Santiago Schnell

Santiago Schnell

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Santiago Schnell

Publications by authors named "Santiago Schnell"

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Characteristic, completion or matching timescales? An analysis of temporary boundaries in enzyme kinetics.

J Theor Biol 2019 Nov 5;481:28-43. Epub 2019 Jan 5.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2019.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612542PMC
November 2019

Information processing by endoplasmic reticulum stress sensors.

J R Soc Interface 2019 Sep 11;16(158):20190288. Epub 2019 Sep 11.

Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1098/rsif.2019.0288DOI Listing
September 2019

Disorder Atlas: Web-based software for the proteome-based interpretation of intrinsic disorder predictions.

Comput Biol Chem 2019 Jul 13;83:107090. Epub 2019 Jul 13.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, MI, USA. Electronic address:

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http://dx.doi.org/10.1016/j.compbiolchem.2019.107090DOI Listing
July 2019

Enhancing career development of postdoctoral trainees: act locally and beyond.

J Physiol 2019 May 31;597(9):2317-2322. Epub 2019 Mar 31.

Office of Graduate & Postdoctoral Studies, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1113/JP277684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6487921PMC
May 2019

Dynamic Recruitment of Single RNAs to Processing Bodies Depends on RNA Functionality.

Mol Cell 2019 05 2;74(3):521-533.e6. Epub 2019 Apr 2.

Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765193017
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http://dx.doi.org/10.1016/j.molcel.2019.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499680PMC
May 2019

Clathrin Heavy Chain Knockdown Impacts CXCR4 Signaling and Post-translational Modification.

Front Cell Dev Biol 2019 8;7:77. Epub 2019 May 8.

Cellular and Molecular Biology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, United States.

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http://dx.doi.org/10.3389/fcell.2019.00077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6518350PMC
May 2019

On the Need to Develop Guidelines for Characterizing and Reporting Intrinsic Disorder in Proteins.

Proteomics 2019 Mar 1;19(6):e1800415. Epub 2019 Mar 1.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA.

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http://dx.doi.org/10.1002/pmic.201800415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6571172PMC
March 2019

"Reproducible" Research in Mathematical Sciences Requires Changes in our Peer Review Culture and Modernization of our Current Publication Approach.

Authors:
Santiago Schnell

Bull Math Biol 2018 12 19;80(12):3095-3105. Epub 2018 Sep 19.

Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.

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http://dx.doi.org/10.1007/s11538-018-0500-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240027PMC
December 2018

Phase-plane geometries in coupled enzyme assays.

Math Biosci 2018 12 24;306:126-135. Epub 2018 Sep 24.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.mbs.2018.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6476317PMC
December 2018

A Kinetic Analysis of Coupled (or Auxiliary) Enzyme Reactions.

Bull Math Biol 2018 12 4;80(12):3154-3183. Epub 2018 Oct 4.

Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.

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http://dx.doi.org/10.1007/s11538-018-0513-4DOI Listing
December 2018

A theory of reactant-stationary kinetics for a mechanism of zymogen activation.

Biophys Chem 2018 11 23;242:34-44. Epub 2018 Aug 23.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bpc.2018.08.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532997PMC
November 2018

How to design an optimal sensor network for the unfolded protein response.

Mol Biol Cell 2018 Sep 26:mbcE18010060. Epub 2018 Sep 26.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, 1137 E. Catherine St., Ann Arbor, MI 48109-5622, USA.

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http://dx.doi.org/10.1091/mbc.E18-01-0060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333173PMC
September 2018

Predicting neuroblastoma using developmental signals and a logic-based model.

Biophys Chem 2018 07 30;238:30-38. Epub 2018 Apr 30.

Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Anatomy and Cell Biology, School of Medicine, University of Kansas, Kansas City, KS 66160, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bpc.2018.04.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6016551PMC
July 2018

Do Cellular Condensates Accelerate Biochemical Reactions? Lessons from Microdroplet Chemistry.

Biophys J 2018 07;115(1):3-8

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, Michigan. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2018.05.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035290PMC
July 2018

Radial WNT5A-Guided Post-mitotic Filopodial Pathfinding Is Critical for Midgut Tube Elongation.

Dev Cell 2018 07;46(2):173-188.e3

Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109-2200, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2018.06.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6084452PMC
July 2018

Inferring Intracellular Signal Transduction Circuitry from Molecular Perturbation Experiments.

Bull Math Biol 2018 05 28;80(5):1310-1344. Epub 2017 Apr 28.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1007/s11538-017-0270-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5660674PMC
May 2018

On the origin of non-membrane-bound organelles, and their physiological function.

J Theor Biol 2017 12 6;434:42-49. Epub 2017 Apr 6.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI 48105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2017.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630510PMC
December 2017

Globalization and changing trends of biomedical research output.

JCI Insight 2017 Jun 15;2(12). Epub 2017 Jun 15.

Departments of Molecular and Integrative Physiology.

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http://dx.doi.org/10.1172/jci.insight.95206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5470885PMC
June 2017

Approaches for the estimation of timescales in nonlinear dynamical systems: Timescale separation in enzyme kinetics as a case study.

Math Biosci 2017 05 6;287:122-129. Epub 2016 Sep 6.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI 48105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.mbs.2016.09.001DOI Listing
May 2017

On the validity and errors of the pseudo-first-order kinetics in ligand-receptor binding.

Math Biosci 2017 05 28;287:3-11. Epub 2016 Sep 28.

Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI 48105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.mbs.2016.09.010DOI Listing
May 2017

The importance of accurately correcting for the natural abundance of stable isotopes.

Anal Biochem 2017 03 11;520:27-43. Epub 2017 Jan 11.

Department of Molecular & Integrative Physiology, Department of Computational Medicine & Bioinformatics and Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ab.2016.12.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343595PMC
March 2017

On the estimation errors of K and V from time-course experiments using the Michaelis-Menten equation.

Biophys Chem 2016 Dec 16;219:17-27. Epub 2016 Sep 16.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI 48105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bpc.2016.09.004DOI Listing
December 2016

Estimation of the lag time in a subsequent monomer addition model for fibril elongation.

Phys Chem Chem Phys 2016 Aug;18(31):21259-68

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. and Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA and Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI 48105, USA.

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http://dx.doi.org/10.1039/c5cp07845hDOI Listing
August 2016

Quantitative proteome-based guidelines for intrinsic disorder characterization.

Biophys Chem 2016 06 5;213:6-16. Epub 2016 Apr 5.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, MI, USA; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bpc.2016.03.005DOI Listing
June 2016

A collection of intrinsic disorder characterizations from eukaryotic proteomes.

Sci Data 2016 06 21;3:160045. Epub 2016 Jun 21.

Department of Molecular &Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan 48109-0622, USA.

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http://dx.doi.org/10.1038/sdata.2016.45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915274PMC
June 2016

Villification in the mouse: Bmp signals control intestinal villus patterning.

Development 2016 Feb 31;143(3):427-36. Epub 2015 Dec 31.

Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA

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http://dx.doi.org/10.1242/dev.130112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760312PMC
February 2016

A computational approach to studying ageing at the individual level.

Proc Biol Sci 2016 Feb;283(1824)

Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA

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http://dx.doi.org/10.1098/rspb.2015.2346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760160PMC
February 2016

Ten Simple Rules for a Computational Biologist's Laboratory Notebook.

Authors:
Santiago Schnell

PLoS Comput Biol 2015 Sep 10;11(9):e1004385. Epub 2015 Sep 10.

Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4565690PMC
September 2015

Evidence for Residual and Partly Reparable Insulin Secretory Function and Maintained β-Cell Gene Expression in Islets From Patients With Type 1 Diabetes.

Diabetes 2015 Jul;64(7):2335-7

Department of Molecular & Integrative Physiology, Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI.

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http://dx.doi.org/10.2337/db15-0434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477347PMC
July 2015

Competitive inhibition reaction mechanisms for the two-step model of protein aggregation.

Biophys Chem 2014 Sep-Oct;193-194:9-19. Epub 2014 Jul 5.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI 48105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bpc.2014.06.006DOI Listing
May 2015

Competitive inhibition reaction mechanisms for the two-step model of protein aggregation.

Biophys Chem 2014 Sep-Oct;193-194:9-19. Epub 2014 Jul 5.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI 48105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bpc.2014.06.006DOI Listing
May 2015

Molecular aspects of pancreatic beta cell failure and diabetes.

Mol Aspects Med 2015 Apr 14;42:1-2. Epub 2015 Jan 14.

Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, MI 48105, USA.

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http://dx.doi.org/10.1016/j.mam.2015.01.002DOI Listing
April 2015

Development, growth and maintenance of β-cell mass: models are also part of the story.

Mol Aspects Med 2015 Apr 23;42:78-90. Epub 2015 Feb 23.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan 48105, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48105, USA; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, Michigan 48105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.mam.2015.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404203PMC
April 2015

Optimal experimental design to estimate statistically significant periods of oscillations in time course data.

PLoS One 2014 3;9(4):e93826. Epub 2014 Apr 3.

Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Department for Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093826PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974819PMC
January 2015

Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study.

Comput Biol Chem 2014 12 21;53PB:242-250. Epub 2014 Sep 21.

Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA. Electronic address:

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http://dx.doi.org/10.1016/j.compbiolchem.2014.09.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254655PMC
December 2014

Connecting the dots: the effects of macromolecular crowding on cell physiology.

Biophys J 2014 Dec;107(12):2761-2766

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, Michigan. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2014.10.051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4269789PMC
December 2014

Inferring the Effects of Honokiol on the Notch Signaling Pathway in SW480 Colon Cancer Cells.

Cancer Inform 2014 13;13(Suppl 5):1-12. Epub 2014 Oct 13.

Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA. ; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA. ; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI, USA.

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http://dx.doi.org/10.4137/CIN.S14060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4218690PMC
November 2014

Surveying the floodgates: estimating protein flux into the endoplasmic reticulum lumen in Saccharomyces cerevisiae.

Front Physiol 2014 13;5:444. Epub 2014 Nov 13.

Department of Molecular & Integrative Physiology, University of Michigan Medical School Ann Arbor, MI, USA ; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School Ann Arbor, MI, USA ; Brehm Center for Diabetes Research, University of Michigan Medical School Ann Arbor, MI, USA.

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http://dx.doi.org/10.3389/fphys.2014.00444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230051PMC
November 2014

Unravelling the impact of obstacles in diffusion and kinetics of an enzyme catalysed reaction.

Phys Chem Chem Phys 2014 Mar;16(10):4492-503

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1039/c3cp52417eDOI Listing
March 2014

Unraveling intestinal stem cell behavior with models of crypt dynamics.

Integr Biol (Camb) 2014 Mar 30;6(3):243-57. Epub 2014 Jan 30.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA.

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http://dx.doi.org/10.1039/c3ib40163dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4007491PMC
March 2014

Validity of the Michaelis-Menten equation--steady-state or reactant stationary assumption: that is the question.

Authors:
Santiago Schnell

FEBS J 2014 Jan 18;281(2):464-72. Epub 2013 Nov 18.

Departments of Molecular & Integrative Physiology and Computational Medicine & Bioinformatics, Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1111/febs.12564DOI Listing
January 2014

Single-molecule enzymology à la Michaelis-Menten.

FEBS J 2014 Jan 2;281(2):518-30. Epub 2014 Jan 2.

School of Biological Sciences and SynthSys, University of Edinburgh, UK.

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http://dx.doi.org/10.1111/febs.12663DOI Listing
January 2014

Network representations and methods for the analysis of chemical and biochemical pathways.

Mol Biosyst 2013 Sep;9(9):2189-200

Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center and Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

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http://dx.doi.org/10.1039/c3mb70052fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755892PMC
September 2013

Circadian rhythms regulate amelogenesis.

Bone 2013 Jul 26;55(1):158-65. Epub 2013 Feb 26.

Department of Orthodontics and Pediatric Dentistry, School of Dentistry, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1016/j.bone.2013.02.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650122PMC
July 2013

Follow-the-leader cell migration requires biased cell-cell contact and local microenvironmental signals.

Phys Biol 2013 Jun 4;10(3):035003. Epub 2013 Jun 4.

Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1088/1478-3975/10/3/035003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3756809PMC
June 2013

Autoimmunity treatment using pMHC-NP-based therapy: designing nanoparticle treatment of autoimmunity with quantitative biology.

Immunol Cell Biol 2013 May 23;91(5):333-4. Epub 2013 Apr 23.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1038/icb.2013.20DOI Listing
May 2013

Network motifs provide signatures that characterize metabolism.

Mol Biosyst 2013 Mar 4;9(3):352-60. Epub 2013 Jan 4.

Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, USA.

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http://dx.doi.org/10.1039/c2mb25346aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619197PMC
March 2013

Unraveling the complex regulatory relationships between metabolism and signal transduction in cancer.

Adv Exp Med Biol 2012 ;736:179-89

Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1007/978-1-4419-7210-1_9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669218PMC
January 2013

More than Skew: Asymmetric Wave Propagation in a Reaction-Diffusion-Convection System.

Biomath (Sofia) 2013;2(1)

Department of Molecular & Integrative Physiology, Department of Computational Medicine & Bioinformatics and Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, Michigan, USA.

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http://dx.doi.org/10.11145/j.biomath.2013.03.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670241PMC
January 2013

Logic-based models in systems biology: a predictive and parameter-free network analysis method.

Integr Biol (Camb) 2012 Nov;4(11):1323-37

Center for Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1039/c2ib20193cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612358PMC
November 2012

Hedgehog-responsive mesenchymal clusters direct patterning and emergence of intestinal villi.

Proc Natl Acad Sci U S A 2012 Sep 10;109(39):15817-22. Epub 2012 Sep 10.

Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1073/pnas.1205669109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465418PMC
September 2012

Computational modelling of cell chain migration reveals mechanisms that sustain follow-the-leader behaviour.

J R Soc Interface 2012 Jul 4;9(72):1576-88. Epub 2012 Jan 4.

Department of Molecular and Integrative Physiology and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1098/rsif.2011.0726DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367809PMC
July 2012

A graphical user interface for a method to infer kinetics and network architecture (MIKANA).

PLoS One 2011 11;6(11):e27534. Epub 2011 Nov 11.

Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027534PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3214083PMC
April 2012

Molecular and circadian controls of ameloblasts.

Eur J Oral Sci 2011 Dec;119 Suppl 1:35-40

Department of Orthodontics and Pediatric Medicine, Center for Computational Medicine and Bioinformatics, University of Michigan Schools of Dentistry and Medicine, Ann Arbor, MI 48109, USA.

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http://deepblue.lib.umich.edu/bitstream/handle/2027.42/90102
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http://doi.wiley.com/10.1111/j.1600-0722.2011.00918.x
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http://dx.doi.org/10.1111/j.1600-0722.2011.00918.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516856PMC
December 2011

Macroscopic simulations of microtubule dynamics predict two steady-state processes governing array morphology.

Comput Biol Chem 2011 Oct 30;35(5):269-81. Epub 2011 Jun 30.

Department of Molecular and Integrative Physiology, Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI 48105, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2011.06.002DOI Listing
October 2011

Expression of clock proteins in developing tooth.

Gene Expr Patterns 2011 Mar-Apr;11(3-4):202-6. Epub 2010 Dec 13.

Department of Orthodontics and Pediatric Dentistry, School of Dentistry, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1016/j.gep.2010.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3073654PMC
July 2011

A model of threshold behavior reveals rescue mechanisms of bystander proteins in conformational diseases.

Biophys J 2011 Apr;100(8):1864-73

Center for Computational Medicine & Bioinformatics, Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, Michigan, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S00063495110031
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http://dx.doi.org/10.1016/j.bpj.2011.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077688PMC
April 2011

Stability of open pathways.

Math Biosci 2010 Dec 26;228(2):147-52. Epub 2010 Sep 26.

Integrated Mathematical Oncology, H. Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA.

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http://dx.doi.org/10.1016/j.mbs.2010.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004284PMC
December 2010

The intranuclear environment.

Methods Mol Biol 2008 ;463:3-19

Indiana University School of Informatics and Biocomplexity Institute, Bloomington, IN, USA.

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http://dx.doi.org/10.1007/978-1-59745-406-3_1DOI Listing
September 2010

Enzyme catalyzed reactions: from experiment to computational mechanism reconstruction.

Comput Biol Chem 2010 Feb 31;34(1):11-8. Epub 2009 Oct 31.

Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, MN 55455, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2009.10.007DOI Listing
February 2010

A model of the unfolded protein response: pancreatic beta-cell as a case study.

Authors:
Santiago Schnell

Cell Physiol Biochem 2009 6;23(4-6):233-44. Epub 2009 May 6.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109-2218, USA.

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http://dx.doi.org/10.1159/000218170DOI Listing
August 2009

Should digestion assays be used to estimate persistence of potential allergens in tests for safety of novel food proteins?

Clin Mol Allergy 2009 Jan 15;7. Epub 2009 Jan 15.

Department of Molecular & Integrative Physiology, and Center for Computational Medicine & Biology, University of Michigan Medical School, 100 Washtenaw Avenue, Palmer Commons 2017, Ann Arbor, MI 48109-2218, USA.

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http://clinicalmolecularallergy.biomedcentral.com/articles/1
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http://dx.doi.org/10.1186/1476-7961-7-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632610PMC
January 2009

Modelling reaction kinetics inside cells.

Essays Biochem 2008 ;45:41-56

Institute for Mathematical Sciences, Imperial College, London, U.K.

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http://dx.doi.org/10.1042/BSE0450041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737326PMC
December 2008

Reactant stationary approximation in enzyme kinetics.

J Phys Chem A 2008 Sep 20;112(37):8654-8. Epub 2008 Aug 20.

Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, USA.

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http://dx.doi.org/10.1021/jp8026226DOI Listing
September 2008

Multiscale modeling of developmental systems. Introduction.

Curr Top Dev Biol 2008 ;81:xvii-xxv

Indiana University School of Informatics and Biocomplexity Institute, 1900 East Tenth Street, Eigenmann Hall 906, Bloomington, Indiana 47406.

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http://dx.doi.org/10.1016/S0070-2153(07)81018-0DOI Listing
January 2008

Mathematical models for somite formation.

Curr Top Dev Biol 2008 ;81:183-203

Centre for Mathematical Biology, Mathematical Institute, University of Oxford, 24-29 St. Giles, Oxford OX1 3LB, United Kingdom.

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http://dx.doi.org/10.1016/S0070-2153(07)81006-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754719PMC
January 2008

Coordinated action of N-CAM, N-cadherin, EphA4, and ephrinB2 translates genetic prepatterns into structure during somitogenesis in chick.

Curr Top Dev Biol 2008 ;81:205-47

Biocomplexity Institute and Department of Physics, 727 East Third Street, Indiana University, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1016/S0070-2153(07)81007-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556964PMC
January 2008

Can tissue surface tension drive somite formation?

Dev Biol 2007 Jul 3;307(2):248-57. Epub 2007 May 3.

Complex Systems Group, Indiana University School of Informatics and Biocomplexity Institute, Eigenmann Hall 906, 1900 East Tenth Street, Bloomington, IN 47406, USA.

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http://dx.doi.org/10.1016/j.ydbio.2007.04.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1992446PMC
July 2007

Is the intrinsic disorder of proteins the cause of the scale-free architecture of protein-protein interaction networks?

Proteomics 2007 Mar;7(6):961-4

Complex Systems Group, Indiana University School of Informatics, Bloomington, IN 47406, USA.

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http://dx.doi.org/10.1002/pmic.200600455DOI Listing
March 2007

Reconstructing biochemical pathways from time course data.

Proteomics 2007 Mar;7(6):828-38

Indiana University School of Informatics and Biocomplexity Institute, Bloomington, IN 47406, USA.

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http://dx.doi.org/10.1002/pmic.200600428DOI Listing
March 2007

A test for measuring the effects of enzyme inactivation.

Biophys Chem 2007 Feb 6;125(2-3):269-74. Epub 2006 Sep 6.

Complex Systems Group, Indiana University School of Informatics, 1900 East Tenth Street, Bloomington, IN 47406, USA.

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http://dx.doi.org/10.1016/j.bpc.2006.08.010DOI Listing
February 2007

The effects of time delays in a phosphorylation-dephosphorylation pathway.

Biophys Chem 2007 Feb 2;125(2-3):286-97. Epub 2006 Oct 2.

Complex Systems Group, Indiana University School of Informatics and Biocomplexity Institute, 1900, East Tenth Street, Bloomington, IN 47406, USA.

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http://dx.doi.org/10.1016/j.bpc.2006.09.001DOI Listing
February 2007

Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map.

Comput Biol Chem 2006 Aug 22;30(4):241-8. Epub 2006 Jun 22.

Indiana University School of Informatics, 1900 East Tenth Street, Bloomington, IN 47406, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2006.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1992444PMC
August 2006

How reaction kinetics with time-dependent rate coefficients differs from generalized mass action.

Chemphyschem 2006 Jul;7(7):1422-4

Indiana University School of Informatics and Biocomplexity Institute, Eigenmann Hall 906, 1900 East Tenth Street, Bloomington, IN 47406, USA.

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http://doi.wiley.com/10.1002/cphc.200600081
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http://dx.doi.org/10.1002/cphc.200600081DOI Listing
July 2006

Why substrate depletion has apparent first-order kinetics in enzymatic digestion.

Comput Biol Chem 2006 Jun 2;30(3):209-14. Epub 2006 May 2.

Indiana University School of Informatics and Biocomplexity Institute, 1900 East Tenth Street, Bloomington, IN 47406, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2006.03.003DOI Listing
June 2006

A multiscale mathematical model of cancer, and its use in analyzing irradiation therapies.

Theor Biol Med Model 2006 Feb 10;3. Epub 2006 Feb 10.

Institute for Theoretical Medicine and Clinical Pharmacology Department, Faculty of Medicine R.T.H Laennec, University of Lyon, Paradin St., P.O.B 8071, 69376 Lyon Cedex 08, France.

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http://dx.doi.org/10.1186/1742-4682-3-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1388194PMC
February 2006

The mechanism distinguishability problem in biochemical kinetics: the single-enzyme, single-substrate reaction as a case study.

C R Biol 2006 Jan 19;329(1):51-61. Epub 2005 Oct 19.

Centre for Mathematical Biology, Mathematical Institute, 24-29 St Giles', Oxford OX1 3LB, UK.

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http://dx.doi.org/10.1016/j.crvi.2005.09.005DOI Listing
January 2006

Bulletin of mathematical biology-facts, figures and comparisons.

Bull Math Biol 2004 Jul;66(4):595-603

Centre for Mathematical Biology, Mathematical Institute, 24-29 St Giles', Oxford OX1 3LB, UK.

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http://dx.doi.org/10.1016/j.bulm.2004.03.003DOI Listing
July 2004

Models for pattern formation in somitogenesis: a marriage of cellular and molecular biology.

C R Biol 2002 Mar;325(3):179-89

Centre for Mathematical Biology, Mathematical Institute, 24-29 St Giles', Oxford OX1 3LB, UK.

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March 2002