Arend Sidow

发表

SHRiMP: Accurate Mapping of Short Color-space Reads

Michael Brudno, Stephen M. Rumble, Adrian V. Dalca, 2009, PLoS Comput. Biol..

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

Lu Zhang, Arend Sidow, Xin Zhou, 2019, GigaScience.

svviz: a read viewer for validating structural variants

Marc L. Salit, Noah Spies, Arend Sidow, 2015 .

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery

Serafim Batzoglou, Arend Sidow, Raheleh Salari, 2013, J. Comput. Biol..

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

Gregory M. Cooper, Arend Sidow, Senthil A. G. Singaravelu, 2004, BMC Bioinformatics.

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery

Serafim Batzoglou, Arend Sidow, Raheleh Salari, 2013, RECOMB.

Aquila_stLFR: assembly based variant calling package for stLFR and hybrid assembly for linked-reads

Xin Zhou, David L. Dill, Yichen Liu, 2019, bioRxiv.

svviz: a read viewer for validating structural variants

Noah Spies, Arend Sidow, Justin M. Zook, 2015, bioRxiv.

Genome-wide reconstruction of complex structural variants using read clouds

Serafim Batzoglou, Noah Spies, Marc Salit, 2016, Nature Methods.

Chaining Algorithms for Alignment of Draft Sequence

Michael Brudno, Serafim Batzoglou, Mukund Sundararajan, 2004, WABI.

genomeview - an extensible python-based genomics visualization engine

Marc L. Salit, Noah Spies, Arend Sidow, 2018 .

Genome-wide reconstruction of complex structural variants using read clouds

Marc L. Salit, Serafim Batzoglou, Noah Spies, 2016 .

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

Serafim Batzoglou, Gregory M. Cooper, Arend Sidow, 2010, PLoS Comput. Biol..

Constructing a meaningful evolutionary average at the phylogenetic center of mass

Arend Sidow, Eric A. Stone, A. Sidow, 2007, BMC Bioinformatics.

Benchmarking challenging small variants with linked and long reads

Andrew Carroll, Giuseppe Narzisi, Chunlin Xiao, 2020 .

- Optical Mapping: a high-throughput single-molecule system for genome-wide restriction mapping - Thesis: "Shotgun optical mapping: a comprehensive statistical and computational analysis"

Arend Sidow, Michael S. Waterman, Anton Valouev, 2012 .

A research roadmap for next-generation sequencing informatics

Russ B. Altman, Euan Ashley, Snehit Prabhu, 2016, Science Translational Medicine.

Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements

Anshul Kundaje, Serafim Batzoglou, Arend Sidow, 2013, Tiny Trans. Comput. Sci..

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

Arend Sidow, Xin Zhou, Lu Zhang, 2019, bioRxiv.

Read clouds uncover variation in complex regions of the human genome

Serafim Batzoglou, Arend Sidow, Yuling Liu, 2015, RECOMB.

Supporting Online Material Materials and Methods Figs. S1 to S6 Table S1 References Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression

Christopher D. Brown, Arend Sidow, A. Sidow, 2022 .

De novo diploid genome assembly for genome-wide structural variant detection

Arend Sidow, Xin Zhou, Ziming Weng, 2019, bioRxiv.

Parsimony or statistics?

Arend Sidow, A. Sidow, 1994, Nature.

Extensive sequencing of seven human genomes to characterize benchmark reference materials

Gintaras Deikus, Ali Bashir, Alex Hastie, 2015, Scientific Data.

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

Mark Gerstein, Gil McVean, Laurent Duret, 2013, Genome research.

Alignment of Genomic DNA LAGAN and Multi-LAGAN : Efficient Tools for Large-Scale Multiple

Michael Brudno, Serafim Batzoglou, Gregory M. Cooper, 2003 .

Aquila: diploid personal genome assembly and comprehensive variant detection based on linked reads

David L. Dill, Arend Sidow, Xin Zhou, 2019, bioRxiv.

Discovery of recurrent structural variants in nasopharyngeal carcinoma

Quynh-Thu Le, Arend Sidow, Anton Valouev, 2014, Genome research.

Estimating the fraction of invariable codons with a capture-recapture method

Terence P. Speed, Arend Sidow, A. Sidow, 1992, Journal of Molecular Evolution.

Single-nucleotide evolutionary constraint scores highlight disease-causing mutations

Jay Shendure, Arend Sidow, Michael J Bamshad, 2010, Nature Methods.

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

Serafim Batzoglou, Arend Sidow, Alex Bishara, 2018, Nature Biotechnology.

Detection of Hidden Intertextuality in the Scientific Publications

Michael Brudno, Serafim Batzoglou, Gregory M. Cooper, 2012 .

Genome evolution during progression to breast cancer

Serafim Batzoglou, Arend Sidow, Raheleh Salari, 2013, Genome research.

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

Daniele Ramazzotti, Serafim Batzoglou, Arend Sidow, 2018, Nature Communications.

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

Lu Zhang, Serafim Batzoglou, Arend Sidow, 2017, bioRxiv.

Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells

Arend Sidow, Anton Valouev, A. Sidow, 2009, Cell.

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

Serafim Batzoglou, Noah Spies, Arend Sidow, 2015, Genome Medicine.

A Cell Cycle Phosphoproteome of the Yeast Centrosome

Arend Sidow, John R. Yates, Jonathan Binkley, 2011, Science.

Sequence First. Ask Questions Later.

Arend Sidow, A. Sidow, 2002, Cell.

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

Arend Sidow, Kalpana Karra, Jonathan Binkley, 2010, Genome research.

Trade-offs in detecting evolutionarily constrained sequence by comparative genomics.

Arend Sidow, Gregory M Cooper, A. Sidow, 2005, Annual review of genomics and human genetics.

Genomic regulatory regions: insights from comparative sequence analysis.

Arend Sidow, Gregory M Cooper, A. Sidow, 2003, Current opinion in genetics & development.

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

Arend Sidow, Anton Valouev, A. Sidow, 2010, Epigenetics & Chromatin.

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

Inna Dubchak, Michael Brudno, Serafim Batzoglou, 2004, Genome research.

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes.

Serafim Batzoglou, Richard M Myers, Arend Sidow, 2010, Genome research.

De novo mutational signature discovery in tumor genomes using SparseSignatures

Robert Tibshirani, Daniele Ramazzotti, Arend Sidow, 2018, bioRxiv.

Inference of functional regions in proteins by quantification of evolutionary constraints

Arend Sidow, A. Sidow, E. Stone, 2002, Proceedings of the National Academy of Sciences of the United States of America.