Systems Biology

bioLQM: a java library for the manipulation and conversion of Logical Qualitative Models of biological networks
Aurélien Naldi

bioRxiv 287011; doi: https://doi.org/10.1101/287011 New Results
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
Emily R. Miraldi, Maria Pokrovskii, Aaron Watters, Dayanne M. Castro, Nicholas De Veaux, Jason A. Hall, June-Yong Lee, Maria Ciofani, Aviv Madar, Nick Carriero, Dan R. Littman, Richard Bonneau

bioRxiv 292987; doi: https://doi.org/10.1101/292987 New Results
Benchmarking optimization methods for parameter estimation in large kinetic models
Alejandro F. Villaverde, Fabian Froehlich, Daniel Weindl, Jan Hasenauer, Julio R Banga

bioRxiv 295006; doi: https://doi.org/10.1101/295006 New Results
Influence of pathway topology and functional class on the molecular evolution of human metabolic genes
Ludovica Montanucci, Hafid Laayouni, Begoña Dobón, Kevin L. Keys, Jaume Bertranpetit, Juli Peretó

bioRxiv 292714; doi: https://doi.org/10.1101/292714 New Results
WASABI: a dynamic iterative framework for gene regulatory network inference
Arnaud Bonnaffoux, Ulysse Herbach, Angelique Richard, Anissa Guillemin, Sandrine Giraud, Pierre-Alexis Gros, Olivier Gandrillon

bioRxiv 292128; doi: https://doi.org/10.1101/292128 New Results
Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models
Olivia Eriksson, Alexandra Jauhiainen, Sara Maad Sasane, Andrei Kramer, Anu G Nair, Carolina Sartorius, Jeanette Hellgren Kotaleski

bioRxiv 294884; doi: https://doi.org/10.1101/294884 New Results
Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis
Mukesh Bansal, Jing He, Michael Peyton, Manjunath Kaustagi, Archana Iyer, Michael Comb, Michael White, John Minna, Andrea Califano

bioRxiv 289603; doi: https://doi.org/10.1101/289603 New Results
Distinct sequence patterns in the active postmortem transcriptome
Peter A Noble, Alexander E Pozhitkov

bioRxiv 293589; doi: https://doi.org/10.1101/293589 New Results
Enter the matrix: factorization uncovers knowledge from omics
Genevieve L. Stein-O'Brien, Raman Arora, Aedin C. Culhane, Alexander Favorov, Lana X. Garmire, Casey Greene, Loyal A. Goff, Yifeng Li, Alioune Ngom, Michael F. Ochs, Yanxun Xu, Elana J. Fertig

bioRxiv 196915; doi: https://doi.org/10.1101/196915 Confirmatory Results
Optimal feedback mechanisms for regulating cell numbers
Saurabh Modi, Abhyudai Singh

bioRxiv 292920; doi: https://doi.org/10.1101/292920 New Results

Systems Biology

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