List of works - Arend Sidow

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

scientific article

A cell cycle phosphoproteome of the yeast centrosome

scientific article published on June 2011

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

scientific article

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

scientific article

A research roadmap for next-generation sequencing informatics

scientific article published on April 2016

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

scientific article

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

scientific article

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

scientific article published in June 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

scientific article (publication date: 6 September 2012)

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

scientific article published on 01 November 2019

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

scientific article published on April 2004

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

scientific article published on 9 April 2015

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

scientific article

Chaining Algorithms for Alignment of Draft Sequence

Characterization of evolutionary rates and constraints in three Mammalian genomes

scientific article published on April 2004

Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations

scientific article published on 10 June 2019

Concepts in solid tumor evolution

scientific article

Constraint and divergence of global gene expression in the mammalian embryo

scientific article published on 14 April 2015

Constructing a meaningful evolutionary average at the phylogenetic center of mass

scientific article published on 26 June 2007

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

scientific article

Determinants of nucleosome organization in primary human cells

scientific article

Discovery of recurrent structural variants in nasopharyngeal carcinoma

scientific article

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

scientific article

Extensive sequencing of seven human genomes to characterize benchmark reference materials

scientific article

Extreme genomic variation in a natural population

scholarly article

Fruit fly family fun.

scientific article published on December 2007

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

scientific article

Functional architecture and evolution of transcriptional elements that drive gene coexpression

scientific article published on 01 September 2007

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

scientific article published on 01 January 2003

Genome evolution during progression to breast cancer

scientific article published on 08 April 2013

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

scientific article

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

scientific article

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

scientific article published on 17 July 2017

Genomic regulatory regions: insights from comparative sequence analysis

scientific article published on December 2003

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

scientific article published on May 2013

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

scientific article

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

scientific article published on 15 October 2018

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

scholarly article

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

scientific article published in June 2007

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

scientific article

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

scientific article

Inference of functional regions in proteins by quantification of evolutionary constraints

scientific article

Inference of tumor phylogenies with improved somatic mutation discovery

scientific article published on November 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

scientific article (publication date: April 2003)

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

scientific article

Mammalian comparative sequence analysis of the Agrp locus

scientific article

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

scientific article

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

scientific article published in Nature Communications

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

scientific article published on 15 November 2004

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

scientific article

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

scientific article published on 17 June 2005

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

scientific article

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

scientific article published on May 1, 2003

Read clouds uncover variation in complex regions of the human genome

scientific article published on 18 August 2015

SHRiMP: accurate mapping of short color-space reads

scientific article

Sequence first. Ask questions later

scientific article

Single-nucleotide evolutionary constraint scores highlight disease-causing mutations

scientific article

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

scientific article published in 2022

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

scientific article

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

scientific article

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

scientific article published on 25 March 2014

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

scientific article

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

scientific article published on 11 March 2013

Trade-offs in detecting evolutionarily constrained sequence by comparative genomics

scientific article

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

scientific article

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

scientific article

svviz: a read viewer for validating structural variants

scientific article published on 18 August 2015

List of works by Arend Sidow

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