Computational Medicine and Bioinformatics, Department of

• Subtyping of common complex diseases and disorders by integrating heterogeneous data. Identifying clusters among women with lower urinary tract symptoms in the LURN study 

  Andreev, VP; Helmuth, ME; Liu, G; Smith, AR; Merion, RM; Yang, CC; Cameron, AP; Jelovsek, JE; Amundsen, CL; Helfand, BT; Bradley, CS; DeLancey, JOL; Griffith, JW; Glaser, AP; Gillespie, BW; Clemens, JQ; Lai, HH (Public Library of Science (PLoS), 2022-06-01)

  (3.6MB)
  
  
• Chromatin information content landscapes inform transcription factor and DNA interactions 

  D'Oliveira Albanus, R; Kyono, Y; Hensley, J; Varshney, A; Orchard, P; Kitzman, JO; Parker, SCJ (2012-07-01)

  (5.6MB)
  
  
• A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures 

  Varshney, Arushi; Kyono, Yasuhiro; Venkateswaran, Elangovan; Wang, Collin; Erdos, Michael; Narisu, Narisu; Albanus, Ricardo; Orchard, Peter; Stitzel, Michael; Collin, Francis; Kitzman, Jacob; Parker, Stephen (2021-07-01)

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• A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures 

  Varshney, A; Kyono, Y; Elangovan, VR; Wang, C; Erdos, MR; Narisu, N; D'Oliveira Albanus, R; Orchard, P; Stitzel, ML; Collins, FS; Kitzman, JO; Parker, SCJ (2015-02-01)

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• A poplar rust effector protein associates with protein disulfide isomerase and enhances plant susceptibility 

  Madina, MH; Rahman, MS; Huang, X; Zhang, Y; Zheng, H; Germain, H (MDPI, 2020-09-01)

  (4.6MB)
  
  
• Scientific benchmarks for guiding macromolecular energy function improvement 

  Leaver-Fay, A; O'Meara, MJ; Tyka, M; Jacak, R; Song, Y; Kellogg, EH; Thompson, J; Davis, IW; Pache, RA; Lyskov, S; Gray, JJ; Kortemme, T; Richardson, JS; Havranek, JJ; Snoeyink, J; Baker, D; Kuhlman, B (Elsevier, 2013-01-01)

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• Maximum geodesic routing in the plane with obstacles 

  O'meara, M; Millman, DL; Snoeyink, J; Verma, V (2010-12-01)

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• Colour Patterns for Polychromatic Four-colourings of Rectangular Subdivisions 

  Haverkort, Herman; Loffler, Maarten; Mumford, Elena; O'Meara, Matthew; Snoeyink, Jack; Speckmann, Bettina

  (185.5KB)
  
  
• Computational Design of Peptides to Block Binding of the SARS-CoV-2 Spike Protein to Human ACE2 

  Huang, Xiaoqiang; Pearce, Robin; Zhang, Yang (2020-03-31)

  (1.6MB)
  
  
• knnAUC: an open-source R package for detecting nonlinear dependence between one continuous variable and one binary variable 

  Li, Yi; Liu, Xiaoyu; Ma, Yanyun; Wang, Yi; Zhou, Weichen; Hao, Meng; Yuan, Zhenghong; Liu, Jie; Xiong, Momiao; Shugart, Yin Y; Wang, Jiucun; Jin, Li (2018-11-22)

  (1.7MB)
  
  
• 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 (2018-05-23)

  (2.6MB)
  
  
• FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods 

  Becker, Timothy; Lee, Wan-Ping; Leone, Joseph; Zhu, Qihui; Zhang, Chengsheng; Liu, Silvia; Sargent, Jack; Shanker, Kritika; Mil-homens, Adam; Cerveira, Eliza; Ryan, Mallory; Cha, Jane; Navarro, Fabio C P; Galeev, Timur; Gerstein, Mark; Mills, Ryan E; Shin, Dong-Guk; Lee, Charles; Malhotra, Ankit (2018-03-20)

  (2.5MB)
  
  
• Maternal Feeding Goals and Restaurant Menu Choices for Young Children 

  Domoff, Sarah E.; Kiefner-Burmeister, Allison; Hoffmann, Debra A.; Musher-Eizenman, Dara (Mary Ann Liebert, Inc., publishers, 2015-08-01)

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• Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications 

  Kolker, Eugene; Özdemir, Vural; Martens, Lennart; Hancock, William; Anderson, Gordon; Anderson, Nathaniel; Aynacioglu, Sukru; Baranova, Ancha; Campagna, Shawn R.; Chen, Rui; Choiniere, John; Dearth, Stephen P.; Feng, Wu-Chun; Ferguson, Lynnette; Fox, Geoffrey; Frishman, Dmitrij; Grossman, Robert; Heath, Allison; Higdon, Roger; Hutz, Mara H.; Janko, Imre; Jiang, Lihua; Joshi, Sanjay; Kel, Alexander; Kemnitz, Joseph W.; Kohane, Isaac S.; Kolker, Natali; Lancet, Doron; Lee, Elaine; Li, Weizhong; Lisitsa, Andrey; Llerena, Adrian; MacNealy-Koch, Courtney; Marshall, Jean-Claude; Masuzzo, Paola; May, Amanda; Mias, George; Monroe, Matthew; Montague, Elizabeth; Mooney, Sean; Nesvizhskii, Alexey; Noronha, Santosh; Omenn, Gilbert; Rajasimha, Harsha; Ramamoorthy, Preveen; Sheehan, Jerry; Smarr, Larry; Smith, Charles V.; Smith, Todd; Snyder, Michael; Rapole, Srikanth; Srivastava, Sanjeeva; Stanberry, Larissa; Stewart, Elizabeth; Toppo, Stefano; Uetz, Peter; Verheggen, Kenneth; Voy, Brynn H.; Warnich, Louise; Wilhelm, Steven W.; Yandl, Gregory (Mary Ann Liebert, Inc., publishers, 2014-01-01)

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• A proximity-based graph clustering method for the identification and application of transcription factor clusters 

  Spadafore, Maxwell; Najarian, Kayvan; Boyle, Alan P. (2017-11-29)

  (1.6MB)
  
  
• Predictive model for inflammation grades of chronic hepatitis B: Large‐scale analysis of clinical parameters and gene expressions 

  Zhou, Weichen; Ma, Yanyun; Zhang, Jun; Hu, Jingyi; Zhang, Menghan; Wang, Yi; Li, Yi; Wu, Lijun; Pan, Yida; Zhang, Yitong; Zhang, Xiaonan; Zhang, Xinxin; Zhang, Zhanqing; Zhang, Jiming; Li, Hai; Lu, Lungen; Jin, Li; Wang, Jiucun; Yuan, Zhenghong; Liu, Jie (Wiley Periodicals, Inc., 2017-11)

  (899.5KB) (461KB)
  
  
• Feature selective temporal prediction of Alzheimer’s disease progression using hippocampus surface morphometry 

  Tsao, Sinchai; Gajawelli, Niharika; Zhou, Jiayu; Shi, Jie; Ye, Jieping; Wang, Yalin; Leporé, Natasha (Wiley Periodicals, Inc., 2017-07)

  (702.3KB) (959.7KB)
  
  
• Stability of methylation markers in head and neck squamous cell carcinoma 

  Virani, Shama; Light, Emily; Peterson, Lisa A.; Sartor, Maureen A.; Taylor, Jeremy M. G.; McHugh, Jonathan B.; Wolf, Gregory T.; Rozek, Laura S. (Wiley Periodicals, Inc., 2016-04)

  (1.4MB) (489KB)
  
  
• The proteomes of the human eye, a highly compartmentalized organ 

  Omenn, Gilbert S. (National Academies PressWiley Periodicals, Inc., 2017-01)

  (406.8KB) (245.5KB)
  
  
• Evolution‐informed modeling improves outcome prediction for cancers 

  Liu, Li; Chang, Yung; Yang, Tao; Noren, David P; Long, Byron; Kornblau, Steven; Qutub, Amina; Ye, Jieping (Wiley Periodicals, Inc.World Scientific, 2017-01)

  (610.1KB) (784.1KB)
  
  

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