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1

Universally Sloppy Parameter Sensitivities in Systems Biology Models

Gutenkunst, Ryan N., Waterfall, Joshua J., Casey, Fergal P., Brown, Kevin S., Myers, Christopher R., Sethna, James P.

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 1.99 MB

english, 2007

2

An introduction to signal extraction in interferometric gravitational wave detectors

Black, Eric D., Gutenkunst, Ryan N.

Journal:

American Journal of Physics

Year:

2003

Language:

english

File:

PDF, 405 KB

english, 2003

3

Sloppiness, robustness, and evolvability in systems biology

Bryan C Daniels, Yan-Jiun Chen, James P Sethna, Ryan N Gutenkunst, Christopher R Myers

Journal:

Current Opinion in Biotechnology

Year:

2008

Language:

english

File:

PDF, 440 KB

english, 2008

4

Extracting Falsifiable Predictions from Sloppy Models

RYAN N. GUTENKUNST, FERGAL P. CASEY, JOSHUA J. WATERFALL, CHRISTOPHER R. MYERS, JAMES P. SETHNA

Journal:

Annals of the New York Academy of Sciences

Year:

2007

Language:

english

File:

PDF, 1.52 MB

english, 2007

5

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

Xu, Xun, Liu, Xin, Ge, Song, Jensen, Jeffrey D, Hu, Fengyi, Li, Xin, Dong, Yang, Gutenkunst, Ryan N, Fang, Lin, Huang, Lei, Li, Jingxiang, He, Weiming, Zhang, Guojie, Zheng, Xiaoming, Zhang, Fumin, Li

Journal:

Nature Biotechnology

Year:

2011

Language:

english

File:

PDF, 1.13 MB

english, 2011

6

Sloppy-Model Universality Class and the Vandermonde Matrix

Waterfall, Joshua J., Casey, Fergal P., Gutenkunst, Ryan N., Brown, Kevin S., Myers, Christopher R., Brouwer, Piet W., Elser, Veit, Sethna, James P.

Journal:

Physical Review Letters

Year:

2006

Language:

english

File:

PDF, 127 KB

english, 2006

7

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

Gutenkunst, Ryan N., Hernandez, Ryan D., Williamson, Scott H., Bustamante, Carlos D., McVean, Gil

Journal:

Year:

2009

Language:

english

File:

PDF, 414 KB

english, 2009

8

[IEEE 2015 IEEE Intelligent Vehicles Symposium (IV) - Seoul, South Korea (2015.6.28-2015.7.1)] 2015 IEEE Intelligent Vehicles Symposium (IV) - Torque-vectoring stability control of a four wheel drive electric vehicle

Jager, Benedict, Neugebauer, Peter, Kriesten, Reiner, Parspour, Nejila, Gutenkunst, Christian

Year:

2015

Language:

english

File:

PDF, 294 KB

english, 2015

9

Demographic history and rare allele sharing among human populations

Simon Gravel, Brenna M. Henn, Ryan N. Gutenkunst, Amit R. Indap, Gabor T. Marth, Andrew G. Clark, Fuli Yu, Richard A. Gibbs, The 1000 Genomes Project and Carlos D. Bustamante

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.18 MB

english, 2011

10

Genomic inferences of domestication events are corroborated by written records in Brassica rapa

Qi, Xinshuai, An, Hong, Ragsdale, Aaron, Hall, Tara E., Gutenkunst, Ryan N., Pires, J. Chris, Barker, Michael S.

Journal:

Molecular Ecology

Year:

2017

Language:

english

File:

PDF, 1.72 MB

english, 2017

11

Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors

Mannakee, Brian K, Balaji, Uthra, Witkiewicz, Agnieszka K, Gutenkunst, Ryan N, Knudsen, Erik S

Journal:

Year:

2018

Language:

english

File:

PDF, 879 KB

english, 2018

12

Approaches for the Homologation of Automated Driving

Düser, Tobias, Abdellatif, Houssem, Gutenkunst, Christian, Gnandt, Christian

Journal:

ATZelectronics worldwide

Year:

2019

Language:

english

File:

PDF, 796 KB

english, 2019

13

Low severity lignite liquefaction: temperature programming to 350 °C in an inorganic solvent system

Virgil I. Stenberg, V. Gutenkunst, J. Nowok, P.G. Sweeny

Journal:

Year:

1989

Language:

english

File:

PDF, 438 KB

english, 1989

14

Inferring resource distributions from Atlantic bluefin tuna movements: An analysis based on net displacement and length of track

Ryan Gutenkunst, Nathaniel Newlands, Molly Lutcavage, Leah Edelstein-Keshet

Journal:

Journal of Theoretical Biology

Year:

2007

Language:

english

File:

PDF, 567 KB

english, 2007

15

Temperature programmed aqueous liquefaction extended to supercritical conditions

P.G. Sweeny, V. Gutenkunst, J. Nowok, V.I. Stenberg

Journal:

Year:

1991

Language:

english

File:

PDF, 459 KB

english, 1991

16

RuleMonkey: software for stochastic simulation of rule-based models

Joshua Colvin, Michael I Monine, Ryan N Gutenkunst, William S Hlavacek, Daniel D Von Hoff, Richard G Posner

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 552 KB

english, 2010

17

Evidence for Increased Levels of Positive and Negative Selection on the X Chromosome versus Autosomes in Humans

Veeramah, K. R., Gutenkunst, R. N., Woerner, A. E., Watkins, J. C., Hammer, M. F.

Journal:

Molecular Biology and Evolution

Year:

2014

Language:

english

File:

PDF, 4.76 MB

english, 2014

18

Loss of amino-terminal acetylation suppresses a prion phenotype by modulating global protein folding

Holmes, William M., Mannakee, Brian K., Gutenkunst, Ryan N., Serio, Tricia R.

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 912 KB

english, 2014

19

Guidelines for visualizing and annotating rule-based models

Chylek, Lily A., Hu, Bin, Blinov, Michael L., Emonet, Thierry, Faeder, James R., Goldstein, Byron, Gutenkunst, Ryan N., Haugh, Jason M., Lipniacki, Tomasz, Posner, Richard G., Yang, Jin, Hlavacek, Wil

Journal:

Molecular BioSystems

Year:

2011

Language:

english

File:

PDF, 1.43 MB

english, 2011

20

Python Unleashed on Systems Biology

Myers, Christopher R., Gutenkunst, Ryan N., Sethna, James P.

Journal:

Computing in Science & Engineering

Year:

2007

Language:

english

File:

PDF, 172 KB

english, 2007

21

Demographic history and rare allele sharing among human populations

Gravel, S., Henn, B. M., Gutenkunst, R. N., Indap, A. R., Marth, G. T., Clark, A. G., Yu, F., Gibbs, R. A., Bustamante, C. D., Altshuler, D. L., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakrav

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 595 KB

english, 2011

22

Variational method for estimating the rate of convergence of Markov-chain Monte Carlo algorithms

Casey, Fergal P., Waterfall, Joshua J., Gutenkunst, Ryan N., Myers, Christopher R., Sethna, James P.

Journal:

Physical Review E

Year:

2008

Language:

english

File:

PDF, 355 KB

english, 2008

23

Testing whether Metazoan Tyrosine Loss Was Driven by Selection against Promiscuous Phosphorylation

Pandya, S., Struck, T. J., Mannakee, B. K., Paniscus, M., Gutenkunst, R. N.

Journal:

Molecular Biology and Evolution

Year:

2015

Language:

english

File:

PDF, 419 KB

english, 2015

24

Sampling strategies for frequency spectrum-based population genomic inference

Robinson, John D, Coffman, Alec J, Hickerson, Michael J, Gutenkunst, Ryan N

Journal:

BMC Evolutionary Biology

Year:

2014

Language:

english

File:

PDF, 705 KB

english, 2014

25

Targets of Balancing Selection in the Human Genome

Andres, A. M., Hubisz, M. J., Indap, A., Torgerson, D. G., Degenhardt, J. D., Boyko, A. R., Gutenkunst, R. N., White, T. J., Green, E. D., Bustamante, C. D., Clark, A. G., Nielsen, R.

Journal:

Molecular Biology and Evolution

Year:

2009

Language:

english

File:

PDF, 365 KB

english, 2009

26

Global distribution of genomic diversity underscores rich complex history of continental human populations

Auton, A., Bryc, K., Boyko, A. R., Lohmueller, K. E., Novembre, J., Reynolds, A., Indap, A., Wright, M. H., Degenhardt, J. D., Gutenkunst, R. N., King, K. S., Nelson, M. R., Bustamante, C. D.

Journal:

Genome Research

Year:

2009

Language:

english

File:

PDF, 930 KB

english, 2009

27

Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics

Smith, Amber M., Adler, Frederick R., McAuley, Julie L., Gutenkunst, Ryan N., Ribeiro, Ruy M., McCullers, Jonathan A., Perelson, Alan S., Antia, Rustom

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 764 KB

english, 2011

28

Kinetics of Coinfection with Influenza A Virus and Streptococcus pneumoniae

Smith, Amber M., Adler, Frederick R., Ribeiro, Ruy M., Gutenkunst, Ryan N., McAuley, Julie L., McCullers, Jonathan A., Perelson, Alan S., Grenfell, Bryan T.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.12 MB

english, 2013

29

Effect of Dedifferentiation on Time to Mutation Acquisition in Stem Cell-Driven Cancers

Jilkine, Alexandra, Gutenkunst, Ryan N., Wang, Edwin

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 949 KB

english, 2014

30

Darwinian and demographic forces affecting human protein coding genes

Nielsen, R., Hubisz, M. J., Hellmann, I., Torgerson, D., Andres, A. M., Albrechtsen, A., Gutenkunst, R., Adams, M. D., Cargill, M., Boyko, A., Indap, A., Bustamante, C. D., Clark, A. G.

Journal:

Genome Research

Year:

2009

Language:

english

File:

PDF, 455 KB

english, 2009

31

L3-subshell alignment of magnesium after electron capture by protons

A. Gutenkunst, S. Zuccatti, W. Mehlhorn

Year:

1994

Language:

english

File:

PDF, 448 KB

english, 1994

32

Computationally efficient composite likelihood statistics for demographic inference

Coffman, Alec J., Hsieh, PingHsun, Gravel, Simon, Gutenkunst, Ryan N.

Journal:

Molecular Biology and Evolution

Year:

2015

Language:

english

File:

PDF, 256 KB

english, 2015

33

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

Hsieh, PingHsun, Veeramah, Krishna R., Lachance, Joseph, Tishkoff, Sarah A., Wall, Jeffrey D., Hammer, Michael F., Gutenkunst, Ryan N.

Journal:

Genome Research

Year:

2016

Language:

english

File:

PDF, 901 KB

english, 2016

34

Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

Hsieh, PingHsun, Woerner, August E., Wall, Jeffrey D., Lachance, Joseph, Tishkoff, Sarah A., Gutenkunst, Ryan N., Hammer, Michael F.

Journal:

Genome Research

Year:

2016

Language:

english

File:

PDF, 721 KB

english, 2016

35

[IEEE 2015 IEEE Vehicle Power and Propulsion Conference (VPPC) - Montreal, QC, Canada (2015.10.19-2015.10.22)] 2015 IEEE Vehicle Power and Propulsion Conference (VPPC) - Novel Classification of Control Strategies for Hybrid Electric Vehicles

Chrenko, Daniela, Gan, Shiyu, Gutenkunst, Christian, Kriesten, Reiner, Le Moyne, Luis

Year:

2015

Language:

english

File:

PDF, 157 KB

english, 2015

36

[IEEE 2015 IEEE Vehicle Power and Propulsion Conference (VPPC) - Montreal, QC, Canada (2015.10.19-2015.10.22)] 2015 IEEE Vehicle Power and Propulsion Conference (VPPC) - Route Generating Algorithm Based on OpenSource Data to Predict the Energy Consumption of Different Vehicles

Gutenkunst, Christian, Chrenko, Daniela, Kriesten, Reiner, Neugebauer, Peter, Jager, Benedict, Giereth, Tom

Year:

2015

Language:

english

File:

PDF, 214 KB

english, 2015

37

Effects of lipoprotein(a) on mesangial cell proliferation and viability

Greiber, S., Kramer-Guth, A., Pavenstadt, H., Gutenkunst, M., Schollmeyer, P., Wanner, C.

Journal:

Nephrology Dialysis Transplantation

Year:

1996

Language:

english

File:

PDF, 3.61 MB

english, 1996

38

Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses

Edwards, Taylor, Tollis, Marc, Hsieh, PingHsun, Gutenkunst, Ryan N., Liu, Zhen, Kusumi, Kenro, Culver, Melanie, Murphy, Robert W.

Journal:

Ecology and Evolution

Year:

2016

Language:

english

File:

PDF, 1.91 MB

english, 2016

39

Triallelic Population Genomics for Inferring Correlated Fitness Effects of Same Site Nonsynonymous Mutations

Ragsdale, A. P., Coffman, A. J., Hsieh, P., Struck, T. J., Gutenkunst, R. N.

Journal:

Year:

2016

Language:

english

File:

PDF, 550 KB

english, 2016

40

Corrigendum: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

Hsieh, PingHsun, Woerner, August E., Wall, Jeffrey D., Lachance, Joseph, Tishkoff, Sarah A., Gutenkunst, Ryan N., Hammer, Michael F.

Journal:

Genome Research

Year:

2016

Language:

english

File:

PDF, 75 KB

english, 2016

41

Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast

Hermansen, Russell A., Mannakee, Brian K., Knecht, Wolfgang, Liberles, David A., Gutenkunst, Ryan N.

Journal:

BMC Evolutionary Biology

Year:

2015

Language:

english

File:

PDF, 1.54 MB

english, 2015

42

Chemical Abundances and Dust in Planetary Nebulae in the Galactic Bulge

Gutenkunst, S., Bernard‐Salas, J., Pottasch, S. R., Sloan, G. C., Houck, J. R.

Journal:

The Astrophysical Journal

Year:

2008

Language:

english

File:

PDF, 706 KB

english, 2008

43

Neon and Sulfur Abundances of Planetary Nebulae in the Magellanic Clouds

Bernard‐Salas, J., Pottasch, S. R., Gutenkunst, S., Morris, P. W., Houck, J. R.

Journal:

The Astrophysical Journal

Year:

2008

Language:

english

File:

PDF, 955 KB

english, 2008

44

Population Genomics of Daphnia pulex

Lynch, M., Gutenkunst, R., Ackerman, M., Spitze, K., Ye, Z., Maruki, T., Jia, Z.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.19 MB

english, 2016

45

Inferring Demographic History Using Two-Locus Statistics

Ragsdale, Aaron P., Gutenkunst, Ryan N.

Journal:

Year:

2017

Language:

english

File:

PDF, 750 KB

english, 2017

46

Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations

Hsieh, PingHsun, Hallmark, Brian, Watkins, Joseph, Karafet, Tatiana M., Osipova, Ludmila P., Gutenkunst, Ryan N., Hammer, Michael F.

Journal:

Molecular Biology and Evolution

Year:

2017

Language:

english

File:

PDF, 1.05 MB

english, 2017

47

A Biophysical Model of Cell Adhesion Mediated by Immunoadhesin Drugs and Antibodies

Gutenkunst, Ryan N., Coombs, Daniel, Starr, Toby, Dustin, Michael L., Goldstein, Byron, Chatenoud, Lucienne

Journal:

Year:

2011

Language:

english

File:

PDF, 255 KB

english, 2011

48

Daily Sampling of an HIV-1 Patient with Slowly Progressing Disease Displays Persistence of Multiple env Subpopulations Consistent with Neutrality

Skar, Helena, Gutenkunst, Ryan N., Wilbe Ramsay, Karin, Alaeus, Annette, Albert, Jan, Leitner, Thomas, Mammano, Fabrizio

Journal:

Year:

2011

Language:

english

File:

PDF, 374 KB

english, 2011

49

The impact of genome-wide association studies on biomedical research publications

Struck, Travis J., Mannakee, Brian K., Gutenkunst, Ryan N.

Journal:

Year:

2018

Language:

english

File:

PDF, 836 KB

english, 2018

50

Diffusion Approximations for Demographic Inference: DaDi

Gutenkunst, Ryan, Hernandez, Ryan, Williamson, Scott, Bustamante, Carlos

Journal:

Nature Precedings

Year:

2010

Language:

english

File:

PDF, 266 KB

english, 2010

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