A thousand empirical adaptive landscapes and their navigability

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Single-base pair differences in a shared motif determine differential Rhodopsin expression

(2015) J. Rister et al.   SCIENCE

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

(2014) Anders Bergström et al.   MOLECULAR BIOLOGY AND EVOLUTION

Conservation of trans-acting circuitry during mammalian regulatory evolution

(2014) Andrew B. Stergachis et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

(2014) Jason D Buenrostro et al.   NATURE BIOTECHNOLOGY

Evolutionary meandering of intermolecular interactions along the drift barrier

(2014) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Robustness and Evolvability of Transcription Factor Binding Sites

(2014) J. L. Payne et al.   SCIENCE

Biophysical Fitness Landscapes for Transcription Factor Binding Sites

(2014) Allan Haldane et al.   PLoS Computational Biology

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Quantitative analyses of empirical fitness landscapes

(2013) Ivan G Szendro et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Genome-wide inference of natural selection on human transcription factor binding sites

(2013) Leonardo Arbiza et al.   NATURE GENETICS

Protein-DNA binding: complexities and multi-protein codes

(2013) T. Siggers et al.   NUCLEIC ACIDS RESEARCH

Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution

(2013) A. I. Ramos et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fitness landscape for nucleosome positioning

(2013) D. Weghorn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive experimental fitness landscape and evolutionary network for small RNA

(2013) J. I. Jimenez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA-binding specificity changes in the evolution of forkhead transcription factors

(2013) S. Nakagawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription factor binding kinetics constrain noise suppression via negative feedback

(2013) Andreas Grönlund et al.   Nature Communications

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

(2012) W. W. Fisher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer

(2011) Christina I. Swanson et al.   CURRENT BIOLOGY

Jury remains out on simple models of transcription factor specificity

(2011) Quaid Morris et al.   NATURE BIOTECHNOLOGY

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity

(2011) D. S. Parker et al.   Science Signaling

Molecular mechanisms of epistasis within and between genes

(2011) Ben Lehner   TRENDS IN GENETICS

Evolutionary Accessibility of Mutational Pathways

(2011) Jasper Franke et al.   PLoS Computational Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape

(2010) Alexandre Dawid et al.   CHAOS

Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes

(2010) Frank J. Poelwijk et al.   JOURNAL OF THEORETICAL BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Specificity landscapes of DNA binding molecules elucidate biological function

(2010) C. D. Carlson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts

(2010) Ryan K. Shultzaberger et al.   PLoS Genetics

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

Analysis of a complete DNA-protein affinity landscape

(2009) W. Rowe et al.   Journal of the Royal Society Interface

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation

(2009) Ville Mustonen et al.   TRENDS IN GENETICS

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites

(2008) V. Mustonen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA