Multiscale Systems Biology and Modeling       

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Multiscale Systems Biology and Modeling - References


2016

Closed-Loop Brain Model of Neocortical Information-Based Exchange

J. Kozloski
Front Neuroanat10, 3, 2016

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin

R. Patro, R. Norel, R. J. Prill, J. Saez-Rodriguez, P. Lorenz, F. Steinbeck, B. Ziems, M. Lu?trek, N. Barbarini, A. Tiengo, R. Bellazzi, H. J. Thiesen, G. Stolovitzky, C. Kingsford
BMC Bioinformatics17, 155, 2016

Influence of metabolic dysfunction on cardiac mechanics in decompensated hypertrophy and heart failure

S. G. Tewari, S. M. Bugenhagen, K. C. Vinnakota, J. J. Rice, P. M. Janssen, D. A. Beard
J. Mol. Cell. Cardiol.94, 162--175, 2016

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis

D. P. Noren, B. L. Long, R. Norel, K. Rrhissorrakrai, K. Hess, C. W. Hu, A. J. Bisberg, A. Schultz, E. Engquist, L. Liu, X. Lin, G. M. Chen, H. Xie, G. A. Hunter, P. C. Boutros, O. Stepanov, T. Norman, S. H. Friend, G. Stolovitzky, S. Kornblau, A. A. Qutu
PLoS Comput. Biol. 12(6), e1004890, 2016

Self-reference in psychosis and depression: a language marker of illness

S. K. Fineberg, J. Leavitt, S. Deutsch-Link, S. Dealy, C. D. Landry, K. Pirruccio, S. Shea, S. Trent, G. Cecchi, P. R. Corlett
Psychol Med 46(12), 2605--2615, 2016
2015

Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge

M. Biehl, P. Sadowski, G. Bhanot, E. Bilal, A. Dayarian, P. Meyer, R. Norel, K. Rhrissorrakrai, M. D. Zeller, S. Hormoz
Bioinformatics 31(4), 453--461, 2015

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge

A. Dayarian, R. Romero, Z. Wang, M. Biehl, E. Bilal, S. Hormoz, P. Meyer, R. Norel, K. Rhrissorrakrai, G. Bhanot, F. Luo, A. L. Tarca
Bioinformatics 31(4), 462--470, 2015

Inter-species pathway perturbation prediction via data-driven detection of functional homology

C. Hafemeister, R. Romero, E. Bilal, P. Meyer, R. Norel, K. Rhrissorrakrai, R. Bonneau, A. L. Tarca
Bioinformatics 31(4), 501--508, 2015

Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets

S. Hormoz, G. Bhanot, M. Biehl, E. Bilal, P. Meyer, R. Norel, K. Rhrissorrakrai, A. Dayarian
Bioinformatics 31(4), 492--500, 2015

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge

K. Rhrissorrakrai, V. Belcastro, E. Bilal, R. Norel, C. Poussin, C. Mathis, R. H. Dulize, N. V. Ivanov, L. Alexopoulos, J. J. Rice, M. C. Peitsch, G. Stolovitzky, P. Meyer, J. Hoeng
Bioinformatics 31(4), 471--483, 2015

A crowd-sourcing approach for the construction of species-specific cell signaling networks

E. Bilal, T. Sakellaropoulos, I. N. Melas, D. E. Messinis, V. Belcastro, K. Rhrissorrakrai, P. Meyer, R. Norel, A. Iskandar, E. Blaese, J. J. Rice, M. C. Peitsch, J. Hoeng, G. Stolovitzky, L. G. Alexopoulos, C. Poussin
Bioinformatics 31(4), 484--491, 2015

Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression

R. Kuffner, N. Zach, R. Norel, J. Hawe, D. Schoenfeld, L. Wang, G. Li, L. Fang, L. Mackey, O. Hardiman, M. Cudkowicz, A. Sherman, G. Ertaylan, M. Grosse-Wentrup, T. Hothorn, J. van Ligtenberg, J. H. Macke, T. Meyer, B. Scholkopf, L. Tran, R. Vaughan, G. S
Nat. Biotechnol. 33(1), 51--57, 2015

Impaired IKs channel activation by Ca(2+)-dependent PKC shows correlation with emotion/arousal-triggered events in LQT1

J. O-Uchi, J. J. Rice, M. H. Ruwald, X. X. Parks, E. Ronzier, A. J. Moss, W. Zareba, C. M. Lopes
J. Mol. Cell. Cardiol.79, 203--211, 2015

DREAMTools: a Python package for scoring collaborative challenges

T. Cokelaer, M. Bansal, C. Bare, E. Bilal, B. M. Bot, E. Chaibub Neto, F. Eduati, A. de la Fuente, M. Gonen, S. M. Hill, B. Hoff, J. R. Karr, R. Kuffner, M. P. Menden, P. Meyer, R. Norel, A. Pratap, R. J. Prill, M. T. Weirauch, J. C. Costello, G. Stolovit
F1000Res4, 1030, 2015

A high-resolution computational model of the deforming human heart

V. Gurev, P. Pathmanathan, J. L. Fattebert, H. F. Wen, J. Magerlein, R. A. Gray, D. F. Richards, J. J. Rice
Biomech Model Mechanobiol 14(4), 829--849, 2015

Variable-Selection Emerges on Top in Empirical Comparison of Whole-Genome Complex-Trait Prediction Methods

D. C. Haws, I. Rish, S. Teyssedre, D. He, A. C. Lozano, P. Kambadur, Z. Karaman, L. Parida
PLoS ONE 10(10), e0138903, 2015

Verification of cardiac mechanics software: benchmark problems and solutions for testing active and passive material behaviour

S. Land, V. Gurev, S. Arens, C. M. Augustin, L. Baron, R. Blake, C. Bradley, S. Castro, A. Crozier, M. Favino, T. E. Fastl, T. Fritz, H. Gao, A. Gizzi, B. E. Griffith, D. E. Hurtado, R. Krause, X. Luo, M. P. Nash, S. Pezzuto, G. Plank, S. Rossi, D. Ruprec
Proc. Math. Phys. Eng. Sci. 471(2184), 20150641
2014

The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells

C. Poussin, C. Mathis, L. G. Alexopoulos, D. E. Messinis, R. H. Dulize, V. Belcastro, I. N. Melas, T. Sakellaropoulos, K. Rhrissorrakrai, E. Bilal, P. Meyer, M. Talikka, S. Boue, R. Norel, J. J. Rice, G. Stolovitzky, N. V. Ivanov, M. C. Peitsch, J. Hoeng
Sci Data1, 140009, 2014

Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages

B. Luan, C. Wang, A. Royyuru, G. Stolovitzky
Nanotechnology 25(26), 265101, 2014

Fabrication of sub-20 nm nanopore arrays in membranes with embedded metal electrodes at wafer scales

J. Bai, D. Wang, S. W. Nam, H. Peng, R. Bruce, L. Gignac, M. Brink, E. Kratschmer, S. Rossnagel, P. Waggoner, K. Reuter, C. Wang, Y. Astier, V. Balagurusamy, B. Luan, Y. Kwark, E. Joseph, M. Guillorn, S. Polonsky, A. Royyuru, S. Papa Rao, G. Stolovitzky
Nanoscale 6(15), 8900--8906, 2014

Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria

P. Meyer, G. Cecchi, G. Stolovitzky
BMC Syst Biol8, 131, 2014
2013

Schizophrenia as a network disease: disruption of emergent brain function in patients with auditory hallucinations

I. Rish, G. Cecchi, B. Thyreau, B. Thirion, M. Plaze, M. L. Paillere-Martinot, C. Martelli, J. L. Martinot, J. B. Poline
PLoS ONE 8(1), e50625, 2013

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

P. Meyer, G. Siwo, D. Zeevi, E. Sharon, R. Norel, E. Segal, G. Stolovitzky, G. Siwo, A. K. Rider, A. Tan, R. S. Pinapati, S. Emrich, N. Chawla, M. T. Ferdig, Y. A. Tung, Y. S. Chen, M. J. Chen, C. Y. Chen, J. M. Knight, S. M. Sahraeian, M. S. Esfahani, R.
Genome Res. 23(11), 1928--1937, 2013

Towards real-time simulation of cardiac electrophysiology in a human heart at high resolution

Richards, David F and Glosli, James N and Draeger, Erik W and Mirin, Arthur A and Chan, Bor and Fattebert, Jean-luc and Krauss, William D and Oppelstrup, Tomas and Butler, Chris J and Gunnels, John A and others
Computer methods in biomechanics and biomedical engineering 16(7), 802--805, Taylor & Francis, 2013

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge

A. L. Tarca, M. Lauria, M. Unger, E. Bilal, S. Boue, K. Kumar Dey, J. Hoeng, H. Koeppl, F. Martin, P. Meyer, P. Nandy, R. Norel, M. Peitsch, J. J. Rice, R. Romero, G. Stolovitzky, M. Talikka, Y. Xiang, C. Zechner, A. Veliz-Cuba, J. Song, H. Nguyen, M. Zel
Bioinformatics 29(22), 2892--2899, 2013
2012

Industrial methodology for process verification in research (IMPROVER): toward systems biology verification

P. Meyer, J. Hoeng, J. J. Rice, R. Norel, J. Sprengel, K. Stolle, T. Bonk, S. Corthesy, A. Royyuru, M. C. Peitsch, G. Stolovitzky
Bioinformatics 28(9), 1193--1201, 2012
 

In Silico Cardiac Risk Assessment in Patients With Long QT SyndromeType 1: Clinical Predictability of Cardiac Models

Ryan Hoefen, Matthias Reumann, Ilan Goldenberg, Arthur J Moss, O Jin, Yiping Gu, Scott McNitt, Wojciech Zareba, Christian Jons, Jorgen K Kanters, others
Journal of the American College of Cardiology 60(21), 2182--2191, Am Coll Cardio Found, 2012

Predictive dynamics of human pain perception

G. A. Cecchi, L. Huang, J. A. Hashmi, M. Baliki, M. V. Centeno, I. Rish, A. V. Apkarian
PLoS Comput. Biol. 8(10), e1002719, 2012
2011

Automated reconstruction of neural tissue and the role of large-scale simulation

J. Kozloski
Neuroinformatics 9(2-3), 133--142, 2011

Orthogonal recursive bisection as data decomposition strategy for massively parallel cardiac simulations

M. Reumann, B. G. Fitch, A. Rayshubskiy, M. C. Pitman, J. J. Rice
Biomed Tech (Berl) 56(3), 129--145, 2011

Verification of systems biology research in the age of collaborative competition

P. Meyer, L. G. Alexopoulos, T. Bonk, A. Califano, C. R. Cho, A. de la Fuente, D. de Graaf, A. J. Hartemink, J. Hoeng, N. V. Ivanov, H. Koeppl, R. Linding, D. Marbach, R. Norel, M. C. Peitsch, J. J. Rice, A. Royyuru, F. Schacherer, J. Sprengel, K. Stolle,
Nat. Biotechnol. 29(9), 811--815, 2011

An Ultrascalable Solution to Large-scale Neural Tissue Simulation

J. Kozloski, J. Wagner
Front Neuroinform5, 15, 2011
2010

A theory of loop formation and elimination by spike timing-dependent plasticity

J. Kozloski, G. A. Cecchi
Front Neural Circuits4, 7, 2010
2009

Strong scaling and speedup to 16,384 processors in cardiac electro-mechanical simulations

M. Reumann, B. G. Fitch, A. Rayshubskiy, D. U. Keller, G. Seemann, O. Dossel, M. C. Pitman, J. J. Rice
Conf Proc IEEE Eng Med Biol Soc2009, 2795--2798

Orthogonal recursive bisection data decomposition for high performance computing in cardiac model simulations: dependence on anatomical geometry

M. Reumann, B. G. Fitch, A. Rayshubskiy, D. U. Keller, G. Seemann, O. Dossel, M. C. Pitman, J. J. Rice
Conf Proc IEEE Eng Med Biol Soc2009, 2799--2802
2008

Spatially-compressed cardiac myofilament models generate hysteresis that is not found in real muscle

J. J. Rice, Y. Tu, C. Poggesi, P. P. De Tombe
Pac Symp Biocomput, 366--377, 2008

Approximate model of cooperative activation and crossbridge cycling in cardiac muscle using ordinary differential equations

J. J. Rice, F. Wang, D. M. Bers, P. P. de Tombe
Biophys. J. 95(5), 2368--2390, 2008

Large scale cardiac modeling on the Blue Gene supercomputer

M. Reumann, B. G. Fitch, A. Rayshubskiy, D. U. Keller, D. L. Weiss, G. Seemann, O. Dossel, M. C. Pitman, J. J. Rice
Conf Proc IEEE Eng Med Biol Soc2008, 577--580
2006

Magnitude and spatial orientation of the hydrophobic moments of multi-domain proteins

R. Zhou, A. Royyuru, P. Athma, F. Suits
Int J Bioinform Res Appl 2(2), 161--176, 2006
2005

Reconstructing biological networks using conditional correlation analysis

J. J. Rice, Y. Tu, G. Stolovitzky
Bioinformatics 21(6), 765--773, 2005

Lasting impressions: motifs in protein-protein maps may provide footprints of evolutionary events

J. J. Rice, A. Kershenbaum, G. Stolovitzky
Proc. Natl. Acad. Sci. U.S.A. 102(9), 3173--3174, 2005

A plausible model for the digital response of p53 to DNA damage

L. Ma, J. Wagner, J. J. Rice, W. Hu, A. J. Levine, G. A. Stolovitzky
Proc. Natl. Acad. Sci. U.S.A. 102(40), 14266--14271, 2005

Adaptive diagnosis in distributed systems

I. Rish, M. Brodie, S. Ma, N. Odintsova, A. Beygelzimer, G. Grabarnik, K. Hernandez
IEEE Trans Neural Netw 16(5), 1088--1109, 2005

p53-Mdm2 loop controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback

J. Wagner, L. Ma, J. J. Rice, W. Hu, A. J. Levine, G. A. Stolovitzky
Syst Biol (Stevenage) 152(3), 109--118, 2005