Lista de obras -

3'-end sequencing for expression quantification (3SEQ) from archival tumor samples

artículo científico publicado en 2010

A cell cycle phosphoproteome of the yeast centrosome

artículo científico publicado en 2011

A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome

artículo científico publicado en 2007

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

artículo científico publicado en 2008

A research roadmap for next-generation sequencing informatics

artículo científico publicado en 2016

ABC: software for interactive browsing of genomic multiple sequence alignment data

artículo científico publicado en 2004

An in vitro-identified high-affinity nucleosome-positioning signal is capable of transiently positioning a nucleosome in vivo

artículo científico publicado en 2010

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

artículo científico publicado en 2007

Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads

scientific article published on 17 February 2021

Architecture of the human regulatory network derived from ENCODE data

artículo científico publicado en 2012

Assessment of human diploid genome assembly with 10x Linked-Reads data

artículo científico publicado en 2019

Automated whole-genome multiple alignment of rat, mouse, and human

artículo científico publicado en 2004

Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia

artículo científico publicado en 2015

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

artículo científico publicado en 2012

Chaining Algorithms for Alignment of Draft Sequence

Characterization of evolutionary rates and constraints in three Mammalian genomes

artículo científico publicado en 2004

Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations

scientific article published on 10 June 2019

Concepts in solid tumor evolution

artículo científico publicado en 2015

Constraint and divergence of global gene expression in the mammalian embryo

artículo científico publicado en 2015

Constructing a meaningful evolutionary average at the phylogenetic center of mass

artículo científico publicado en 2007

De novo discovery of a tissue-specific gene regulatory module in a chordate

artículo científico publicado en 2005

Determinants of nucleosome organization in primary human cells

artículo científico publicado en 2011

Discovery of recurrent structural variants in nasopharyngeal carcinoma

artículo científico publicado en 2013

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

artículo científico publicado en 2010

Extensive sequencing of seven human genomes to characterize benchmark reference materials

artículo científico publicado en 2016

Extreme genomic variation in a natural population

artículo científico publicado en 2007

Fruit fly family fun.

artículo científico

Functional analyses of variants reveal a significant role for dominant negative and common alleles in oligogenic Bardet-Biedl syndrome

artículo científico publicado en 2010

Functional architecture and evolution of transcriptional elements that drive gene coexpression

artículo científico publicado en 2007

Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail

artículo científico publicado en 2003

Genome evolution during progression to breast cancer

artículo científico publicado en 2013

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

artículo científico publicado en 2004

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

artículo científico publicado en 2008

Genome-wide reconstruction of complex structural variants using read clouds.

artículo científico

Genomic regulatory regions: insights from comparative sequence analysis

artículo científico publicado en 2003

Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses

artículo científico publicado en 2013

HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data.

artículo científico publicado en 2018

High-quality genome sequences of uncultured microbes by assembly of read clouds

artículo científico publicado en 2018

Identification Of The Disease-Causing Mutation In Autosomal Dominant Familial Immune Thrombocytopenia By Genome-Wide Linkage Analysis and Whole Genome Sequencing ⬇️

artículo científico publicado en 2013

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

artículo científico publicado en 2007

Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members

artículo científico publicado en 2008

Identifying a high fraction of the human genome to be under selective constraint using GERP++.

artículo científico publicado en 2010

Inference of functional regions in proteins by quantification of evolutionary constraints

artículo científico publicado en 2002

Inference of tumor phylogenies with improved somatic mutation discovery

artículo científico publicado en 2013

Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells

scientific journal article

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

artículo científico publicado en 2003

Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells

artículo científico publicado en 2016

Mammalian comparative sequence analysis of the Agrp locus

artículo científico publicado en 2007

Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta

artículo científico publicado en 2014

Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival

artículo científico publicado en 2018

Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance

artículo científico publicado en 2004

Phenotype-genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence

artículo científico publicado en 2005

Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity

artículo científico publicado en 2005

ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses

artículo científico publicado en 2009

Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes ⬇️

artículo científico publicado el 1 de mayo de 2003

Read clouds uncover variation in complex regions of the human genome

artículo científico publicado en 2015

SHRiMP: accurate mapping of short color-space reads

artículo científico publicado en 2009

Sequence first. Ask questions later

artículo científico publicado en 2002

Single-nucleotide evolutionary constraint scores highlight disease-causing mutations

artículo científico publicado en 2010

SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples

artículo científico publicado en 2022

Structural and molecular evolutionary analysis of Agouti and Agouti-related proteins

artículo científico publicado en 2006

The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution

artículo científico publicado en 2008

The future of sequencing: convergence of intelligent design and market Darwinism

artículo científico publicado en 2014

The integrity of a cholesterol-binding pocket in Niemann-Pick C2 protein is necessary to control lysosome cholesterol levels.

artículo científico publicado en 2003

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

artículo científico publicado en 2013

Trade-offs in detecting evolutionarily constrained sequence by comparative genomics

artículo científico publicado en 2005

Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines

artículo científico publicado en 2013

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

artículo científico publicado en 2012

svviz: a read viewer for validating structural variants

artículo científico publicado en 2015

Lista de obras de

3'-end sequencing for expression quantification (3SEQ) from archival tumor samples

A cell cycle phosphoproteome of the yeast centrosome

A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

A research roadmap for next-generation sequencing informatics

ABC: software for interactive browsing of genomic multiple sequence alignment data

An in vitro-identified high-affinity nucleosome-positioning signal is capable of transiently positioning a nucleosome in vivo

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads

Architecture of the human regulatory network derived from ENCODE data

Assessment of human diploid genome assembly with 10x Linked-Reads data

Automated whole-genome multiple alignment of rat, mouse, and human

Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia

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

Chaining Algorithms for Alignment of Draft Sequence

Characterization of evolutionary rates and constraints in three Mammalian genomes

Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations

Concepts in solid tumor evolution

Constraint and divergence of global gene expression in the mammalian embryo

Constructing a meaningful evolutionary average at the phylogenetic center of mass

De novo discovery of a tissue-specific gene regulatory module in a chordate

Determinants of nucleosome organization in primary human cells

Discovery of recurrent structural variants in nasopharyngeal carcinoma

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

Extensive sequencing of seven human genomes to characterize benchmark reference materials

Extreme genomic variation in a natural population

Fruit fly family fun.

Functional analyses of variants reveal a significant role for dominant negative and common alleles in oligogenic Bardet-Biedl syndrome

Functional architecture and evolution of transcriptional elements that drive gene coexpression

Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail

Genome evolution during progression to breast cancer

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

Genome-wide reconstruction of complex structural variants using read clouds.

Genomic regulatory regions: insights from comparative sequence analysis

Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses

HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data.

High-quality genome sequences of uncultured microbes by assembly of read clouds

Identification Of The Disease-Causing Mutation In Autosomal Dominant Familial Immune Thrombocytopenia By Genome-Wide Linkage Analysis and Whole Genome Sequencing ⬇️

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members

Identifying a high fraction of the human genome to be under selective constraint using GERP++.

Inference of functional regions in proteins by quantification of evolutionary constraints

Inference of tumor phylogenies with improved somatic mutation discovery

Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells

Mammalian comparative sequence analysis of the Agrp locus

Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta

Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival

Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance

Phenotype-genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence

Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity

ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses

Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes ⬇️

Read clouds uncover variation in complex regions of the human genome

SHRiMP: accurate mapping of short color-space reads

Sequence first. Ask questions later

Single-nucleotide evolutionary constraint scores highlight disease-causing mutations

SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples

Structural and molecular evolutionary analysis of Agouti and Agouti-related proteins

The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution

The future of sequencing: convergence of intelligent design and market Darwinism

The integrity of a cholesterol-binding pocket in Niemann-Pick C2 protein is necessary to control lysosome cholesterol levels.

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

Trade-offs in detecting evolutionarily constrained sequence by comparative genomics

Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

svviz: a read viewer for validating structural variants