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2020 – today
- 2024
[i1]Benedikt Geiger, Peter J. Park:
On the Connection Between Non-negative Matrix Factorization and Latent Dirichlet Allocation. CoRR abs/2405.20542 (2024)- 2022
- [j28]Soohyun Lee, Clara R. Bakker
, Carl Vitzthum, Burak Han Alver, Peter J. Park:
Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs. Bioinform. 38(6): 1729-1731 (2022) - 2021
- [j27]Minseok Kwon, Soohyun Lee, Michele Berselli, Chong Chu, Peter J. Park:
BamSnap: a lightweight viewer for sequencing reads in BAM files. Bioinform. 37(2): 263-264 (2021) - [j26]Dhawal Jain, Chong Chu, Burak Han Alver, Soohyun Lee, Eunjung Alice Lee, Peter J. Park:
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data. Bioinform. 37(8): 1045-1051 (2021) - 2020
- [j25]Connor A. Horton, Burak Han Alver, Peter J. Park:
GiniQC: a measure for quantifying noise in single-cell Hi-C data. Bioinform. 36(9): 2902-2904 (2020) - [j24]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:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j23]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:
Genomic basis for RNA alterations in cancer. Nat. 578(7793): 129-136 (2020)
2010 – 2019
- 2019
- [j22]Soohyun Lee, Jeremy Johnson, Carl Vitzthum, Koray Kirli, Burak Han Alver, Peter J. Park:
Tibanna: software for scalable execution of portable pipelines on the cloud. Bioinform. 35(21): 4424-4426 (2019) - 2016
- [j21]Jae-Yong Nam, Nayoung K. D. Kim, Sang Cheol Kim, Je-Gun Joung, Ruibin Xi, Semin Lee, Peter J. Park, Woong-Yang Park:
Evaluation of somatic copy number estimation tools for whole-exome sequencing data. Briefings Bioinform. 17(2): 185-192 (2016) - 2015
- [j20]Kyung-Ah Sohn, Joshua Wing Kei Ho, Djordje Djordjevic, Hyun-hwan Jeong, Peter J. Park, Ju Han Kim:
hiHMM: Bayesian non-parametric joint inference of chromatin state maps. Bioinform. 31(13): 2066-2074 (2015) - [j19]Soohyun Lee, Chae Hwa Seo, Burak Han Alver, Sanghyuk Lee, Peter J. Park:
EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering. BMC Bioinform. 16: 278:1-278:16 (2015) - [j18]James C. McClay, Peter J. Park, Mark G. Janczewski, Laura Heermann Langford:
Standard for improving emergency information interoperability: the HL7 data elements for emergency department systems. J. Am. Medical Informatics Assoc. 22(3): 529-535 (2015) - 2014
- [j17]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:
Comparative analysis of metazoan chromatin organization Open. Nat. 512(7515): 449-452 (2014) - 2013
- [j16]Nils Gehlenborg, Michael S. Noble, Gad Getz, Lynda Chin, Peter J. Park:
Nozzle: a report generation toolkit for data analysis pipelines. Bioinform. 29(8): 1089-1091 (2013) - [c6]James C. McClay, Peter J. Park, Sandra D. Marr, Laura Heermann Langford:
The HL7 Standards-Based Model of Emergency Care Information. MedInfo 2013: 1180 - 2012
- [j15]Alexander Lex, Marc Streit, Hans-Jörg Schulz, Christian Partl, Dieter Schmalstieg, Peter J. Park, Nils Gehlenborg:
StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization. Comput. Graph. Forum 31(3pt3): 1175-1184 (2012) - [c5]James C. McClay, Laura Heermann Langford, Kevin Coonan, Donald Kamens, Peter J. Park:
The HL7 Specification of the Data Elements for Emergency Department Systems (DEEDS). AMIA 2012 - 2010
- [j14]Shouyong Peng, Mitzi I. Kuroda, Peter J. Park:
Quantized correlation coefficient for measuring reproducibility of ChIP-chip data. BMC Bioinform. 11: 399 (2010) - [j13]Tae-Min Kim, Lovelace J. Luquette, Ruibin Xi, Peter J. Park:
rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data. BMC Bioinform. 11: 432 (2010)
2000 – 2009
- 2009
- [j12]Peter J. Park, Sek Won Kong, Toma Tebaldi, Weil R. Lai, Simon Kasif, Isaac S. Kohane:
Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinform. 25(23): 3121-3127 (2009) - [j11]Peter J. Park, J. Manjourides, Marco Bonetti, Marcello Pagano:
A permutation test for determining significance of clusters with applications to spatial and gene expression data. Comput. Stat. Data Anal. 53(12): 4290-4300 (2009) - 2008
- [j10]Hyunju Lee, Sek Won Kong, Peter J. Park:
Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes. Bioinform. 24(7): 889-896 (2008) - [j9]Weil R. Lai, Vidhu Choudhary, Peter J. Park:
CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. Bioinform. 24(7): 1014-1015 (2008) - [j8]Michael Y. Tolstorukov, Vidhu Choudhary, Wilma K. Olson, Victor Zhurkin, Peter J. Park:
nuScore: a web-interface for nucleosome positioning predictions. Bioinform. 24(12): 1456-1458 (2008) - 2007
- [j7]Shouyong Peng, Artyom A. Alekseyenko, Erica Larschan, Mitzi I. Kuroda, Peter J. Park:
Normalization and experimental design for ChIP-chip data. BMC Bioinform. 8 (2007) - 2006
- [j6]Sek Won Kong, William T. Pu, Peter J. Park:
A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinform. 22(19): 2373-2380 (2006) - 2005
- [j5]Sek Won Kong, Kyu Baek Hwang, Richard D. Kim, Byoung-Tak Zhang, Steven A. Greenberg, Isaac S. Kohane, Peter J. Park:
CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays. Bioinform. 21(9): 2116-2117 (2005) - [j4]Weil R. Lai, Mark D. Johnson, Raju Kucherlapati, Peter J. Park:
Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinform. 21(19): 3763-3770 (2005) - 2004
- [j3]Kyu Baek Hwang, Sek Won Kong, Steven A. Greenberg, Peter J. Park:
Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinform. 5: 159 (2004) - 2003
- [j2]Martin Kulldorff, Toshiro Tango, Peter J. Park:
Power comparisons for disease clustering tests. Comput. Stat. Data Anal. 42(4): 665-684 (2003) - [c4]Winston Patrick Kuo, Eduardo Mendez, Chu Chen, Mark Whipple, Greg Farell, Nicholas Agoff, Peter J. Park:
Functional Relationships Between Gene Pairs in Oral Squamous Cell Carcinoma. AMIA 2003 - 2002
- [j1]Peter J. Park, Atul J. Butte, Isaac S. Kohane:
Comparing expression profiles of genes with similar promoter regions. Bioinform. 18(12): 1576-1584 (2002) - [c3]Winston Patrick Kuo, Tor-Kristian Jenssen, Peter J. Park, Mark W. Lingen, Rifat Hasina, Lucila Ohno-Machado:
Gene expression levels in different stages of progression in oral squamous cell carcinoma. AMIA 2002 - [c2]Peter J. Park, Lu Tian, Isaac S. Kohane:
Linking gene expression data with patient survival times using partial least squares. ISMB 2002: 120-127 - 2001
- [c1]Peter J. Park, Marcello Pagano, Marco Bonetti:
A Nonparametric Scoring Algorithm for Identifying Informative Genes from Microarray Data. Pacific Symposium on Biocomputing 2001: 52-63
Coauthor Index
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