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Liu, Tongyu, Mi, Lin, Xiong, Jing, Orchard, Peter, Yu, Qi, Yu, Lei, Zhao, Xu-Yun, Meng, Zhuo-Xian, Parker, Stephen C. J., Lin, Jiandie D., Li, Siming
Published in Nature communications (13.05.2020)
Published in Nature communications (13.05.2020)
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CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images
Tao, Yicheng, Feng, Fan, Luo, Xin, Reihsmann, Conrad V, Hopkirk, Alexander L, Cartailler, Jean-Philippe, Brissova, Marcela, Parker, Stephen C J, Saunders, Diane C, Liu, Jie
Published in PLoS computational biology (28.08.2024)
Published in PLoS computational biology (28.08.2024)
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FixItFelix: improving genomic analysis by fixing reference errors
Behera, Sairam, LeFaive, Jonathon, Orchard, Peter, Mahmoud, Medhat, Paulin, Luis F, Farek, Jesse, Soto, Daniela C, Parker, Stephen C J, Smith, Albert V, Dennis, Megan Y, Zook, Justin M, Sedlazeck, Fritz J
Published in Genome Biology (21.02.2023)
Published in Genome Biology (21.02.2023)
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BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues
Zou, Luli S, Erdos, Michael R, Taylor, D Leland, Chines, Peter S, Varshney, Arushi, Parker, Stephen C J, Collins, Francis S, Didion, John P
Published in BMC genomics (23.05.2018)
Published in BMC genomics (23.05.2018)
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Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome
Parker, Stephen C. J., Hansen, Loren, Abaan, Hatice Ozel, Tullius, Thomas D., Margulies, Elliott H.
Published in Science (American Association for the Advancement of Science) (17.04.2009)
Published in Science (American Association for the Advancement of Science) (17.04.2009)
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Multi-omic profiling of pituitary thyrotropic cells and progenitors
Daly, Alexandre Z, Dudley, Lindsey A, Peel, Michael T, Liebhaber, Stephen A, Parker, Stephen C J, Camper, Sally A
Published in BMC biology (15.04.2021)
Published in BMC biology (15.04.2021)
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A Map of Minor Groove Shape and Electrostatic Potential from Hydroxyl Radical Cleavage Patterns of DNA
Bishop, Eric P, Rohs, Remo, Parker, Stephen C. J, West, Sean M, Liu, Peng, Mann, Richard S, Honig, Barry, Tullius, Thomas D
Published in ACS chemical biology (16.12.2011)
Published in ACS chemical biology (16.12.2011)
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Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection
Shibata, Yoichiro, Sheffield, Nathan C, Fedrigo, Olivier, Babbitt, Courtney C, Wortham, Matthew, Tewari, Alok K, London, Darin, Song, Lingyun, Lee, Bum-Kyu, Iyer, Vishwanath R, Parker, Stephen C J, Margulies, Elliott H, Wray, Gregory A, Furey, Terrence S, Crawford, Gregory E
Published in PLoS genetics (01.06.2012)
Published in PLoS genetics (01.06.2012)
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Super-enhancers delineate disease-associated regulatory nodes in T cells
Vahedi, Golnaz, Kanno, Yuka, Furumoto, Yasuko, Jiang, Kan, Parker, Stephen C. J., Erdos, Michael R., Davis, Sean R., Roychoudhuri, Rahul, Restifo, Nicholas P., Gadina, Massimo, Tang, Zhonghui, Ruan, Yijun, Collins, Francis S., Sartorelli, Vittorio, O’Shea, John J.
Published in Nature (London) (23.04.2015)
Published in Nature (London) (23.04.2015)
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Machine Learning to Predict Anti–Tumor Necrosis Factor Drug Responses of Rheumatoid Arthritis Patients by Integrating Clinical and Genetic Markers
Guan, Yuanfang, Zhang, Hongjiu, Quang, Daniel, Wang, Ziyan, Parker, Stephen C. J., Pappas, Dimitrios A., Kremer, Joel M., Zhu, Fan
Published in Arthritis & rheumatology (Hoboken, N.J.) (01.12.2019)
Published in Arthritis & rheumatology (Hoboken, N.J.) (01.12.2019)
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Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle
Taylor, D. Leland, Jackson, Anne U., Narisu, Narisu, Hemani, Gibran, Erdos, Michael R., Chines, Peter S., Swift, Amy, Idol, Jackie, Didion, John P., Welch, Ryan P., Kinnunen, Leena, Saramies, Jouko, Lakka, Timo A., Laakso, Markku, Tuomilehto, Jaakko, Parker, Stephen C. J., Koistinen, Heikki A., Smith, George Davey, Boehnke, Michael, Scott, Laura J., Birney, Ewan, Collins, Francis S.
Published in Proceedings of the National Academy of Sciences - PNAS (28.05.2019)
Published in Proceedings of the National Academy of Sciences - PNAS (28.05.2019)
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Towards the identification of essential genes using targeted genome sequencing and comparative analysis
Gustafson, Adam M, Snitkin, Evan S, Parker, Stephen C J, DeLisi, Charles, Kasif, Simon
Published in BMC genomics (19.10.2006)
Published in BMC genomics (19.10.2006)
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Chromatin information content landscapes inform transcription factor and DNA interactions
D’Oliveira Albanus, Ricardo, Kyono, Yasuhiro, Hensley, John, Varshney, Arushi, Orchard, Peter, Kitzman, Jacob O., Parker, Stephen C. J.
Published in Nature communications (26.02.2021)
Published in Nature communications (26.02.2021)
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Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
Orchard, Peter, Manickam, Nandini, Ventresca, Christa, Vadlamudi, Swarooparani, Varshney, Arushi, Rai, Vivek, Kaplan, Jeremy, Lalancette, Claudia, Mohlke, Karen L, Gallagher, Katherine, Burant, Charles F, Parker, Stephen C J
Published in Genome research (01.12.2021)
Published in Genome research (01.12.2021)
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CHD7 promotes neural progenitor differentiation in embryonic stem cells via altered chromatin accessibility and nascent gene expression
Yao, Hui, Hannum, Douglas F., Zhai, Yiwen, Hill, Sophie F., Albanus, Ricardo D.’Oliveira, Lou, Wenjia, Skidmore, Jennifer M., Sanchez, Gilson, Saiakhova, Alina, Bielas, Stephanie L., Scacheri, Peter, Ljungman, Mats, Parker, Stephen C. J., Martin, Donna M.
Published in Scientific reports (15.10.2020)
Published in Scientific reports (15.10.2020)
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Accurate and comprehensive sequencing of personal genomes
Ajay, Subramanian S, Parker, Stephen C J, Abaan, Hatice Ozel, Fajardo, Karin V Fuentes, Margulies, Elliott H
Published in Genome research (01.09.2011)
Published in Genome research (01.09.2011)
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Family-Based Analysis of Candidate Genes for Polycystic Ovary Syndrome
Ewens, Kathryn G, Stewart, Douglas R, Ankener, Wendy, Urbanek, Margrit, McAllister, Jan M, Chen, Chen, Baig, K. Maravet, Parker, Stephen C. J, Margulies, Elliot H, Legro, Richard S, Dunaif, Andrea, Strauss, Jerome F, Spielman, Richard S
Published in The journal of clinical endocrinology and metabolism (01.05.2010)
Published in The journal of clinical endocrinology and metabolism (01.05.2010)
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A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures
Varshney, Arushi, Kyono, Yasuhiro, Elangovan, Venkateswaran Ramamoorthi, Wang, Collin, Erdos, Michael R, Narisu, Narisu, Albanus, Ricardo D'Oliveira, Orchard, Peter, Stitzel, Michael L, Collins, Francis S, Kitzman, Jacob O, Parker, Stephen C J
Published in Diabetes (New York, N.Y.) (01.07.2021)
Published in Diabetes (New York, N.Y.) (01.07.2021)
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Global Epigenomic Analysis of Primary Human Pancreatic Islets Provides Insights into Type 2 Diabetes Susceptibility Loci
Stitzel, Michael L., Sethupathy, Praveen, Pearson, Daniel S., Chines, Peter S., Song, Lingyun, Erdos, Michael R., Welch, Ryan, Parker, Stephen C.J., Boyle, Alan P., Scott, Laura J., Margulies, Elliott H., Boehnke, Michael, Furey, Terrence S., Crawford, Gregory E., Collins, Francis S.
Published in Cell metabolism (03.11.2010)
Published in Cell metabolism (03.11.2010)
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