Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data

(2014) Yaron Orenstein et al.   NUCLEIC ACIDS RESEARCH

Spdef Null Mice Lack Conjunctival Goblet Cells and Provide a Model of Dry Eye

(2013) Christina K. Marko et al.   AMERICAN JOURNAL OF PATHOLOGY

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

The diversity of zinc-finger genes on human chromosome 19 provides an evolutionary mechanism for defense against inherited endogenous retroviruses

(2013) S Lukic et al.   CELL DEATH AND DIFFERENTIATION

Brk regulates wing disc growth in part via repression of Myc expression

(2013) Nikolaos Doumpas et al.   EMBO REPORTS

Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

(2013) M. S. Enuameh et al.   GENOME RESEARCH

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He et al.   NATURE METHODS

Transcriptional Networks Controlling the Cell Cycle

(2013) Martin Bonke et al.   G3-Genes Genomes Genetics

Intestinal stem cell function in Drosophila and mice

(2012) Huaqi Jiang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Canonical and atypical E2Fs regulate the mammalian endocycle

(2012) Hui-Zi Chen et al.   NATURE CELL BIOLOGY

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

(2012) J. Wang et al.   NUCLEIC ACIDS RESEARCH

An Orchestrated Program Regulating Secretory Pathway Genes and Cargos by the Transmembrane Transcription Factor CREB-H

(2012) Sónia Barbosa et al.   TRAFFIC

The endocrine pancreas: insights into development, differentiation, and diabetes

(2012) Teresa L. Mastracci et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Inheritance of Stress-Induced, ATF-2-Dependent Epigenetic Change

(2011) Ki-Hyeon Seong et al.   CELL

High-throughput protein expression screening and purification in Escherichia coli

(2011) Renaud Vincentelli et al.   METHODS

Automated protein-DNA interaction screening of Drosophila regulatory elements

(2011) Korneel Hens et al.   NATURE METHODS

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

Origin of Pax and Six gene families in sponges: Single PaxB and Six1/2 orthologs in Chalinula loosanoffi

(2010) April Hill et al.   DEVELOPMENTAL BIOLOGY

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

(2010) Gong-Hong Wei et al.   EMBO JOURNAL

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

(2010) A. Jolma et al.   GENOME RESEARCH

Changes in Hox genes’ structure and function during the evolution of the squamate body plan

(2010) Nicolas Di-Poï et al.   NATURE

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

(2010) Lihua Julie Zhu et al.   NUCLEIC ACIDS RESEARCH

Lineage-specific expansion of DNA-binding transcription factor families

(2010) Varodom Charoensawan et al.   TRENDS IN GENETICS

Conservation and divergence in developmental networks: a view from Drosophila myogenesis

(2009) Lucia Ciglar et al.   CURRENT OPINION IN CELL BIOLOGY

Development of the genetic code: Insights from a fungal codon reassignment

(2009) Gabriela R. Moura et al.   FEBS LETTERS

The Ets-Domain Transcription Factor Spdef Promotes Maturation of Goblet and Paneth Cells in the Intestinal Epithelium

(2009) Alex Gregorieff et al.   GASTROENTEROLOGY

The Drosophila DHR96 nuclear receptor binds cholesterol and regulates cholesterol homeostasis

(2009) M. A. Horner et al.   GENES & DEVELOPMENT

SPDEF is required for mouse pulmonary goblet cell differentiation and regulates a network of genes associated with mucus production

(2009) Gang Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database

(2009) Ulrike Pfreundt et al.   NUCLEIC ACIDS RESEARCH

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Natural similarity measures between position frequency matrices with an application to clustering

(2008) Utz J. Pape et al.   BIOINFORMATICS

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Growth regulation by Dpp: an essential role for Brinker and a non-essential role for graded signaling levels

(2008) G. Schwank et al.   DEVELOPMENT

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

(2008) Marcus B. Noyes et al.   NUCLEIC ACIDS RESEARCH

The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

(2008) K. J Peterson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES