Network of epistatic interactions within a yeast snoRNA

The fitness landscape of a tRNA gene

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Mutational interference mapping experiment (MIME) for studying RNA structure and function

(2015) Redmond P Smyth et al.   NATURE METHODS

Pervasive degeneracy and epistasis in a protein-protein interface

(2015) A. I. Podgornaia et al.   SCIENCE

A Systematic Survey of an Intragenic Epistatic Landscape

(2014) Claudia Bank et al.   MOLECULAR BIOLOGY AND EVOLUTION

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

Inferring fitness landscapes by regression produces biased estimates of epistasis

(2014) J. Otwinowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II

(2013) Hannes Braberg et al.   CELL

Genotype to Phenotype Mapping and the Fitness Landscape of the E. coli lac Promoter

(2013) Jakub Otwinowski et al.   PLoS One

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

(2011) Wiebke Wlotzka et al.   EMBO JOURNAL

A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

(2011) Trevor Hinkley et al.   NATURE GENETICS

The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing

(2011) Laura M. Dutca et al.   NUCLEIC ACIDS RESEARCH

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Molecular mechanisms of epistasis within and between genes

(2011) Ben Lehner   TRENDS IN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness

(2010) Margarita V. Meer et al.   NATURE

Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

(2010) Xionglei He et al.   NATURE GENETICS

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Fitness and its role in evolutionary genetics

(2009) H. Allen Orr   NATURE REVIEWS GENETICS

Compensatory mutations are repeatable and clustered within proteins

(2009) B. H. Davis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS