PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition

Tensor decomposition for multiple-tissue gene expression experiments

(2016) Victoria Hore et al.   NATURE GENETICS

Peak shape clustering reveals biological insights

(2015) Marzia A. Cremona et al.   BMC BIOINFORMATICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

(2015) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution

(2014) Melissa J Hubisz et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Predicting the human epigenome from DNA motifs

(2014) John W Whitaker et al.   NATURE METHODS

Transcription factor binding predicts histone modifications in human cell lines

(2014) Dan Benveniste et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

(2014) Genevieve D. Erwin et al.   PLoS Computational Biology

MMDiff: quantitative testing for shape changes in ChIP-Seq data sets

(2013) Gabriele Schweikert et al.   BMC GENOMICS

The Developmental Brain Gene NPAS3 Contains the Largest Number of Accelerated Regulatory Sequences in the Human Genome

(2013) Gretel B. Kamm et al.   MOLECULAR BIOLOGY AND EVOLUTION

Many human accelerated regions are developmental enhancers

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

Function and Regulation of AUTS2, a Gene Implicated in Autism and Human Evolution

(2013) Nir Oksenberg et al.   PLoS Genetics

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Scalable tensor factorizations for incomplete data

(2010) Evrim Acar et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Matrix Factorization Techniques for Recommender Systems

(2009) Yehuda Koren et al.   COMPUTER

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Tensor Decompositions and Applications

(2009) Tamara G. Kolda et al.   SIAM REVIEW

Interacting haplotypes at the NPAS3 locus alter risk of schizophrenia and bipolar disorder

(2008) B S Pickard et al.   MOLECULAR PSYCHIATRY

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE