for Bioinformatics and Computational Biology, University of Maryland, College Park (S.H.); Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, CA (E.A.A.); Department of Cardiovascular Medicine, Cleveland Clinic, OH (C.S.M., W.H.W.T.); and Howard Hughes Medical Institute and Cincinnati Children's Hospital Medical Center, OH (M.M., J.D.M.).

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http://dx.doi.org/10.1161/CIRCGEN.117.001901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5858599PMC
March 2018

Putative functional genes in idiopathic dilated cardiomyopathy.

Sci Rep 2018 01 8;8(1):66. Epub 2018 Jan 8.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA.

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http://dx.doi.org/10.1038/s41598-017-18524-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5758757PMC
January 2018

Prediction and Subtyping of Hypertension from Pan-Tissue Transcriptomic and Genetic Analyses.

Genetics 2017 11 12;207(3):1121-1134. Epub 2017 Sep 12.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742

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http://dx.doi.org/10.1534/genetics.117.300280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676229PMC
November 2017

A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer.

PLoS Comput Biol 2017 Nov 30;13(11):e1005793. Epub 2017 Nov 30.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005793DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708603PMC
November 2017

Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters.

Genome Res 2017 04 21;27(4):553-566. Epub 2017 Feb 21.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA.

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http://dx.doi.org/10.1101/gr.212050.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378174PMC
April 2017

A pathway-centric view of spatial proximity in the 3D nucleome across cell lines.

Sci Rep 2016 12 15;6:39279. Epub 2016 Dec 15.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.

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http://dx.doi.org/10.1038/srep39279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5157015PMC
December 2016

Heterogeneity of transcription factor binding specificity models within and across cell lines.

Genome Res 2016 08 16;26(8):1110-23. Epub 2016 Jun 16.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA; Department of Cell and Molecular Biology, University of Maryland, College Park, Maryland 20742, USA.

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http://dx.doi.org/10.1101/gr.199166.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971765PMC
August 2016

Evolutionarily conserved network properties of intrinsically disordered proteins.

PLoS One 2015 14;10(5):e0126729. Epub 2015 May 14.

Center for Bioinformatics and Computational Biology, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126729PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4431869PMC
February 2016

Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer.

BMC Cancer 2016 Feb 11;16:88. Epub 2016 Feb 11.

Department of Cell and Molecular Biology, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA.

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http://dx.doi.org/10.1186/s12885-016-2128-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750190PMC
February 2016

High-Throughput Identification of Cis-Regulatory Rewiring Events in Yeast.

Mol Biol Evol 2015 Dec 23;32(12):3047-63. Epub 2015 Sep 23.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park

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http://dx.doi.org/10.1093/molbev/msv203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009955PMC
December 2015

Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution.

PLoS Comput Biol 2015 Nov 6;11(11):e1004603. Epub 2015 Nov 6.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636164PMC
November 2015

Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability.

Nat Commun 2015 Oct 12;6:8555. Epub 2015 Oct 12.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA.

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http://dx.doi.org/10.1038/ncomms9555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4633824PMC
October 2015

Chromatin and Genomic determinants of alternative splicing.

ACM BCB 2015 Sep;2015:345-354

Center for Bioinformatics and Computational Biology, University of Maryland.

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http://dx.doi.org/10.1145/2808719.2808755DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558438PMC
September 2015

RNA-Seq identifies novel myocardial gene expression signatures of heart failure.

Genomics 2015 Feb 17;105(2):83-9. Epub 2014 Dec 17.

Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S08887543140026
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http://dx.doi.org/10.1016/j.ygeno.2014.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684258PMC
February 2015

Developmental expression of chicken FOXN1 and putative target genes during feather development.

Int J Dev Biol 2014 ;58(1):57-64

Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA.

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http://dx.doi.org/10.1387/ijdb.130023syDOI Listing
January 2015

Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals.

BMC Genomics 2014 Jun 26;15:526. Epub 2014 Jun 26.

Department of Cell Biology and Molecular Genetics, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, MD 20742, USA.

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http://dx.doi.org/10.1186/1471-2164-15-526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085337PMC
June 2014

Determinants of expression variability.

Nucleic Acids Res 2014 Apr 15;42(6):3503-14. Epub 2014 Jan 15.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/nar/gkt1364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973347PMC
April 2014

Next-generation sequencing and epigenomics research: a hammer in search of nails.

Genomics Inform 2014 Mar 31;12(1):2-11. Epub 2014 Mar 31.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20740, USA.

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http://dx.doi.org/10.5808/GI.2014.12.1.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990762PMC
March 2014

CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation.

Nucleic Acids Res 2014 Jan 10;42(2):774-89. Epub 2013 Oct 10.

Department of Cell & Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA, Program of Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA and Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/nar/gkt910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902912PMC
January 2014

Epigenomic model of cardiac enhancers with application to genome wide association studies.

Pac Symp Biocomput 2013 :92-102

Center for Bioinformatics and Computational Biology, University of Maryland, College park, MD 20742, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581590PMC
December 2013

Widespread evidence of viral miRNAs targeting host pathways.

BMC Bioinformatics 2013 21;14 Suppl 2:S3. Epub 2013 Jan 21.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.

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http://dx.doi.org/10.1186/1471-2105-14-S2-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549839PMC
September 2013

Correlated evolution of positions within mammalian cis elements.

PLoS One 2013 8;8(2):e55521. Epub 2013 Feb 8.

Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055521PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568137PMC
September 2013

Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation.

BMC Genomics 2013 21;14 Suppl 1:S15. Epub 2013 Jan 21.

School of Computer Science and Technology, Soochow University, Suzhou 215006, China.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-14-S1-S15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549814PMC
August 2013

Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers.

Nucleic Acids Res 2013 Aug 21;41(14):6828-38. Epub 2013 May 21.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20740, USA.

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http://dx.doi.org/10.1093/nar/gkt374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737527PMC
August 2013

Three independent determinants of protein evolutionary rate.

J Mol Evol 2013 Mar 12;76(3):98-111. Epub 2013 Feb 12.

Department of Medical Biotechnology, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, South Korea.

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http://dx.doi.org/10.1007/s00239-013-9543-6DOI Listing
March 2013

Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation.

BMC Cancer 2013 Mar 22;13:144. Epub 2013 Mar 22.

James Buchanan Brady Urological Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.

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http://dx.doi.org/10.1186/1471-2407-13-144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3618251PMC
March 2013

Intrinsically disordered proteins and conformational noise: implications in cancer.

Cell Cycle 2013 Jan 19;12(1):26-31. Epub 2012 Dec 19.

Division of Bioengineering, California Institute of Technology; Pasadena, CA USA.

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http://dx.doi.org/10.4161/cc.23178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570512PMC
January 2013

Why transcription factor binding sites are ten nucleotides long.

Genetics 2012 Nov 10;192(3):973-85. Epub 2012 Aug 10.

Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1534/genetics.112.143370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522170PMC
November 2012

Myocardin-like protein 2 regulates TGFβ signaling in embryonic stem cells and the developing vasculature.

Development 2012 Oct 16;139(19):3531-42. Epub 2012 Aug 16.

University of Pennsylvania Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104-4283, USA.

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http://dx.doi.org/10.1242/dev.082222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436110PMC
October 2012

Functional divergence of gene duplicates - a domain-centric view.

BMC Evol Biol 2012 Jul 27;12:126. Epub 2012 Jul 27.

Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1186/1471-2148-12-126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426493PMC
July 2012

Epigenomic and RNA structural correlates of polyadenylation.

RNA Biol 2011 May-Jun;8(3):529-37. Epub 2011 May 1.

Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218514PMC
http://dx.doi.org/10.4161/rna.8.3.15194DOI Listing
May 2012

Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1.

BMC Evol Biol 2011 Oct 15;11:302. Epub 2011 Oct 15.

Penn Center for Bioinformatics, 1424 Blockley Hall, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA 19104 USA.

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http://dx.doi.org/10.1186/1471-2148-11-302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207924PMC
October 2011

A tutorial of the poisson random field model in population genetics.

Adv Bioinformatics 2008 2:257864. Epub 2008 Jul 2.

Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1155/2008/257864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775679PMC
July 2011

Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis.

Nucleic Acids Res 2011 Jul 5;39(12):e78. Epub 2011 Apr 5.

Genomics and Computational Biology Program, 700 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130287PMC
July 2011

Regulation of lung endoderm progenitor cell behavior by miR302/367.

Development 2011 Apr 24;138(7):1235-45. Epub 2011 Feb 24.

Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1242/dev.061762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3050657PMC
April 2011

Gene coexpression network topology of cardiac development, hypertrophy, and failure.

Circ Cardiovasc Genet 2011 Feb 2;4(1):26-35. Epub 2010 Dec 2.

Department of Internal Medicine and the Division of Cardiovascular Medicine, Stanford Hospital and Clinics, and Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1161/CIRCGENETICS.110.941757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324316PMC
February 2011

Regulating the regulators: modulators of transcription factor activity.

Methods Mol Biol 2010 ;674:297-312

Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1007/978-1-60761-854-6_19DOI Listing
December 2010

Young proteins experience more variable selection pressures than old proteins.

Genome Res 2010 Nov 4;20(11):1574-81. Epub 2010 Oct 4.

Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1101/gr.109595.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2963820PMC
November 2010

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

Genome Biol 2009 18;10(11):R131. Epub 2009 Nov 18.

Penn Center for Bioinformatics, Department of Genetics, 415 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1186/gb-2009-10-11-r131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091324PMC
July 2010

Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons.

Genome Biol 2009 1;10(7):R72. Epub 2009 Jul 1.

Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1186/gb-2009-10-7-r72DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728526PMC
January 2010

Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families.

Nucleic Acids Res 2010 Jan 19;38(3):738-49. Epub 2009 Nov 19.

Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1093/nar/gkp989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817486PMC
January 2010

Mimosa: mixture model of co-expression to detect modulators of regulatory interaction.

Algorithms Mol Biol 2010 Jan 4;5. Epub 2010 Jan 4.

Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Pennsylvania, USA.

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http://almob.biomedcentral.com/articles/10.1186/1748-7188-5-
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http://dx.doi.org/10.1186/1748-7188-5-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826332PMC
January 2010

Evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure.

Circ Cardiovasc Genet 2009 Jun 31;2(3):212-9. Epub 2009 Mar 31.

Department of Biostatistics and Epidemiology, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.

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http://dx.doi.org/10.1161/CIRCGENETICS.108.816686DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157251PMC
June 2009

Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians.

Clin Endocrinol (Oxf) 2009 May 15;70(5):698-705. Epub 2008 Aug 15.

Cardiovascular Institute, Institute for Translational Medicine and Therapeutics, and Department of Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA.

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http://dx.doi.org/10.1111/j.1365-2265.2008.03375.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108432PMC
May 2009

The evolution of Fox genes and their role in development and disease.

Nat Rev Genet 2009 Apr;10(4):233-40

Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1038/nrg2523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2733165PMC
April 2009

PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes.

Nucleic Acids Res 2009 Jan 15;37(Database issue):D66-71. Epub 2008 Oct 15.

Penn Center for Bioinformatics, Department of Genetics and Department of Computer Science, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1093/nar/gkn731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686453PMC
January 2009

Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity.

PLoS One 2008 Sep 1;3(9):e3122. Epub 2008 Sep 1.

Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003122PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518851PMC
September 2008

Genome-wide analysis of natural selection on human cis-elements.

PLoS One 2008 Sep 10;3(9):e3137. Epub 2008 Sep 10.

Department of Genetics, School of Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003137PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2522239PMC
September 2008

Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development.

Development 2008 Aug 9;135(16):2729-38. Epub 2008 Jul 9.

Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1242/dev.024539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596970PMC
August 2008

Eukaryotic transcription factor binding sites--modeling and integrative search methods.

Bioinformatics 2008 Jun 21;24(11):1325-31. Epub 2008 Apr 21.

Penn Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn198DOI Listing
June 2008

Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression.

PLoS One 2008 Jun 4;3(6):e2345. Epub 2008 Jun 4.

Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadephia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002345PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394658PMC
June 2008

TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance.

Nucleic Acids Res 2007 25;35(21):7360-71. Epub 2007 Oct 25.

Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkm885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2189735PMC
January 2008

MetaProm: a neural network based meta-predictor for alternative human promoter prediction.

BMC Genomics 2007 Oct 17;8:374. Epub 2007 Oct 17.

Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1186/1471-2164-8-374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2194789PMC
October 2007

Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes.

Virology 2007 Aug 25;365(1):60-9. Epub 2007 Apr 25.

Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6076, USA.

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http://dx.doi.org/10.1016/j.virol.2007.02.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705903PMC
August 2007

Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation.

Nucleic Acids Res 2007 22;35(10):3203-13. Epub 2007 Apr 22.

Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104-6021, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkm201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904283PMC
June 2007

Patterns of sequence conservation in presynaptic neural genes.

Genome Biol 2006 ;7(11):R105

Penn Center for Bioinformatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1186/gb-2006-7-11-r105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794582PMC
March 2007

Recurring genomic breaks in independent lineages support genomic fragility.

BMC Evol Biol 2006 Nov 7;6:90. Epub 2006 Nov 7.

Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1186/1471-2148-6-90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636669PMC
November 2006

Selection of target sites for mobile DNA integration in the human genome.

PLoS Comput Biol 2006 Nov;2(11):e157

Department of Family and Preventive Medicine, School of Medicine, University of California San Diego, La Jolla, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0020157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664696PMC
November 2006

Transcriptional genomics associates FOX transcription factors with human heart failure.

Circulation 2006 Sep 4;114(12):1269-76. Epub 2006 Sep 4.

Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.

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http://dx.doi.org/10.1161/CIRCULATIONAHA.106.632430DOI Listing
September 2006

A mammalian promoter model links cis elements to genetic networks.

Biochem Biophys Res Commun 2006 Aug 21;347(1):166-77. Epub 2006 Jun 21.

Penn Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, 19104-6021, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S0006291X0601363
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http://dx.doi.org/10.1016/j.bbrc.2006.06.062DOI Listing
August 2006

Dense subgraph computation via stochastic search: application to detect transcriptional modules.

Bioinformatics 2006 Jul;22(14):e117-23

Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl260DOI Listing
July 2006

Functional analysis of Hes-1 in preadipocytes.

Mol Endocrinol 2006 Mar 10;20(3):698-705. Epub 2005 Nov 10.

Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.

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https://academic.oup.com/mend/article-lookup/doi/10.1210/me.
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http://dx.doi.org/10.1210/me.2005-0325DOI Listing
March 2006

Genome-wide analysis of retroviral DNA integration.

Nat Rev Microbiol 2005 Nov;3(11):848-58

University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104-6076, USA.

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http://www.nature.com/articles/nrmicro1263
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http://dx.doi.org/10.1038/nrmicro1263DOI Listing
November 2005

Generalizations of Markov model to characterize biological sequences.

BMC Bioinformatics 2005 Sep 6;6:219. Epub 2005 Sep 6.

Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104-6021, USA.

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http://dx.doi.org/10.1186/1471-2105-6-219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1236913PMC
September 2005

Enhanced position weight matrices using mixture models.

Bioinformatics 2005 Jun;21 Suppl 1:i204-12

Department of Genetics, University of Pennsylvania Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti1001DOI Listing
June 2005

A note on efficient computation of haplotypes via perfect phylogeny.

J Comput Biol 2004 ;11(5):858-66

Department of Computer Science & Engineering, University of California at San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1089/cmb.2004.11.858DOI Listing
March 2005

Transcriptional regulation of protein complexes and biological pathways.

Mamm Genome 2003 Sep;14(9):611-9

Informatics Research, Celera Genomics, 45 West Gude Drive, Rockville, Maryland 20850, USA.

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http://dx.doi.org/10.1007/s00335-002-2260-xDOI Listing
September 2003

Combinatorial algorithms for design of DNA arrays.

Adv Biochem Eng Biotechnol 2002 ;77:1-19

Department of Mathematics, University of Southern California, Los Angeles 90089-1113, USA.

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http://dx.doi.org/10.1007/3-540-45713-5_1DOI Listing
October 2002

Predicting transcription factor synergism.

Nucleic Acids Res 2002 Oct;30(19):4278-84

Informatics Research, Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC140535PMC
http://dx.doi.org/10.1093/nar/gkf535DOI Listing
October 2002

Identification of transcription factor binding sites in the human genome sequence.

Mamm Genome 2002 Sep;13(9):510-4

Informatics Research, Celera Corporation, Rockville, Maryland 20850, USA.

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http://dx.doi.org/10.1007/s00335-002-2175-6DOI Listing
September 2002