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Marino, S and Gideon, HP and Gong, C and Mankad, S and McCrone, JT and Lin, PL and Linderman, JJ and Flynn, JAL and Kirschner, DE (2016) Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome. PLoS Computational Biology, 12 (4). ISSN 1553-734X

Wang, T and Ren, Z and Ding, Y and Fang, Z and Sun, Z and MacDonald, ML and Sweet, RA and Wang, J and Chen, W (2016) FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks. PLoS Computational Biology, 12 (2). ISSN 1553-734X

Dalziel, BD and Bjørnstad, ON and van Panhuis, WG and Burke, DS and Metcalf, CJE and Grenfell, BT (2016) Persistent Chaos of Measles Epidemics in the Prevaccination United States Caused by a Small Change in Seasonal Transmission Patterns. PLoS Computational Biology, 12 (2). ISSN 1553-734X

Donovan, RM and Tapia, JJ and Sullivan, DP and Faeder, JR and Murphy, RF and Dittrich, M and Zuckerman, DM (2016) Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. PLoS Computational Biology, 12 (2). ISSN 1553-734X

Lu, S and Lu, KN and Cheng, SY and Hu, B and Ma, X and Nystrom, N and Lu, X (2015) Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets. PLoS Computational Biology, 11 (8). ISSN 1553-734X

Ocker, GK and Litwin-Kumar, A and Doiron, B (2015) Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses. PLoS Computational Biology, 11 (8). ISSN 1553-734X

Ziraldo, C and Solovyev, A and Allegretti, A and Krishnan, S and Henzel, MK and Sowa, GA and Brienza, D and An, G and Mi, Q and Vodovotz, Y (2015) A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury. PLoS Computational Biology, 11 (6). ISSN 1553-734X

Brown, JW and Bullitt, E and Sriswasdi, S and Harper, S and Speicher, DW and McKnight, CJ (2015) The Physiological Molecular Shape of Spectrin: A Compact Supercoil Resembling a Chinese Finger Trap. PLoS Computational Biology, 11 (6). ISSN 1553-734X

Egan, P and Moore, J and Schunn, C and Cagan, J and LeDuc, P (2015) Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity. PLoS Computational Biology, 11 (4). ISSN 1553-734X

Zhou, P and Burton, SD and Snyder, AC and Smith, MA and Urban, NN and Kass, RE (2015) Establishing a Statistical Link between Network Oscillations and Neural Synchrony. PLoS Computational Biology, 11 (10). ISSN 1553-734X

Malkin, AD and Sheehan, RP and Mathew, S and Federspiel, WJ and Redl, H and Clermont, G (2015) A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis. PLoS Computational Biology, 11 (10). ISSN 1553-734X

Cheng, MH and Bahar, I (2014) Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle. PLoS Computational Biology, 10 (10). ISSN 1553-734X

General, IJ and Liu, Y and Blackburn, ME and Mao, W and Gierasch, LM and Bahar, I (2014) ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones. PLoS Computational Biology, 10 (5). ISSN 1553-734X

Hogg, JS and Harris, LA and Stover, LJ and Nair, NS and Faeder, JR (2014) Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems. PLoS Computational Biology, 10 (4). ISSN 1553-734X

Das, A and Gur, M and Cheng, MH and Jo, S and Bahar, I and Roux, B (2014) Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model. PLoS Computational Biology, 10 (4). ISSN 1553-734X

Erwin, GD and Oksenberg, N and Truty, RM and Kostka, D and Murphy, KK and Ahituv, N and Pollard, KS and Capra, JA (2014) Integrating Diverse Datasets Improves Developmental Enhancer Prediction. PLoS Computational Biology, 10 (6). ISSN 1553-734X

Parikh, AP and Curtis, RE and Kuhn, I and Becker-Weimann, S and Bissell, M and Xing, EP and Wu, W (2014) Network Analysis of Breast Cancer Progression and Reversal Using a Tree-Evolving Network Algorithm. PLoS Computational Biology, 10 (7). ISSN 1553-734X

Solovyev, A and Mi, Q and Tzen, YT and Brienza, D and Vodovotz, Y (2013) Hybrid Equation/Agent-Based Model of Ischemia-Induced Hyperemia and Pressure Ulcer Formation Predicts Greater Propensity to Ulcerate in Subjects with Spinal Cord Injury. PLoS Computational Biology, 9 (5). ISSN 1553-734X

Coronnello, C and Hartmaier, R and Arora, A and Huleihel, L and Pandit, KV and Bais, AS and Butterworth, M and Kaminski, N and Stormo, GD and Oesterreich, S and Benos, PV (2012) Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density. PLoS Computational Biology, 8 (12). ISSN 1553-734X

Kurkcuoglu, Z and Bakan, A and Kocaman, D and Bahar, I and Doruker, P (2012) Coupling between Catalytic Loop Motions and Enzyme Global Dynamics. PLoS Computational Biology, 8 (9). ISSN 1553-734X

Selivanov, VA and Cascante, M and Friedman, M and Schumaker, MF and Trucco, M and Votyakova, TV (2012) Multistationary and Oscillatory Modes of Free Radicals Generation by the Mitochondrial Respiratory Chain Revealed by a Bifurcation Analysis. PLoS Computational Biology, 8 (9). ISSN 1553-734X

Litwin-Kumar, A and Chacron, MJ and Doiron, B (2012) The Spatial Structure of Stimuli Shapes the Timescale of Correlations in Population Spiking Activity. PLoS Computational Biology, 8 (9). ISSN 1553-734X

Rosenbaum, R and Rubin, J and Doiron, B (2012) Short term synaptic depression imposes a frequency dependent filter on synaptic information transfer. PLoS Computational Biology, 8 (6). ISSN 1553-734X

Rho, Young-Ah and Prescott, Steven A. (2012) Identification of Molecular Pathologies Sufficient to Cause Neuropathic Excitability in Primary Somatosensory Afferents Using Dynamical Systems Theory. PLoS Computational Biology, 8 (5). e1002524 - e1002524.

Song, SOK and Hogg, J and Peng, ZY and Parker, R and Kellum, JA and Clermont, G (2012) Ensemble models of neutrophil trafficking in severe sepsis. PLoS Computational Biology, 8 (3). ISSN 1553-734X

Litwin-Kumar, A and Oswald, AMM and Urban, NN and Doiron, B (2011) Balanced synaptic input shapes the correlation between neural spike trains. PLoS Computational Biology, 7 (12). ISSN 1553-734X

Kilpatrick, ZP and Ermentrout, B (2011) Sparse gamma rhythms arising through clustering in adapting neuronal networks. PLoS Computational Biology, 7 (11). ISSN 1553-734X

Hayut, I and Fanselow, EE and Connors, BW and Golomb, D (2011) LTS and FS inhibitory interneurons, short-term synaptic plasticity, and cortical circuit dynamics. PLoS Computational Biology, 7 (10). ISSN 1553-734X

Doyon, Nicolas and Prescott, Steven A. and Castonguay, Annie and Godin, Antoine G. and Kröger, Helmut and De Koninck, Yves (2011) Efficacy of Synaptic Inhibition Depends on Multiple, Dynamically Interacting Mechanisms Implicated in Chloride Homeostasis. PLoS Computational Biology, 7 (9). e1002149 - e1002149.

Marcos, E and Crehuet, R and Bahar, I (2011) Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members. PLoS Computational Biology, 7 (9). ISSN 1553-734X

Rule, M and Stoffregen, M and Ermentrout, B (2011) A model for the origin and properties of flicker-induced geometric phosphenes. PLoS Computational Biology, 7 (9). ISSN 1553-734X

Selivanov, VA and Votyakova, TV and Pivtoraiko, VN and Zeak, J and Sukhomlin, T and Trucco, M and Roca, J and Cascante, M (2011) Reactive oxygen species production by forward and reverse electron fluxes in the mitochondrial respiratory chain. PLoS Computational Biology, 7 (3). ISSN 1553-734X

Chalancon, G and Kosloff, M and Osmanbeyoglu, HU and Saraswathi, S (2010) Plos computational biology conference postcards from ISMB 2010. PLoS Computational Biology, 6 (11). ISSN 1553-734X

Liu, Y and Gierasch, LM and Bahar, I (2010) Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs. PLoS Computational Biology, 6 (9). ISSN 1553-734X

Gai, Y and Doiron, B and Rinzel, J (2010) Slope-based stochastic resonance: How noise enables phasic neurons to encode slow signals. PLoS Computational Biology, 6 (6). 1 - 22. ISSN 1553-734X

Lezon, TR and Bahar, I (2010) Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology. PLoS Computational Biology, 6 (6). 1 - 12. ISSN 1553-734X

Marcos, E and Crehuet, R and Bahar, I (2010) On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm. PLoS Computational Biology, 6 (4). ISSN 1553-734X

Marella, S and Ermentrout, B (2010) Amplification of asynchronous inhibition-mediated synchronization by feedback in recurrent networks. PLoS Computational Biology, 6 (2). ISSN 1553-734X

Ekins, Sean and Kortagere, Sandhya and Iyer, Manisha and Reschly, Erica J. and Lill, Markus A. and Redinbo, Matthew R. and Krasowski, Matthew D. (2009) Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR. PLoS Computational Biology, 5 (12). e1000594 - e1000594.

Selivanov, VA and Votyakova, TV and Zeak, JA and Trucco, M and Roca, J and Cascante, M (2009) Bistability of mitochondrial respiration underlies paradoxical reactive oxygen species generation induced by anoxia. PLoS Computational Biology, 5 (12). ISSN 1553-734X

Ermentrout, B and Simons, DJ and Land, PW (2009) Subbarrel patterns in somatosensory cortical barrels can emerge from local dynamic instabilities. PLoS Computational Biology, 5 (10). ISSN 1553-734X

Lezon, TR and Sali, A and Bahar, I (2009) Global motions of the nuclear pore complex: Insights from elastic network models. PLoS Computational Biology, 5 (9). ISSN 1553-734X

Yang, Z and Májek, P and Bahar, I (2009) Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL. PLoS Computational Biology, 5 (4). ISSN 1553-734X

Barua, D and Faeder, JR and Haugh, JM (2009) A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases. PLoS Computational Biology, 5 (4). ISSN 1553-734X

Ly, C and Doiron, B (2009) Divisive Gain Modulation with Dynamic Stimuli in Integrate-and-Fire Neurons. PLoS Computational Biology, 5 (4). ISSN 1553-734X

Kim, M and Maly, IV (2009) Deterministic mechanical model of T-killer cell polarization reproduces the wandering of aim between simultaneously engaged targets. PLoS Computational Biology, 5 (1). ISSN 1553-734X

Camacho, CJ and Katsumata, Y and Ascherman, DP (2008) Structural and thermodynamic approach to peptide immunogenicity. PLoS Computational Biology, 4 (11). ISSN 1553-734X

Vazquez, A and De Menezes, MA and Barabási, AL and Oltvai, ZN (2008) Impact of limited solvent capacity on metabolic rate, enzyme activities, and metabolite concentrations of S. cerevisiae glycolysis. PLoS Computational Biology, 4 (10). ISSN 1553-734X

Vodovotz, Y and Csete, M and Bartels, J and Chang, S and An, G (2008) Translational systems biology of inflammation. PLoS Computational Biology, 4 (4). ISSN 1553-734X

Ernst, J and Beg, QK and Kay, KA and Balázsi, G and Oltvai, ZN and Bar-Joseph, Z (2008) A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Computational Biology, 4 (3). ISSN 1553-734X

Marino, S and Sud, D and Plessner, H and Lin, PL and Chan, J and Flynn, JAL and Kirschner, DE (2007) Differences in reactivation of tuberculosis induced from anti-tnf treatments are based on bioavailability in granulomatous tissue. PLoS Computational Biology, 3 (10). 1909 - 1924. ISSN 1553-734X

Chennubhotla, C and Bahar, I (2007) Erratum: Signal propagation in proteins and relation to equilibrium fluctuations (PLoS Computational Biology (2007) 3, 9, (e172) DOI: 10.1371/journal.pcbi.0030172)). PLoS Computational Biology, 3 (10). 2043 - ?. ISSN 1553-734X

Lee, J and Li, Z and Brower-Sinning, R and John, B (2007) Regulatory circuit of human microRNA biogenesis. PLoS Computational Biology, 3 (4). 721 - 732. ISSN 1553-734X

Mahony, S and Auron, PE and Benos, PV (2007) DNA familial binding profiles made easy: Comparison of various motif alignment and clustering strategies. PLoS Computational Biology, 3 (3). 0578 - 0591. ISSN 1553-734X

Zenker, S and Rubin, J and Clermont, G (2007) From inverse problems in mathematical physiology to quantitative differential diagnoses. PLoS Computational Biology, 3 (11). 2072 - 2086. ISSN 1553-734X

Azad, RK and Lawrence, JG (2005) Use of artificial genomes in assessing methods for atypical gene detection. PLoS Computational Biology, 1 (6). 0461 - 0473. ISSN 1553-734X