Works by Park, Peter J.

Results: 116

Transcriptional control of a whole chromosome: emerging models for dosage compensation.

Published in:

Nature Structural & Molecular Biology, 2014, v. 21, n. 2, p. 118, doi. 10.1038/nsmb.2763

By:

Ferrari, Francesco;
Alekseyenko, Artyom A;
Park, Peter J;
Kuroda, Mitzi I

Publication type:

Article

Impact of chromatin structure on sequence variability in the human genome.

Published in:

Nature Structural & Molecular Biology, 2011, v. 18, n. 4, p. 510, doi. 10.1038/nsmb.2012

By:

Tolstorukov, Michael Y.;
Volfovsky, Natalia;
Stephens, Robert M.;
Park, Peter J.

Publication type:

Article

Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation.

Published in:

Nature Structural & Molecular Biology, 2009, v. 16, n. 8, p. 825, doi. 10.1038/nsmb.1644

By:

Gelbart, Marnie E.;
Larschan, Erica;
Shouyong Peng;
Park, Peter J.;
Kuroda, Mitzi I.

Publication type:

Article

The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome.

Published in:

Nature Structural & Molecular Biology, 2008, v. 15, n. 12, p. 1318, doi. 10.1038/nsmb.1520

By:

Sural, Tuba H.;
Peng, Shouyong;
Li, Bing;
Workman, Jerry L.;
Park, Peter J.;
Kuroda, Mitzi I.

Publication type:

Article

hiHMM: Bayesian non-parametric joint inference of chromatin state maps.

Published in:

Bioinformatics, 2015, v. 31, n. 13, p. 2066, doi. 10.1093/bioinformatics/btv117

By:

Kyung-Ah Sohn;
Ho, Joshua W. K.;
Djordjevic, Djordje;
Hyun-hwan Jeong;
Park, Peter J.;
Ju Han Kim

Publication type:

Article

Nozzle: a report generation toolkit for data analysis pipelines.

Published in:

Bioinformatics, 2013, v. 29, n. 8, p. 1089, doi. 10.1093/bioinformatics/btt085

By:

Gehlenborg, Nils;
Noble, Michael S.;
Getz, Gad;
Chin, Lynda;
Park, Peter J.

Publication type:

Article

Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance.

Published in:

Bioinformatics, 2009, v. 25, n. 23, p. 3121, doi. 10.1093/bioinformatics/btp559

By:

Park, Peter J.;
Sek Won Kong;
Tebaldi, Toma;
Lai, Weil R.;
Kasif, Simon;
Kohane, Isaac S.

Publication type:

Article

nuScore: a web-interface for nucleosome positioning predictions.

Published in:

Bioinformatics, 2008, v. 24, n. 12, p. 1456

By:

Michael Y. Tolstorukov;
Vidhu Choudhary;
Wilma K. Olson;
Victor B. Zhurkin;
Peter J. Park

Publication type:

Article

nuScore: a web-interface for nucleosome positioning predictions.

Published in:

Bioinformatics, 2008, v. 24, n. 12, p. 1456

By:

Michael Y. Tolstorukov;
Vidhu Choudhary;
Wilma K. Olson;
Victor B. Zhurkin;
Peter J. Park

Publication type:

Article

Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes.

Published in:

Bioinformatics, 2008, v. 24, n. 7, p. 889, doi. 10.1093/bioinformatics/btn034

By:

Hyunju Lee;
Sek Won Kong;
Peter J. Park

Publication type:

Article

CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms.

Published in:

Bioinformatics, 2008, v. 24, n. 7, p. 1014, doi. 10.1093/bioinformatics/btn067

By:

Weil Lai;
Vidhu Choudhary;
Peter J. Park

Publication type:

Article

A multivariate approach for integrating genome-wide expression data and biological knowledge.

Published in:

Bioinformatics, 2006, v. 22, n. 19, p. 2373, doi. 10.1093/bioinformatics/btl401

By:

Kong, Sek Won;
Pu, William T.;
Park, Peter J.

Publication type:

Article

Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data.

Published in:

Bioinformatics, 2005, v. 21, n. 19, p. 3763, doi. 10.1093/bioinformatics/bti611

By:

Weil R. Lai;
Mark D. Johnson;
Raju Kucherlapati;
Peter J. Park

Publication type:

Article

Detecting structural variations in the human genome using next generation sequencing.

Published in:

Briefings in Functional Genomics, 2010, v. 9, n. 5/6, p. 405, doi. 10.1093/bfgp/elq025

By:

Ruibin Xi;
Tae-Min Kim;
Park, Peter J.

Publication type:

Article

Genomics of MPNST (GeM) Consortium: Rationale and Study Design for Multi-Omic Characterization of NF1-Associated and Sporadic MPNSTs.

Published in:

Genes, 2020, v. 11, n. 4, p. 1, doi. 10.3390/genes11040387

By:

Miller, David T.;
Cortés-Ciriano, Isidro;
Pillay, Nischalan;
Hirbe, Angela C.;
Snuderl, Matija;
Bui, Marilyn M.;
Piculell, Katherine;
Al-Ibraheemi, Alyaa;
Dickson, Brendan C.;
Hart, Jesse;
Jones, Kevin;
Jordan, Justin T.;
Kim, Raymond H.;
Lindsay, Daniel;
Yoshihiro Nishida;
Ullrich, Nicole J.;
Xia Wang;
Park, Peter J.;
Flanagan, Adrienne M.

Publication type:

Article

Phenotypic plasticity of the threespine stickleback Gasterosteus aculeatus telencephalon in response to experience in captivity.

Published in:

Current Zoology, 2012, v. 58, n. 1, p. 189, doi. 10.1093/czoolo/58.1.189

By:

Park, Peter J.;
Chase, Ivan;
Bell, Michael A.

Publication type:

Article

Dysregulation of cancer genes by recurrent intergenic fusions.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02076-2

By:

Yun, Jae Won;
Yang, Lixing;
Park, Hye-Young;
Lee, Chang-Woo;
Cha, Hongui;
Shin, Hyun-Tae;
Noh, Ka-Won;
Choi, Yoon-La;
Park, Woong-Yang;
Park, Peter J.

Publication type:

Article

HiNT: a computational method for detecting copy number variations and translocations from Hi-C data.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-01986-5

By:

Wang, Su;
Lee, Soohyun;
Chu, Chong;
Jain, Dhawal;
Kerpedjiev, Peter;
Nelson, Geoffrey M.;
Walsh, Jennifer M.;
Alver, Burak H.;
Park, Peter J.

Publication type:

Article

A Panel-Based Mutational Signature of Mismatch Repair Deficiency is Associated With Durable Response to Pembrolizumab in Metastatic Castration-Resistant Prostate Cancer.

Published in:

Clinical Genitourinary Cancer, 2024, v. 22, n. 2, p. 558, doi. 10.1016/j.clgc.2024.01.011

By:

Boiarsky, Daniel;
Gulhan, Doga C.;
Savignano, Hunter;
Lakshminarayanan, Gitanjali;
McClure, Heather M.;
Silver, Rebecca;
Hirsch, Michelle S.;
Sholl, Lynette M.;
Choudhury, Atish D.;
Ananda, Guruprasad;
Park, Peter J.;
Tewari, Alok K.;
Berchuck, Jacob E.

Publication type:

Article

Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway.

Published in:

Nature Medicine, 2010, v. 16, n. 12, p. 1429, doi. 10.1038/nm.2251

By:

Jagani, Zainab;
Mora-Blanco, E. Lorena;
Sansam, Courtney G.;
McKenna, Elizabeth S.;
Wilson, Boris;
Chen, Dongshu;
Klekota, Justin;
Tamayo, Pablo;
Nguyen, Phuong T. L.;
Tolstorukov, Michael;
Park, Peter J.;
Yoon-Jae Cho;
Hsiao, Kathy;
Buonamici, Silvia;
Pomeroy, Scott L.;
Mesirov, Jill P.;
Ruffner, Heinz;
Bouwmeester, Tewis;
Luchansky, Sarah J.;
Murtie, Joshua

Publication type:

Article

Intron retention is a widespread mechanism of tumor-suppressor inactivation.

Published in:

Nature Genetics, 2015, v. 47, n. 11, p. 1242, doi. 10.1038/ng.3414

By:

Jung, Hyunchul;
Lee, Donghoon;
Lee, Jongkeun;
Park, Donghyun;
Kim, Yeon Jeong;
Park, Woong-Yang;
Hong, Dongwan;
Park, Peter J;
Lee, Eunjung

Publication type:

Article

Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells.

Published in:

Nature Genetics, 2012, v. 44, n. 7, p. 831, doi. 10.1038/ng0712-831b

By:

Stadtfeld, Matthias;
Apostolou, Effie;
Ferrari, Francesco;
Choi, Jiho;
Walsh, Ryan M;
Chen, Taiping;
Ooi, Steen S K;
Kim, Sang Yong;
Bestor, Timothy H;
Shioda, Toshi;
Park, Peter J;
Hochedlinger, Konrad

Publication type:

Article

Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells.

Published in:

Nature Genetics, 2012, v. 44, n. 4, p. 398, doi. 10.1038/ng.1110

By:

Stadtfeld, Matthias;
Apostolou, Effie;
Ferrari, Francesco;
Choi, Jiho;
Walsh, Ryan M;
Chen, Taiping;
Ooi, Steen S K;
Kim, Sang Yong;
Bestor, Timothy H;
Shioda, Toshi;
Park, Peter J;
Hochedlinger, Konrad

Publication type:

Article

Evidence for dosage compensation between the X chromosome and autosomes in mammals.

Published in:

2011

By:

Kharchenko, Peter V;
Xi, Ruibin;
Park, Peter J

Publication type:

Letter

The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression.

Published in:

Nature Genetics, 2008, v. 40, n. 6, p. 794, doi. 10.1038/ng.126

By:

Mueller, Jacob L.;
Mahadevaiah, Shantha K.;
Park, Peter J.;
Warburton, Peter E.;
Page, David C.;
Turner, James M. A.

Publication type:

Article

Thyroid hormone-related regulation of gene expression in human fatty liver.

Published in:

2009

By:

Pihlajamäki, Jussi;
Boes, Tanner;
Kim, Eun-Young;
Dearie, Farrell;
Kim, Brian W;
Schroeder, Joshua;
Mun, Edward;
Nasser, Imad;
Park, Peter J;
Bianco, Antonio C;
Goldfine, Allison B;
Patti, Mary Elizabeth

Publication type:

journal article

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis.

Published in:

BMC Genomics, 2011, v. 12, n. 1, p. 134, doi. 10.1186/1471-2164-12-134

By:

Ho, Joshua W. K.;
Bishop, Eric;
Karchenko, Peter V.;
Nègre, Nicolas;
White, Kevin P.;
Park, Peter J.

Publication type:

Article

Hallmarks of pluripotency.

Published in:

Nature, 2015, v. 525, n. 7570, p. 469, doi. 10.1038/nature15515

By:

De Los Angeles, Alejandro;
Ferrari, Francesco;
Xi, Ruibin;
Fujiwara, Yuko;
Benvenisty, Nissim;
Deng, Hongkui;
Hochedlinger, Konrad;
Jaenisch, Rudolf;
Lee, Soohyun;
Leitch, Harry G.;
Lensch, M. William;
Lujan, Ernesto;
Pei, Duanqing;
Rossant, Janet;
Wernig, Marius;
Park, Peter J.;
Daley, George Q.

Publication type:

Article

Comparing expression profiles of genes with similar promoter regions.

Published in:

Bioinformatics, 2002, v. 18, n. 12, p. 1576, doi. 10.1093/bioinformatics/18.12.1576

By:

Park, Peter J.;
Butte, Atul J.;
Kohane, Isaac S.

Publication type:

Article

Linking gene expression data with patient survival times using partial least squares.

Published in:

Bioinformatics, 2002, v. 18, p. S120, doi. 10.1093/bioinformatics/18.suppl_1.S120

By:

Park, Peter J.;
Tian, Lu;
Kohane, Isaac S.

Publication type:

Article

Single-cell gene fusion detection by scFusion.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28661-6

By:

Jin, Zijie;
Huang, Wenjian;
Shen, Ning;
Li, Juan;
Wang, Xiaochen;
Dong, Jiqiao;
Park, Peter J.;
Xi, Ruibin

Publication type:

Article

Identification of regions in the HOX cluster that can confer repression in a Polycomb-dependent manner.

Published in:

2013

By:

Woo, Caroline J.;
Kharchenko, Peter V.;
Daheron, Laurence;
Park, Peter J.;
Kingston, Robert E.

Publication type:

Conference Paper/Materials

Gene Expression Analysis Reveals the Cell Cycle and Kinetochore Genes Participating in Ischemia Reperfusion Injury and Early Development in Kidney.

Published in:

PLoS ONE, 2011, v. 6, n. 9, p. 1, doi. 10.1371/journal.pone.0025679

By:

Kim, Tae-Min;
Ramírez, Victoria;
Barrera-Chimal, Jonatan;
Bobadilla, Norma A.;
Park, Peter J.;
Vaidya, Vishal S.

Publication type:

Article

Unphosphorylated SR-Like Protein Npl3 Stimulates RNA Polymerase II Elongation.

Published in:

PLoS ONE, 2008, v. 3, n. 9, p. 1, doi. 10.1371/journal.pone.0003273

By:

Dermody, Jessica L.;
Dreyfuss, Jonathan M.;
Villén, Judit;
Ogundipe, Babatunde;
Gygi, Steven P.;
Park, Peter J.;
Ponticelli, Alfred S.;
Moore, Claire L.;
Buratowski, Stephen;
Bucheli, Miriam E.

Publication type:

Article

The BabySeq project: implementing genomic sequencing in newborns.

Published in:

2018

By:

Holm, Ingrid A.;
Agrawal, Pankaj B.;
Ceyhan-Birsoy, Ozge;
Christensen, Kurt D.;
Fayer, Shawn;
Frankel, Leslie A.;
Genetti, Casie A.;
Krier, Joel B.;
LaMay, Rebecca C.;
Levy, Harvey L.;
McGuire, Amy L.;
Parad, Richard B.;
Park, Peter J.;
Pereira, Stacey;
Rehm, Heidi L.;
Schwartz, Talia S.;
Waisbren, Susan E.;
Yu, Timothy W.;
The BabySeq Project Team;
Green, Robert C.

Publication type:

journal article

Standard for improving emergency information interoperability: the HL7 data elements for emergency department systems.

Published in:

Journal of the American Medical Informatics Association, 2015, v. 22, n. 3, p. 529, doi. 10.1093/jamia/ocu040

By:

McClay, James C.;
Park, Peter J.;
Janczewski, Mark G.;
Heermann Langford, Laura

Publication type:

Article

Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation.

Published in:

Human Molecular Genetics, 2015, v. 24, n. 9, p. 2442, doi. 10.1093/hmg/ddv006

By:

Biagioli, Marta;
Ferrari, Francesco;
Mendenhall, Eric M.;
Yijing Zhang;
Erdin, Serkan;
Vijayvargia, Ravi;
Vallabh, Sonia M.;
Solomos, Nicole;
Manavalan, Poornima;
Ragavendran, Ashok;
Ozsolak, Fatih;
Jong Min Lee;
Talkowski, Michael E.;
Gusella, James F.;
Macdonald, Marcy E.;
Park, Peter J.;
Ihn Sik Seong

Publication type:

Article

A Wnt-Bmp Feedback Circuit Controls Intertissue Signaling Dynamics in Tooth Organogenesis.

Published in:

Science Signaling, 2012, v. 5, n. 206, p. 1, doi. 10.1126/scisignal.2002414

By:

O'Connell, Daniel J.;
Ho, Joshua W. K.;
Mammoto, Tadanori;
Turbe-Doan, Annick;
O'Connell, Joyce T.;
Haseley, Psalm S.;
Koo, Samuel;
Kamiya, Nobuhiro;
Ingber, Donald E.;
Park, Peter J.;
Maas, Richard L.

Publication type:

Article

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 278, doi. 10.1186/s12859-015-0704-z

By:

Lee, Soohyun;
Seo, Chae Hwa;
Alver, Burak Han;
Lee, Sanghyuk;
Park, Peter J.

Publication type:

Article

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0704-z

By:

Soohyun Lee;
Chae Hwa Seo;
Alver, Burak Han;
Sanghyuk Lee;
Park, Peter J.

Publication type:

Article

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.

Published in:

PLoS Genetics, 2016, v. 12, n. 10, p. 1, doi. 10.1371/journal.pgen.1006385

By:

Saini, Natalie;
Roberts, Steven A.;
Klimczak, Leszek J.;
Chan, Kin;
Grimm, Sara A.;
Dai, Shuangshuang;
Fargo, David C.;
Boyer, Jayne C.;
Kaufmann, William K.;
Taylor, Jack A.;
Lee, Eunjung;
Cortes-Ciriano, Isidro;
Park, Peter J.;
Schurman, Shepherd H.;
Malc, Ewa P.;
Mieczkowski, Piotr A.;
Gordenin, Dmitry A.

Publication type:

Article

KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs.

Published in:

Journal of Clinical Investigation, 2013, v. 123, n. 2, p. 727, doi. 10.1172/JCI64535

By:

Tzatsos, Alexandros;
Paskaleva, Polina;
Ferrari, Francesco;
Deshpande, Vikram;
Stoykova, Svetlana;
Contino, Gianmarco;
Wong, Kwok-Kin;
Fei Lan;
Trojer, Patrick;
Park, Peter J.;
Bardeesy, Nabeel

Publication type:

Article

Overcoming evasive resistance from vascular endothelial growth factor a inhibition in sarcomas by genetic or pharmacologic targeting of hypoxia-inducible factor 1α.

Published in:

International Journal of Cancer, 2013, v. 132, n. 1, p. 29, doi. 10.1002/ijc.27666

By:

Kim, Yeo‐Jung;
Lee, Hae‐June;
Kim, Tae‐Min;
Eisinger‐Mathason, T.S. Karin;
Zhang, Alexia Y.;
Schmidt, Benjamin;
Karl, Daniel L.;
Nakazawa, Michael S.;
Park, Peter J.;
Simon, M. Celeste;
Yoon, Sam S.

Publication type:

Article

Design and analysis of ChIP-seq experiments for DNA-binding proteins.

Published in:

Nature Biotechnology, 2008, v. 26, n. 12, p. 1351, doi. 10.1038/nbt.1508

By:

Kharchenko, Peter V;
Tolstorukov, Michael Y;
Park, Peter J

Publication type:

Article

Spt6 Regulates Intragenic and Antisense Transcription, Nucleosome Positioning, and Histone Modifications Genome-Wide in Fission Yeast.

Published in:

Molecular & Cellular Biology, 2013, v. 33, n. 24, p. 4779, doi. 10.1128/MCB.01068-13

By:

DeGennaro, Christine M.;
Alver, Burak H.;
Marguerat, Samuel;
Stepanova, Ekaterina;
Davis, Christopher P.;
Bähler, Jürg;
Park, Peter J.;
Winston, Fred

Publication type:

Article

Variable Requirements for DNA-Binding Proteins at Polycomb-Dependent Repressive Regions in Human HOX Clusters.

Published in:

Molecular & Cellular Biology, 2013, v. 33, n. 16, p. 3274, doi. 10.1128/MCB.00275-13

By:

Woo, Caroline J.;
Kharchenko, Peter V.;
Daheron, Laurence;
Park, Peter J.;
Kingston, Robert E.

Publication type:

Article

Variable Requirements for DNA-Binding Proteins at Polycomb-Dependent Repressive Regions in Human HOX Clusters.

Published in:

Molecular & Cellular Biology, 2013, v. 33, n. 15, p. 3274, doi. 10.1128/MCB.00275-13

By:

Woo, Caroline J.;
Kharchenko, Peter V.;
Daheron, Laurence;
Park, Peter J.;
Kingston, Robert E.

Publication type:

Article

ChIP-seq: advantages and challenges of a maturing technology.

Published in:

2009

By:

Park, Peter J.

Publication type:

journal article

Evaluation of somatic copy number estimation tools for whole-exome sequencing data.

Published in:

Briefings in Bioinformatics, 2016, v. 17, n. 2, p. 185, doi. 10.1093/bib/bbv055

By:

Jae-Yong Nam;
Kim, Nayoung K. D.;
Sang Cheol Kim;
Je-Gun Joung;
Ruibin Xi;
Lee, Semin;
Park, Peter J.;
Woong-Yang Park

Publication type:

Article

Expression profiling of uterine leiomyomata cytogenetic subgroups reveals distinct signatures in matched myometrium: transcriptional profiling of the t(12;14) and evidence in support of predisposing genetic heterogeneity.

Published in:

Human Molecular Genetics, 2012, v. 21, n. 10, p. 2312, doi. 10.1093/hmg/dds051

By:

Hodge, Jennelle C.;
Kim, Tae-Min;
Dreyfuss, Jonathan M.;
Somasundaram, Priya;
Christacos, Nicole C.;
Rousselle, Marissa;
Quade, Bradley J.;
Park, Peter J.;
Stewart, Elizabeth A.;
Morton, Cynthia C.

Publication type:

Article