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Submissions from 2014

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Higher-order chromatin domains link eQTLs with the expression of far-away genes., Geet Duggal, Hao Wang, and Carl Kingsford

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Identification of alternative topological domains in chromatin., Darya Filippova, Rob Patro, Geet Duggal, and Carl Kingsford

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Parameter discovery in stochastic biological models using simulated annealing and statistical model checking., Faraz Hussain, Sumit Kumar Jha, Susmit Jha, and Christopher J. Langmead

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Learning Sequence Determinants of Protein:protein Interaction Specificity with Sparse Graphical Models., Hetunandan Kamisetty, Bornika Ghosh, Christopher J. Langmead, and Chris Bailey-Kellogg

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Efficient discovery of responses of proteins to compounds using active learning., Joshua D. Kangas, Armaghan W. Naik, and Robert F. Murphy

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Generative models of conformational dynamics., Christopher J. Langmead

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Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms., Rob Patro, Stephen M. Mount, and Carl Kingsford

Submissions from 2013

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Resolving spatial inconsistencies in chromosome conformation measurements., Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, and Carl Kingsford

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The Marker State Space (MSS) method for classifying clinical samples., Brian P. Fallon, Bryan Curnutte, Kevin A. Maupin, Katie Partyka, Sunguk Choi, Randall E. Brand, Christopher J. Langmead, Waibhav Tembe, and Brian B. Haab

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Predicting protein interactions via parsimonious network history inference., Rob Patro and Carl Kingsford

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Label-free detection of neuronal differentiation in cell populations using high-throughput live-cell imaging of PC12 cells., Sebastian Weber, María L. Fernández-Cachón, Juliana M. Nascimento, Steffen Knauer, Barbara Offermann, Robert F. Murphy, Melanie Boerries, and Hauke Busch

Submissions from 2012

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Biological imaging software tools., Kevin W. Eliceiri, Michael R. Berthold, Ilya G. Goldberg, Luis Ibáñez, B. B. Manjunath, Maryann E. Martone, Robert F. Murphy, Hanchuan Peng, Anne L. Plant, Badrinath Roysam, Nico Stuurman, Jason R. Swedlow, Pavel Tomancak, and Anne E. Carpenter

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Coral: an integrated suite of visualizations for comparing clusterings., Darya Filippova, Aashish Gadani, and Carl Kingsford

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Exploring behaviors of stochastic differential equation models of biological systems using change of measures., Sumit Kumar Jha and Christopher J. Langmead

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Automated analysis and reannotation of subcellular locations in confocal images from the Human Protein Atlas., Jieyue Li, Justin Newberg, Mathias Uhlén, Emma Lundberg, and Robert F. Murphy

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Protein subcellular location pattern classification in cellular images using latent discriminative models., Jieyue Li, Liang Xiong, Jeff Schneider, and Robert F. Murphy

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A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors., Subhodeep Moitra, Kalyan C. Tirupula, Judith Klein-Seetharaman, and Christopher J. Langmead

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CellOrganizer: Image-derived models of subcellular organization and protein distribution., Robert F. Murphy

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Learning generative models of molecular dynamics., Narges Sharif Razavian, Hetunandan Kamisetty, and Christopher J. Langmead

Submissions from 2011

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Serum biomarker panels for the detection of pancreatic cancer., Randall E Brand, Brian M. Nolen, Herbert J. Zeh, Peter J. Allen, Mohamad A. Eloubeidi, Michael Goldberg, Eric Elton, Juan P. Arnoletti, John D. Christein, Selwyn M. Vickers, Christopher J. Langmead, Douglas P. Landsittel, David C. Whitcomb, William E. Grizzle, Anna E. Lokshin, and Randall E. Brand

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Discriminative motif finding for predicting protein subcellular localization., Tien-ho Lin, Robert F. Murphy, and Ziv Bar-Joseph

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An active role for machine learning in drug development., Robert F. Murphy

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Image-derived, three-dimensional generative models of cellular organization., Tao Peng and Robert F. Murphy

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Discovering conformational sub-states relevant to protein function., Arvind Ramanathan, Andrej J. Savol, Christopher J. Langmead, Pratul K. Agarwal, and Chakra S. Chennubhotla

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The von Mises Graphical Model: Expectation Propagation for Inference (CMU-CS-11-130/CMU-CB-11-102), Narges Sharif Razavian, Hetunandan Kamisetty, and Christopher J. Langmead

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The von Mises Graphical Model: Regularized Structure and Parameter Learning (CMU-CS-11-129/CMU-CB-11-101), Narges Sharif Razavian, Hetunandan Kamisetty, and Christopher J. Langmead

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The von Mises Graphical Model: Structure Learning (CMU-CS-11-108 / CMU-CB-11-100), Narges Sharif Razavian, Hetunandan Kamisetty, and Christopher J. Langmead

Submissions from 2010

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Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing., Luis Pedro Coelho, Tao Peng, and Robert F. Murphy

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A Graphical Model to Determine the Subcellular Protein Location in Artificial Tissues., Estelle Glory-Afshar, Elvira Osuna-Highley, Brian Granger, and Robert F. Murphy

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Communicating subcellular distributions., Robert F. Murphy