In silico design of context-responsive mammalian promoters with user-defined functionality

Overloaded and stressed: whole-cell considerations for bacterial synthetic biology

(2016) Olivier Borkowski et al.   CURRENT OPINION IN MICROBIOLOGY

Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators

(2016) David van Dijk et al.   GENOME RESEARCH

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

(2016) Sushil Tripathi et al.   Database-The Journal of Biological Databases and Curation

Sp1 and the ‘hallmarks of cancer’

(2015) Kate Beishline et al.   FEBS Journal

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

Synthetic promoters for CHO cell engineering

(2014) Adam J. Brown et al.   BIOTECHNOLOGY AND BIOENGINEERING

The endoplasmic reticulum and unfolded protein response in the control of mammalian recombinant protein production

(2014) Hirra Hussain et al.   BIOTECHNOLOGY LETTERS

The Transcription Factor Titration Effect Dictates Level of Gene Expression

(2014) Robert C. Brewster et al.   CELL

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

(2014) Eilon Sharon et al.   GENOME RESEARCH

The grammar of transcriptional regulation

(2014) Shira Weingarten-Gabbay et al.   HUMAN GENETICS

Physical constraints determine the logic of bacterial promoter architectures

(2014) Daphne Ezer et al.   NUCLEIC ACIDS RESEARCH

Target competition: transcription factors enter the limelight

(2014) Florian A Karreth et al.   GENOME BIOLOGY

Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression

(2014) Daphne Ezer et al.   Computational and Structural Biotechnology Journal

Block decoys: Transcription-factor decoys designed for in vitro gene regulation studies

(2013) Adam J. Brown et al.   ANALYTICAL BIOCHEMISTRY

TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors

(2013) Konika Chawla et al.   BIOINFORMATICS

Molecular mechanisms of ETS transcription factor-mediated tumorigenesis

(2013) Adwitiya Kar et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Oncogenic RAS directs silencing of tumor suppressor genes through ordered recruitment of transcriptional repressors

(2013) N. Wajapeyee et al.   GENES & DEVELOPMENT

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants

(2013) Ilaria Mogno et al.   GENOME RESEARCH

Bile acid-controlled transgene expression in mammalian cells and mice

(2013) Katrin Rössger et al.   METABOLIC ENGINEERING

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

(2013) Robin P Smith et al.   NATURE GENETICS

Synergistic and tunable human gene activation by combinations of synthetic transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

Precise and reliable gene expression via standard transcription and translation initiation elements

(2013) Vivek K Mutalik et al.   NATURE METHODS

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Multi-chromatic control of mammalian gene expression and signaling

(2013) Konrad Müller et al.   NUCLEIC ACIDS RESEARCH

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

Repair of Strand Breaks by Homologous Recombination

(2013) M. Jasin et al.   Cold Spring Harbor Perspectives in Biology

The Keap1-Nrf2 pathway: Mechanisms of activation and dysregulation in cancer

(2013) Emilia Kansanen et al.   Redox Biology

Functional heterogeneity and heritability in CHO cell populations

(2012) Sarah L. Davies et al.   BIOTECHNOLOGY AND BIOENGINEERING

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

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

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Stress management at the ER: Regulators of ER stress-induced apoptosis

(2012) Adrienne M. Gorman et al.   PHARMACOLOGY & THERAPEUTICS

A mechanistic understanding of production instability in CHO cell lines expressing recombinant monoclonal antibodies

(2011) Minsoo Kim et al.   BIOTECHNOLOGY AND BIOENGINEERING

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

(2010) Christina I. Swanson et al.   DEVELOPMENTAL CELL

DNA methylation contributes to loss in productivity of monoclonal antibody-producing CHO cell lines

(2010) Yuansheng Yang et al.   JOURNAL OF BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis

(2010) Mary Ellen Moynahan et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Synthetic design of strong promoters

(2010) M. R. Schlabach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Designing and engineering evolutionary robust genetic circuits

(2010) Sean C Sleight et al.   Journal of Biological Engineering

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Regulation of gene expression via the core promoter and the basal transcriptional machinery

(2009) Tamar Juven-Gershon et al.   DEVELOPMENTAL BIOLOGY

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

The words of the regulatory code are arranged in a variable manner in highly conserved enhancers

(2008) Sepand Rastegar et al.   DEVELOPMENTAL BIOLOGY

Models of transcription factor binding: Sensitivity of activation functions to model assumptions

(2008) Dominique Chu et al.   JOURNAL OF THEORETICAL BIOLOGY

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions

(2008) Thomas Manke et al.   PLoS Computational Biology