Author details

Full Name

Arend Sidow

Affiliation

ORCID

Career Start Year

1990

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
35779264	SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples.	STAR Protoc	2022
33597536	Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads.	Nature Communications	2021
36700103	Aquila_stLFR: diploid genome assembly based structural variant calling package for stLFR linked-reads.		2021
34181655	De novo mutational signature discovery in tumor genomes using SparseSignatures.	PLoS Comput Biol	2021
33575568	diploid genome assembly for genome-wide structural variant detection.	NAR Genomics and Bioinformatics	2020
31182087	Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations.	BMC Med Genomics	2019
31769805	Assessment of human diploid genome assembly with 10x Linked-Reads data.	GigaScience	2019
30320765	High-quality genome sequences of uncultured microbes by assembly of read clouds.	Nat Biotechnol	2018
29914369	HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data.	BMC Genomics	2018
30367051	Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival.	Nat Commun	2018
28714986	Genome-wide reconstruction of complex structural variants using read clouds.	Nat Methods	2017
27271295	Extensive sequencing of seven human genomes to characterize benchmark reference materials.	Sci Data	2016
27099173	A research roadmap for next-generation sequencing informatics.	Sci Transl Med	2016
26797145	Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells.	Science	2016
26286554	Read clouds uncover variation in complex regions of the human genome.	Genome Research	2015
25918554	Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia.	Genome Med	2015
25871848	Constraint and divergence of global gene expression in the mammalian embryo.	Elife	2015
25733351	Concepts in solid tumor evolution.	Trends Genet	2015
26286809	svviz: a read viewer for validating structural variants.	Bioinformatics	2015
25000818	The future of sequencing: convergence of intelligent design and market Darwinism.	Genome Biol	2014
24214394	Discovery of recurrent structural variants in nasopharyngeal carcinoma.	Genome Res	2014
24594094	Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta.	Developmental Biology	2014
23568837	Genome evolution during progression to breast cancer.	Genome Research	2013
24195709	Inference of tumor phylogenies with improved somatic mutation discovery.	Journal of Computational Biology	2013
24138567	Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines.	BMC Genomics	2013
23478400	The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.	Genome Res	2013
23651856	Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses.	Genes and Development	2013
22955619	Architecture of the human regulatory network derived from ENCODE data.	Nature	2012
22955991	ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.	Genome Res	2012
22955985	Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.	Genome Res	2012
21602827	Determinants of nucleosome organization in primary human cells.	Nature	2011
21700874	A cell cycle phosphoproteome of the yeast centrosome.	Science	2011
20498079	Functional analyses of variants reveal a significant role for dominant negative and common alleles in oligogenic Bardet-Biedl syndrome.	Proc Natl Acad Sci U S A	2010
21152010	Identifying a high fraction of the human genome to be under selective constraint using GERP++.	PLoS Comput Biol	2010
20354513	Single-nucleotide evolutionary constraint scores highlight disease-causing mutations.	Nat Methods	2010
19846609	ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses.	Genome Res	2010
20067941	Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes.	Genome Res	2010
20594331	An in vitro-identified high-affinity nucleosome-positioning signal is capable of transiently positioning a nucleosome in vivo.	Epigenetics Chromatin	2010
20098735	3'-end sequencing for expression quantification (3SEQ) from archival tumor samples.	PLoS One	2010
20064375	Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells.	Cell	2009
19461883	SHRiMP: accurate mapping of short color-space reads.	PLoS Comput Biol	2009
18519652	The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution.	Genome Res	2008
19160518	Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.	Nat Methods	2008
18477713	A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.	Genome Res	2008
18254951	Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members.	BMC Evol Biol	2008
18160030	Fruit fly family fun.	Cell	2007
17567995	Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.	Genome Res	2007
17374142	A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome.	Genome Biol	2007
17372217	Extreme genomic variation in a natural population.	Proc Natl Acad Sci U S A	2007
17594490	Constructing a meaningful evolutionary average at the phylogenetic center of mass.	BMC Bioinformatics	2007