Peter J. Park

According to our database, Peter J. Park authored at least 35 papers between 2001 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

On the Connection Between Non-negative Matrix Factorization and Latent Dirichlet Allocation.

Benedikt Geiger, Peter J. Park

CoRR, 2024

2022

Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs.

Soohyun Lee, Clara R. Bakker, Carl Vitzthum, Burak Han Alver, Peter J. Park

Bioinform., 2022

2021

BamSnap: a lightweight viewer for sequencing reads in BAM files.

Minseok Kwon, Soohyun Lee, Michele Berselli, Chong Chu, Peter J. Park

Bioinform., 2021

HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data.

Dhawal Jain, Chong Chu, Burak Han Alver, Soohyun Lee, Eunjung Alice Lee, Peter J. Park

Bioinform., 2021

2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora

Nat., 2020

Genomic basis for RNA alterations in cancer.

Claudia Calabrese, Natalie R. Davidson, Deniz Demircioglu, Nuno A. Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban, Liliana Greger, Siliang Li, Dongbing Liu, Marc D. Perry, Qian Xiang, Fan Zhang, Junjun Zhang, Peter Bailey, Serap Erkek, Katherine A. Hoadley, Yong Hou, Matthew R. Huska, Helena Kilpinen, Jan O. Korbel, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarström, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G. Stark, Hong Su, Patrick Tan, Sebastian M. Waszak, Christina K. Yung, Shida Zhu, Philip Awadalla, Matthew Meyerson, B. F. Francis Ouellette, Kui Wu, Huanming Yang, Samirkumar B. Amin, Aurélien Chateigner, Isidro Cortés-Ciriano, Brian Craft, Milana Frenkel-Morgenstern, Mary Goldman, Ekta Khurana, Fabien C. Lamaze, Chang Li, Xiaobo Li, Xinyue Li, Xingmin Liu, Morten Muhlig Nielsen, Akinyemi I. Ojesina, Peter J. Park, Jakob Skou Pedersen, Bin Tean Teh, Jian Wang, Heng Xiong, Sergei Yakneen, Chen Ye, Xiuqing Zhang, Liangtao Zheng, Jingchun Zhu, Chad Creighton, Jonathan Göke, Roland F. Schwarz, Oliver Stegle, Zemin Zhang, Alvis Brazma, Gunnar Rätsch, Angela N. Brooks

Nat., 2020

GiniQC: a measure for quantifying noise in single-cell Hi-C data.

Connor A. Horton, Burak Han Alver, Peter J. Park

Bioinform., 2020

2019

Tibanna: software for scalable execution of portable pipelines on the cloud.

Soohyun Lee, Jeremy Johnson, Carl Vitzthum, Koray Kirli, Burak Han Alver, Peter J. Park

Bioinform., 2019

2016

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

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

Briefings Bioinform., 2016

2015

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

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

J. Am. Medical Informatics Assoc., 2015

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

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

BMC Bioinform., 2015

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

Kyung-Ah Sohn, Joshua Wing Kei Ho, Djordje Djordjevic, Hyun-hwan Jeong, Peter J. Park, Ju Han Kim

Bioinform., 2015

2014

Comparative analysis of metazoan chromatin organization Open.

Joshua Wing Kei Ho, Youngsook L. Jung, Tao Liu, Burak Han Alver, Soohyun Lee, Kohta Ikegami, Kyung-Ah Sohn, Aki Minoda, Michael Y. Tolstorukov, Alex Appert, Stephen C. J. Parker, Tingting Gu, Anshul Kundaje, Nicole C. Riddle, Eric Bishop, Thea A. Egelhofer, Sheng'en Shawn Hu, Artyom A. Alekseyenko, Andreas Rechtsteiner, Dalal Asker, Jason A. Belsky, Sarah K. Bowman, Q. Brent Chen, Ron A.-J. Chen, Daniel S. Day, Yan Dong, Andrea C. Dose, Xikun Duan, Charles B. Epstein, Sevinc Ercan, Elise A. Feingold, Francesco Ferrari, Jacob M. Garrigues, Nils Gehlenborg, Peter J. Good, Psalm Haseley, Daniel He, Moritz Herrmann, Michael M. Hoffman, Tess E. Jeffers, Peter V. Kharchenko, Paulina Kolasinska-Zwierz, Chitra V. Kotwaliwale, Nischay Kumar, Sasha A. Langley, Erica Larschan, Isabel Latorre, Maxwell W. Libbrecht, Xueqiu Lin, Richard Park, Michael J. Pazin, Hoang N. Pham, Annette Plachetka, Bo Qin, Yuri B. Schwartz, Noam Shoresh, Przemyslaw Stempor, Anne Vielle, Chengyang Wang, Christina M. Whittle, Huiling Xue, Robert E. Kingston, Ju Han Kim, Bradley E. Bernstein, Abby F. Dernburg, Vincenzo Pirrotta, Mitzi I. Kuroda, William S. Noble, Thomas D. Tullius, Manolis Kellis, David M. MacAlpine, Susan Strome, Sarah C. R. Elgin, Xiaole Shirley Liu, Jason D. Lieb, Julie Ahringer, Gary H. Karpen, Peter J. Park

Nat., 2014

2013

Nozzle: a report generation toolkit for data analysis pipelines.

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

Bioinform., 2013

The HL7 Standards-Based Model of Emergency Care Information.

James C. McClay, Peter J. Park, Sandra D. Marr, Laura Heermann Langford

Proceedings of the MEDINFO 2013, 2013

2012

StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization.

Alexander Lex, Marc Streit, Hans-Jörg Schulz, Christian Partl, Dieter Schmalstieg, Peter J. Park, Nils Gehlenborg

Comput. Graph. Forum, 2012

The HL7 Specification of the Data Elements for Emergency Department Systems (DEEDS).

James C. McClay, Laura Heermann Langford, Kevin Coonan, Donald Kamens, Peter J. Park

Proceedings of the AMIA 2012, 2012

2010

Quantized correlation coefficient for measuring reproducibility of ChIP-chip data.

Shouyong Peng, Mitzi I. Kuroda, Peter J. Park

BMC Bioinform., 2010

rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data.

Tae-Min Kim, Lovelace J. Luquette, Ruibin Xi, Peter J. Park

BMC Bioinform., 2010

2009

A permutation test for determining significance of clusters with applications to spatial and gene expression data.

Peter J. Park, J. Manjourides, Marco Bonetti, Marcello Pagano

Comput. Stat. Data Anal., 2009

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

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

Bioinform., 2009

2008

nuScore: a web-interface for nucleosome positioning predictions.

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

Bioinform., 2008

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

Hyunju Lee, Sek Won Kong, Peter J. Park

Bioinform., 2008

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

Weil R. Lai, Vidhu Choudhary, Peter J. Park

Bioinform., 2008

2007

Normalization and experimental design for ChIP-chip data.

Shouyong Peng, Artyom A. Alekseyenko, Erica Larschan, Mitzi I. Kuroda, Peter J. Park

BMC Bioinform., 2007

2006

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

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

Bioinform., 2006

2005

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

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

Bioinform., 2005

CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays.

Sek Won Kong, Kyu Baek Hwang, Richard D. Kim, Byoung-Tak Zhang, Steven A. Greenberg, Isaac S. Kohane, Peter J. Park

Bioinform., 2005

2004

Combining gene expression data from different generations of oligonucleotide arrays.

Kyu Baek Hwang, Sek Won Kong, Steven A. Greenberg, Peter J. Park

BMC Bioinform., 2004

2003

Power comparisons for disease clustering tests.

Martin Kulldorff, Toshiro Tango, Peter J. Park

Comput. Stat. Data Anal., 2003

Functional Relationships Between Gene Pairs in Oral Squamous Cell Carcinoma.

Winston Patrick Kuo, Eduardo Mendez, Chu Chen, Mark Whipple, Greg Farell, Nicholas Agoff, Peter J. Park

Proceedings of the AMIA 2003, 2003

2002

Comparing expression profiles of genes with similar promoter regions.

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

Bioinform., 2002

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

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

Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

Gene expression levels in different stages of progression in oral squamous cell carcinoma.

Winston Patrick Kuo, Tor-Kristian Jenssen, Peter J. Park, Mark W. Lingen, Rifat Hasina, Lucila Ohno-Machado

Proceedings of the AMIA 2002, 2002

2001

A Nonparametric Scoring Algorithm for Identifying Informative Genes from Microarray Data.

Peter J. Park, Marcello Pagano, Marco Bonetti

Proceedings of the 6th Pacific Symposium on Biocomputing, 2001