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1

Metastable Evolutionary Dynamics: Crossing Fitness Barriers or Escaping via Neutral Paths?

Erik van Nimwegen, James P. Crutchfield

Journal:

Bulletin of Mathematical Biology

Year:

2000

Language:

english

File:

PDF, 562 KB

english, 2000

2

Statistical Dynamics of the Royal Road Genetic Algorithm

Erik van Nimwegen, James P. Crutchfield, Melanie Mitchell

Journal:

Theoretical Computer Science

Year:

1999

Language:

english

File:

PDF, 635 KB

english, 1999

3

Photoconductive response of polycrystalline Cu0.5Ag0.5InSe2thin films

Erik Van Nimwegen, James P. Crutchfield

Journal:

Journal of Materials Science: Materials in Electronics

Year:

2001

Language:

english

File:

PDF, 391 KB

english, 2001

4

A meta-analysis of the cognitive and motivational effects of serious games.

Wouters, Pieter, van Nimwegen, Christof, van Oostendorp, Herre, van der Spek, Erik D.

Journal:

Journal of Educational Psychology

Year:

2013

Language:

english

File:

PDF, 200 KB

english, 2013

5

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Suzuki, Harukazu, Forrest, Alistair R R, van Nimwegen, Erik, Daub, Carsten O, Balwierz, Piotr J, Irvine, Katharine M, Lassmann, Timo, Ravasi, Timothy, Hasegawa, Yuki, de Hoon, Michiel J L

Journal:

Nature Genetics

Year:

2009

Language:

english

File:

PDF, 980 KB

english, 2009

6

Optimizing Epochal Evolutionary Search: Population-Size Dependent Theory

Erik Van Nimwegen, James P. Crutchfield

Journal:

Machine Learning

Year:

2001

Language:

english

File:

PDF, 391 KB

english, 2001

7

Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria

Galbusera, Luca, Bellement-Theroue, Gwendoline, Urchueguia, Arantxa, Julou, Thomas, van Nimwegen, Erik, Signore, Giovanni

Journal:

Year:

2020

File:

PDF, 3.44 MB

2020

8

Dynamics of One-pass Germinal Center Models: Implications for Affinity Maturation

Mihaela Oprea, Erik van Nimwegen, Alan S. Perelson

Journal:

Bulletin of Mathematical Biology

Year:

2000

Language:

english

File:

PDF, 320 KB

english, 2000

9

Optimizing epochal evolutionary search: population-size independent theory

Erik van Nimwegen, James P. Crutchfield

Journal:

Computer Methods in Applied Mechanics and Engineering

Year:

2000

Language:

english

File:

PDF, 324 KB

english, 2000

10

Finite populations induce metastability in evolutionary search

Erik van Nimwegen, James P Crutchfield, Melanie Mitchell

Journal:

Physics Letters A

Year:

1997

Language:

english

File:

PDF, 729 KB

english, 1997

11

Co-expression of FBN1 with mesenchyme-specific genes in mouse cell lines: implications for phenotypic variability in Marfan syndrome

Summers, Kim M, Raza, Sobia, van Nimwegen, Erik, Freeman, Thomas C, Hume, David A

Journal:

European Journal of Human Genetics

Year:

2010

Language:

english

File:

PDF, 369 KB

english, 2010

12

Transformation fingerprint: induced STAT3-C, v-Src and Ha-Ras cause small initial changes but similar established profiles in mRNA

Paz, Keren, Socci, Nicholas D, van Nimwegen, Erik, Viale, Agnes, Darnell, James E

Journal:

Year:

2004

Language:

english

File:

PDF, 229 KB

english, 2004

13

The types and prevalence of alternative splice forms

Mihaela Zavolan, Erik van Nimwegen

Journal:

Current Opinion in Structural Biology

Year:

2006

Language:

english

File:

PDF, 165 KB

english, 2006

14

The types and prevalence of alternative splice forms [Current Opinion in Structural Biology 2006, 16:362–367]

Mihaela Zavolan, Erik van Nimwegen

Journal:

Current Opinion in Structural Biology

Year:

2006

Language:

english

File:

PDF, 89 KB

english, 2006

15

Scaling laws in functional genome content across prokaryotic clades and lifestyles

Nacho Molina, Erik van Nimwegen

Journal:

Trends in Genetics

Year:

2009

Language:

english

File:

PDF, 726 KB

english, 2009

16

Scaling laws in the functional content of genomes

Erik van Nimwegen

Journal:

Trends in Genetics

Year:

2003

Language:

english

File:

PDF, 125 KB

english, 2003

17

Identification of clustered microRNAs using anab initioprediction method

Alain Sewer, Nicodème Paul, Pablo Landgraf, Alexei Aravin, Sébastien Pfeffer, Michael J Brownstein, Thomas Tuschl, Erik van Nimwegen, Mihaela Zavolan

Journal:

BMC Bioinformatics

Year:

2005

Language:

english

File:

PDF, 518 KB

english, 2005

18

Correction: Inference of miRNA targets using evolutionary conservation and pathway analysis

Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 139 KB

english, 2007

19

Inference of miRNA targets using evolutionary conservation and pathway analysis

Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 809 KB

english, 2007

20

Finding regulatory elements and regulatory motifs: a general probabilistic framework

Erik van Nimwegen

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 979 KB

english, 2007

21

Computational analysis of small RNA cloning data

Philipp Berninger, Dimos Gaidatzis, Erik van Nimwegen, Mihaela Zavolan

Journal:

Year:

2008

Language:

english

File:

PDF, 203 KB

english, 2008

22

The evolution of domain-content in bacterial genomes

Nacho Molina, Erik van Nimwegen

Journal:

Year:

2008

Language:

english

File:

PDF, 353 KB

english, 2008

23

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets

Khorshid, Mohsen, Hausser, Jean, Zavolan, Mihaela, van Nimwegen, Erik

Journal:

Year:

2013

Language:

english

File:

PDF, 758 KB

english, 2013

24

Sox4 Is a Master Regulator of Epithelial-Mesenchymal Transition by Controlling Ezh2 Expression and Epigenetic Reprogramming

Tiwari, Neha, Tiwari, Vijay K., Waldmeier, Lorenz, Balwierz, Piotr J., Arnold, Phil, Pachkov, Mikhail, Meyer-Schaller, Nathalie, Schübeler, Dirk, van Nimwegen, Erik, Christofori, Gerhard

Journal:

Year:

2013

Language:

english

File:

PDF, 4.41 MB

english, 2013

25

Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates ofE. coli

Niels Hofsteenge, Erik van Nimwegen, Olin K Silander

Journal:

BMC Microbiology

Year:

2013

Language:

english

File:

PDF, 297 KB

english, 2013

26

An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants

Vigano, Maria Alessandra, Ivanek, Robert, Balwierz, Piotr, Berninger, Philipp, van Nimwegen, Erik, Karjalainen, Klaus, Rolink, Antonius

Journal:

European Journal of Immunology

Year:

2014

Language:

english

File:

PDF, 3.02 MB

english, 2014

27

Neutral Evolution of Mutational Robustness

Erik van Nimwegen, James P. Crutchfield and Martijn Huynen

Journal:

Proceedings of the National Academy of Sciences

Year:

1999

Language:

english

File:

PDF, 1.17 MB

english, 1999

28

Absence of Interleukin-17 Receptor A Signaling Prevents Autoimmune Inflammation of the Joint and Leads to a Th2-like Phenotype in Collagen-Induced Arthritis

Corneth, Odilia B. J., Mus, Adriana M. C., Asmawidjaja, Patrick S., Klein Wolterink, Roel G. J., van Nimwegen, Menno, Brem, Maarten D., Hofman, Yara, Hendriks, Rudi W., Lubberts, Erik

Journal:

Arthritis & Rheumatology

Year:

2014

Language:

english

File:

PDF, 479 KB

english, 2014

29

Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells

Gruber, Andreas R., Martin, Georges, Müller, Philipp, Schmidt, Alexander, Gruber, Andreas J., Gumienny, Rafal, Mittal, Nitish, Jayachandran, Rajesh, Pieters, Jean, Keller, Walter, van Nimwegen, Erik,

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 1.09 MB

english, 2014

30

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

Burger, Lukas, van Nimwegen, Erik

Journal:

Molecular Systems Biology

Year:

2008

Language:

english

File:

PDF, 336 KB

english, 2008

31

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development

Schertel, Claus, Albarca, Monica, Rockel-Bauer, Claudia, Kelley, Nicholas W., Bischof, Johannes, Hens, Korneel, van Nimwegen, Erik, Basler, Konrad, Deplancke, Bart

Journal:

Genome Research

Year:

2015

Language:

english

File:

PDF, 4.48 MB

english, 2015

32

Quantifying the strength of miRNA–target interactions

Breda, Jeremie, Rzepiela, Andrzej J., Gumienny, Rafal, van Nimwegen, Erik, Zavolan, Mihaela

Journal:

Year:

2015

Language:

english

File:

PDF, 1.47 MB

english, 2015

33

Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli

Brewster, Robert C., Jones, Daniel L., Phillips, Rob, van Nimwegen, Erik

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 851 KB

english, 2012

34

SPA: A Probabilistic Algorithm for Spliced Alignment

van Nimwegen, Erik, Paul, Nicodeme, Sheridan, Robert, Zavolan, Mihaela

Journal:

Year:

2006

Language:

english

File:

PDF, 978 KB

english, 2006

35

Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability

ten Tusscher, Kirsten H., Hogeweg, Paulien, van Nimwegen, Erik

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.92 MB

english, 2011

36

Trade-Offs and Constraints in Allosteric Sensing

Martins, Bruno M.C., Swain, Peter S., van Nimwegen, Erik

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.22 MB

english, 2011

37

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

Burger, Lukas, van Nimwegen, Erik, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 748 KB

english, 2010

38

Cooperative Adaptive Responses in Gene Regulatory Networks with Many Degrees of Freedom

Inoue, Masayo, Kaneko, Kunihiko, van Nimwegen, Erik

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.11 MB

english, 2013

39

Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers

Ozonov, Evgeniy A., van Nimwegen, Erik, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.36 MB

english, 2013

40

A Simple Physical Model Predicts Small Exon Length Variations

Chern, Tzu-Ming, van Nimwegen, Erik, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, Zavolan, Mihaela

Journal:

Year:

2006

Language:

english

File:

PDF, 374 KB

english, 2006

41

PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny

Siddharthan, Rahul, Siggia, Eric D., van Nimwegen, Erik

Journal:

PLoS Computational Biology

Year:

2005

Language:

english

File:

PDF, 460 KB

english, 2005

42

ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data

Pemberton-Ross, Peter J., Pachkov, Mikhail, van Nimwegen, Erik

Journal:

Year:

2015

Language:

english

File:

PDF, 2.06 MB

english, 2015

43

Corrigendum to “Quantifying the strength of miRNA–target interactions” [Methods (2015) 90–99]

Breda, Jeremie, Rzepiela, Andrzej J., Gumienny, Rafal, van Nimwegen, Erik, Zavolan, Mihaela

Journal:

Year:

2016

Language:

english

File:

PDF, 445 KB

english, 2016

44

The Genomic Context and Corecruitment of SP1 Affect ERRα Coactivation by PGC-1α in Muscle Cells

Salatino, Silvia, Kupr, Barbara, Baresic, Mario, van Nimwegen, Erik, Handschin, Christoph

Journal:

Molecular Endocrinology

Year:

2016

Language:

english

File:

PDF, 3.37 MB

english, 2016

45

A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology

Vissers, Lisenka E.L.M., van Nimwegen, Kirsten J.M., Schieving, Jolanda H., Kamsteeg, Erik-Jan, Kleefstra, Tjitske, Yntema, Helger G., Pfundt, Rolph, van der Wilt, Gert Jan, Krabbenborg, Lotte, Brunne

Journal:

Genetics in Medicine

Year:

2017

Language:

english

File:

PDF, 588 KB

english, 2017

46

Corrigendum: DNA-binding factors shape the mouse methylome at distal regulatory regions

Stadler, Michael B., Murr, Rabih, Burger, Lukas, Ivanek, Robert, Lienert, Florian, Schöler, Anne, van Nimwegen, Erik, Wirbelauer, Christiane, Oakeley, Edward J., Gaidatzis, Dimos, Tiwari, Vijay K., Sc

Journal:

Year:

2012

Language:

english

File:

PDF, 36 KB

english, 2012

47

Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels

Tippmann, Sylvia C, Ivanek, Robert, Gaidatzis, Dimos, Schöler, Anne, Hoerner, Leslie, van Nimwegen, Erik, Stadler, Peter F, Stadler, Michael B, Schübeler, Dirk

Journal:

Molecular Systems Biology

Year:

2012

Language:

english

File:

PDF, 387 KB

english, 2012

48

Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software

Kaiser, Matthias, Jug, Florian, Julou, Thomas, Deshpande, Siddharth, Pfohl, Thomas, Silander, Olin K., Myers, Gene, van Nimwegen, Erik

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 1.76 MB

english, 2018

49

Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC

Gruber, Andreas J., Schmidt, Ralf, Ghosh, Souvik, Martin, Georges, Gruber, Andreas R., van Nimwegen, Erik, Zavolan, Mihaela

Journal:

Year:

2018

Language:

english

File:

PDF, 4.48 MB

english, 2018

50

Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8)

Tiwari, Neha, Meyer-Schaller, Nathalie, Arnold, Phil, Antoniadis, Helena, Pachkov, Mikhail, van Nimwegen, Erik, Christofori, Gerhard, Katz, Elad

Journal:

Year:

2013

Language:

english

File:

PDF, 1.83 MB

english, 2013

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