Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling

The influence of thermal signals during embryonic development on intrasexual and sexually dimorphic gene expression and circulating steroid hormones in American alligator hatchlings ( Alligator mississippiensis )

(2016) Jessica A. McCoy et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

A Novel Candidate Gene for Temperature-Dependent Sex Determination in the Common Snapping Turtle

(2016) Anthony L. Schroeder et al.   GENETICS

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

A Novel Candidate Gene for Temperature-Dependent Sex Determination in the Common Snapping Turtle

(2016) Anthony L. Schroeder et al.   GENETICS

Estrogen Receptor 1 (ESR1; ERα), not ESR2 (ERβ), Modulates Estrogen-Induced Sex Reversal in the American Alligator, a Species With Temperature-Dependent Sex Determination

(2015) Satomi Kohno et al.   ENDOCRINOLOGY

Sex reversal triggers the rapid transition from genetic to temperature-dependent sex

(2015) Clare E. Holleley et al.   NATURE

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ragout--a reference-assisted assembly tool for bacterial genomes

(2014) M. Kolmogorov et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes

(2014) Alexander Suh et al.   Genome Biology and Evolution

The Staurotypus Turtles and Aves Share the Same Origin of Sex Chromosomes but Evolved Different Types of Heterogametic Sex Determination

(2014) Taiki Kawagoshi et al.   PLoS One

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

(2014) R. E. Green et al.   SCIENCE

Complex evolutionary trajectories of sex chromosomes across bird taxa

(2014) Q. Zhou et al.   SCIENCE

HAL: a hierarchical format for storing and analyzing multiple genome alignments

(2013) Glenn Hickey et al.   BIOINFORMATICS

Differential Incubation Temperatures Result in Dimorphic DNA Methylation Patterning of the SOX9 and Aromatase Promoters in Gonads of Alligator (Alligator mississippiensis) Embryos1

(2013) Benjamin B. Parrott et al.   BIOLOGY OF REPRODUCTION

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K-T boundary in Madagascar

(2012) A. Crottini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

(2011) David Martin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SyMAP v3.4: a turnkey synteny system with application to plant genomes

(2011) Carol Soderlund et al.   NUCLEIC ACIDS RESEARCH

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

(2011) Jarrod A. Chapman et al.   PLoS One

MapMi: automated mapping of microRNA loci

(2010) Jose Afonso Guerra-Assuncao et al.   BMC BIOINFORMATICS

Genetic network underlying temperature-dependent sex determination is endogenously regulated by temperature in isolated cultured Trachemys scripta gonads

(2010) Christina M. Shoemaker-Daly et al.   DEVELOPMENTAL DYNAMICS

WNT4 is required for normal ovarian follicle development and female fertility

(2010) Alexandre Boyer et al.   FASEB JOURNAL

CCCTC-binding Factor Acts Upstream of FOXA1 and Demarcates the Genomic Response to Estrogen

(2010) Yu Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Potential Contributions of Heat Shock Proteins to Temperature-Dependent Sex Determination in the American Alligator

(2010) S. Kohno et al.   Sexual Development

Blurring the edges in vertebrate sex determination

(2009) Lindsey A Barske et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands

(2009) Willem-Jan Welboren et al.   EMBO JOURNAL

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

CCCTC-Binding Factor Confines the Distal Action of Estrogen Receptor

(2008) Chang S. Chan et al.   CANCER RESEARCH

Is regulation of aromatase expression in reptiles the key to understanding temperature-dependent sex determination?

(2008) Valentine A. Lance   Journal of Experimental Zoology Part A-Ecological Genetics and Physiology

Steroid signaling and temperature-dependent sex determination—Reviewing the evidence for early action of estrogen during ovarian determination in turtles

(2008) Mary Ramsey et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY