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Lista de obras de Anshul Kundaje

A classification-based framework for predicting and analyzing gene regulatory response

artículo científico publicado en 2006

A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization

A common pattern of DNase-I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization

A comparative encyclopedia of DNA elements in the mouse genome

artículo científico publicado en 2014

A predictive model of the oxygen and heme regulatory network in yeast

artículo científico publicado en 2008

An Arntl2-Driven Secretome Enables Lung Adenocarcinoma Metastatic Self-Sufficiency

artículo científico publicado en 2016

An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development

artículo científico publicado en 2016

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

artículo científico publicado en 2017

Architecture of the human regulatory network derived from ENCODE data

artículo científico publicado en 2012

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

artículo científico publicado en 2022

Author Correction: Perspectives on ENCODE

artículo científico publicado en 2022

Base-resolution models of transcription-factor binding reveal soft motif syntax

artículo científico publicado en 2021

ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation

artículo científico publicado en 2018

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

artículo científico publicado en 2012

Challenges and recommendations for epigenomics in precision health.

artículo científico publicado en 2017

Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci

artículo científico publicado en 2015

Characterization of the direct targets of FOXO transcription factors throughout evolution

artículo científico publicado en 2016

Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging

artículo científico publicado en 2023

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans.

artículo científico publicado en 2017

Chromatin accessibility dynamics reveal novel functional enhancers inC. elegans

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

artículo científico publicado en 2012

Combining sequence and time series expression data to learn transcriptional modules

artículo científico publicado en 2005

Comparative analysis of metazoan chromatin organization

artículo científico publicado en 2014

Comparative analysis of regulatory information and circuits across distant species

artículo científico publicado en 2014

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease

artículo científico publicado en 2015

Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution

artículo científico publicado en 2015

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays.

artículo científico publicado en 2019

Defining functional DNA elements in the human genome

artículo científico publicado en 2014

Denoising genome-wide histone ChIP-seq with convolutional neural networks

artículo científico publicado en 2017

Denoising genome-wide histone ChIP-seq with convolutional neural networks

scholarly article published 7 May 2016

Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers

artículo científico publicado en 2018

Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster

artículo científico publicado en 2014

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.

artículo científico publicado en 2017

Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data

artículo científico publicado en 2017

Expanded encyclopaedias of DNA elements in the human and mouse genomes

artículo científico publicado en 2020

Extensive variation in chromatin states across humans

artículo científico publicado en 2013

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

artículo científico publicado en 2015

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

artículo científico publicado en 2015

Genetic Effects on Transcriptome Profiles in Colon Epithelium Provide Functional Insights for Genetic Risk Loci

artículo científico publicado en 2021

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens

artículo científico publicado en 2017

Genome-wide enhancer maps link risk variants to disease genes

scientific article published on 07 April 2021

GenomeDISCO: A concordance score for chromosome conformation capture experiments using random walks on contact map graphs

GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs

scholarly article by Oana Ursu published in August 2018

GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs

artículo científico publicado en 2019

Gkmexplain: Fast and Accurate Interpretation of Nonlinear Gapped k-mer Support Vector Machines Using Integrated Gradients

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

artículo científico publicado en 2015

H3K4me3 breadth is linked to cell identity and transcriptional consistency.

artículo científico publicado en 2014

High-Throughput Characterization of Cascade type I-E CRISPR Guide Efficacy Reveals Unexpected PAM Diversity and Target Sequence Preferences

artículo científico publicado en 2017

Homogeneity in the association of body mass index with type 2 diabetes across the UK Biobank: A Mendelian randomization study

scientific article published on 10 December 2019

Impact of regulatory variation across human iPSCs and differentiated cells

Impact of regulatory variation across human iPSCs and differentiated cells.

artículo científico publicado en 2017

Impact of the X Chromosome and sex on regulatory variation

artículo científico publicado en 2016

Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution

Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution

artículo científico publicado en 2017

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts

scientific article published on 01 July 2019

Integrative annotation of chromatin elements from ENCODE data

artículo científico publicado en 2012

Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin

artículo científico publicado en 2018

Kipoi: accelerating the community exchange and reuse of predictive models for genomics

Landscape of cohesin-mediated chromatin loops in the human genome

artículo científico publicado en 2020

Large-scale quality analysis of published ChIP-seq data

artículo científico publicado en 2014

Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis

artículo científico publicado en 2021

Learning regulatory programs that accurately predict differential expression with MEDUSA.

artículo científico publicado en 2007

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

artículo científico publicado en 2016

Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.

artículo científico publicado en 2017

Linking disease associations with regulatory information in the human genome

artículo científico publicado en 2012

Long noncoding RNAs are rarely translated in two human cell lines

artículo científico publicado en 2012

Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types

artículo científico publicado en 2016

Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility

scientific article published on 08 July 2019

Modeling gene expression using chromatin features in various cellular contexts

artículo científico publicado en 2012

Molecular definition of a metastatic lung cancer state reveals a targetable CD109-Janus kinase-Stat axis

artículo científico publicado en 2017

Motif Discovery Through Predictive Modeling of Gene Regulation

article

Opportunities and challenges for transcriptome-wide association studies

artículo científico publicado en 2019

Opportunities and obstacles for deep learning in biology and medicine.

artículo científico publicado en 2018

Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response

Predicting gene expression in massively parallel reporter assays: A comparative study

artículo científico publicado en 2017

Predicting genetic regulatory response using classification.

artículo científico publicado en 2004

Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures

Principles of regulatory information conservation between mouse and human

artículo científico publicado en 2014

PyBoost: A parallelized Python implementation of 2D boosting with hierarchies

Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution.

artículo científico publicado en 2015

Regulatory analysis of the C. elegans genome with spatiotemporal resolution

artículo científico publicado en 2014

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

artículo científico publicado en 2019

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

artículo científico publicado en 2014

Reverse-complement parameter sharing improves deep learning models for genomics

scholarly article published 27 January 2017

STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma

artículo científico publicado en 2013

Semi-automated genome annotation using epigenomic data and Segway

Separable Fully Connected Layers Improve Deep Learning Models For Genomics

scholarly article published 5 June 2017

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

artículo científico publicado en 2012

Short tandem repeats bind transcription factors to tune eukaryotic gene expression

artículo científico publicado en 2023

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases

artículo científico publicado en 2020

Spectrogram Analysis of Genomes

Statistical analysis of MPSS measurements: application to the study of LPS-activated macrophage gene expression

artículo científico publicado en 2005

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

scientific article published on 27 June 2019

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

artículo científico publicado en 2019

The chromatin organization of a chlorarachniophyte nucleomorph genome

artículo científico publicado en 2022

Transcription factors bind negatively selected sites within human mtDNA genes

artículo científico publicado en 2014

Transcriptome-wide association studies: opportunities and challenges

Transparency and reproducibility in artificial intelligence

artículo científico publicado en 2020

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

artículo científico publicado en 2012

Umap and Bismap: quantifying genome and methylome mappability

Umap and Bismap: quantifying genome and methylome mappability

artículo científico publicado en 2018

Vicus: Exploiting local structures to improve network-based analysis of biological data.

artículo científico publicado en 2017

fastISM: performant<i>in silico</i>saturation mutagenesis for convolutional neural networks

artículo científico publicado en 2022

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