PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions by Qiao, Wenlian, Quon, Gerald, Csaszar, Elizabeth, Yu, Mei, Morris, Quaid D., Zandstra, Peter W.

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Modular Composition of Gene Transcription Networks by Gyorgy, Andras, Del Vecchio, Domitilla

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In Vivo Volume and Hemoglobin Dynamics of Human Red Blood Cells by Malka, Roy, Higgins, John M., Manalis, Scott R, Delgado, Francisco Feijo

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Two dynamic regimes in the human gut microbiome by Gibbons, Sean Michael, Kearney, Sean M, Smillie, Chris S, Alm, Eric J

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BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods by Gorgolewski, Krzysztof J., Alfaro-Almagro, Fidel, Auer, Tibor, Bellec, Pierre, Chakravarty, M. Mallar, Churchill, Nathan W., Cohen, Alexander Li, Craddock, R. Cameron, Devenyi, Gabriel A., Eklund, Anders, Esteban, Oscar, Flandin, Guillaume, Ghosh, Satrajit S., Guntupalli, J. Swaroop, Jenkinson, Mark, Keshavan, Anisha, Kiar, Gregory, Liem, Franziskus, Raamana, Pradeep Reddy, Raffelt, David, Steele, Christopher J., Quirion, Pierre-Olivier, Smith, Robert E., Strother, Stephen C., Wang, Yida, Yarkoni, Tal, Poldrack, Russell A., Capota, Mihai, Varoquaux, Gael, Ghosh, Satrajit S

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Mechanobiological model for simulation of injured cartilage degradation via pro-inflammatory cytokines and mechanical stimulus by Eskelinen, Atte SA, Tanska, Petri, Florea, Cristina, Orozco, Gustavo A, Julkunen, Petro, Grodzinsky, Alan J, Korhonen, Rami K

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Robust point-process Granger causality analysis in presence of exogenous temporal modulations and trial-by-trial variability in spike trains by Casile, Antonino, Faghih, Rose T, Brown, Emery N

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Data-driven Mechanistic Modeling of 3D Human Genome by Qi, Yifeng

“…The manuscript associated with this study is published in PLoS Computational Biology, 15.6, e1007024 (2019). In the second chapter, we expand the spatial scale of the model to study the organization of the global diploid human genome in the entire nucleus. …”
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A high-throughput screening approach to discovering good forms of inspired visual representation by Pinto, Nicolas, Doukhan, David, DiCarlo, James, Cox, David D.

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Computational analysis of viscoelastic properties of crosslinked actin networks by Hwang, Wonmuk, Lee, Hyungsuk, Kim, Taeyoon, Kamm, Roger Dale

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A Neural Computational Model of Incentive Salience by Zhang, Jun, Berridge, Kent C., Tindell, Amy J., Smith, Kyle S., Aldridge, J. Wayne

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The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data by Samaga, Regina, Saez-Rodriguez, Julio, Alexopoulos, Leonidas G., Sorger, Peter K., Klamt, Steffen

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Within- and cross-modal distance information disambiguate visual size- perception by Battaglia, Peter W., Kersten, Daniel, Machulla, Tonja, Schrater, Paul R., Ernst, Marc O., Di Luca, Massimiliano

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Optimal workloop energetics of muscle-actuated systems: an impedance view by Farahat, Waleed A., Herr, Hugh M.

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An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data by Ramsköld, Daniel, Sandberg, Rickard, Burge, Christopher B, Wang, Eric T

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A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis by Luengo-Oroz, Miguel A., Duloquin, Louise, Savy, Thierry, Rizzi, Barbara, Desnoulez, Sophie, Kergosien, Yannick L., Bourgine, Paul, Castro Gonzalez, Carlos, Doursat, Rene, Peyrieras, Nadine, Santos, Andres, Ledesma-Carbayo, Maria J.

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Kinetic modeling of H2O2 dynamics in the mitochondria of HeLa cells by Stein, Kassi T, Moon, Sun Jin, Nguyen, Athena N, Sikes, Hadley D

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BETASCAN: Probable beta-amyloids Identified by Pairwise Probabilistic Analysis by Bryan, Allen W., Menke, Matthew E., Cowen, Lenore J., Lindquist, Susan, Berger Leighton, Bonnie

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Information Flow Analysis of Interactome Networks by Liu, Kesheng, Ge, Hui, Ross, Brian Christopher, Missiuro, Patrycja Vasilyev, Zhao, Guoyan, Liu, Jun S., Zou, Lihua

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A High-Throughput Screening Approach to Discovering Good Forms of Biologically Inspired Visual Representation by Cox, David D., Pinto, Nicolas, Doukhan, David, DiCarlo, James

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