FixItFelix: improving genomic analysis by fixing reference errors von 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

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BAF60a deficiency uncouples chromatin accessibility and cold sensitivity from white fat browning von 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

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CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images von 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

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BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues von Zou, Luli S, Erdos, Michael R, Taylor, D Leland, Chines, Peter S, Varshney, Arushi, Parker, Stephen C J, Collins, Francis S, Didion, John P

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Machine Learning to Predict Anti–Tumor Necrosis Factor Drug Responses of Rheumatoid Arthritis Patients by Integrating Clinical and Genetic Markers von Guan, Yuanfang, Zhang, Hongjiu, Quang, Daniel, Wang, Ziyan, Parker, Stephen C. J., Pappas, Dimitrios A., Kremer, Joel M., Zhu, Fan

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Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome von Parker, Stephen C. J., Hansen, Loren, Abaan, Hatice Ozel, Tullius, Thomas D., Margulies, Elliott H.

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Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection von 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

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A simple model for water table fluctuations in response to precipitation von Park, Eungyu, Parker, J.C.

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Multi-omic profiling of pituitary thyrotropic cells and progenitors von Daly, Alexandre Z, Dudley, Lindsey A, Peel, Michael T, Liebhaber, Stephen A, Parker, Stephen C J, Camper, Sally A

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Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle von 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.

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Super-enhancers delineate disease-associated regulatory nodes in T cells von 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.

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A Map of Minor Groove Shape and Electrostatic Potential from Hydroxyl Radical Cleavage Patterns of DNA von Bishop, Eric P, Rohs, Remo, Parker, Stephen C. J, West, Sean M, Liu, Peng, Mann, Richard S, Honig, Barry, Tullius, Thomas D

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Automated region of interest analysis of dynamic Ca²+ signals in image sequences von Francis, Michael, Qian, Xun, Charbel, Chimène, Ledoux, Jonathan, Parker, J C, Taylor, Mark S

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Chromatin information content landscapes inform transcription factor and DNA interactions von D’Oliveira Albanus, Ricardo, Kyono, Yasuhiro, Hensley, John, Varshney, Arushi, Orchard, Peter, Kitzman, Jacob O., Parker, Stephen C. J.

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CHD7 promotes neural progenitor differentiation in embryonic stem cells via altered chromatin accessibility and nascent gene expression von 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.

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Modeling field-scale dense nonaqueous phase liquid dissolution kinetics in heterogeneous aquifers von Parker, J.C, Park, E

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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 von 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

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Usability of Geographic Information: Current challenges and future directions von Brown, M., Sharples, S., Harding, J., Parker, C.J., Bearman, N., Maguire, M., Forrest, D., Haklay, M., Jackson, M.

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Towards the identification of essential genes using targeted genome sequencing and comparative analysis von Gustafson, Adam M, Snitkin, Evan S, Parker, Stephen C J, DeLisi, Charles, Kasif, Simon

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Accurate and comprehensive sequencing of personal genomes von Ajay, Subramanian S, Parker, Stephen C J, Abaan, Hatice Ozel, Fajardo, Karin V Fuentes, Margulies, Elliott H

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