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

by Xin Zhou, Serafim Batzoglou, Arend Sidow, Lu Zhang
Published 2018-06-01

De novo mutational signature discovery in tumor genomes using SparseSignatures.

by Avantika Lal, Keli Liu, Robert Tibshirani, Arend Sidow, Daniele Ramazzotti
Published 2021-06-01

Mammalian comparative sequence analysis of the Agrp locus.

by Christopher B Kaelin, Gregory M Cooper, Arend Sidow, Gregory S Barsh
Published 2007-08-01

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

by Daniele Ramazzotti, Avantika Lal, Bo Wang, Serafim Batzoglou, Arend Sidow
Published 2018-10-01

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

by Xin Zhou, Lu Zhang, Ziming Weng, David L. Dill, Arend Sidow
Published 2021-02-01

Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations

by Avantika Lal, Daniele Ramazzotti, Ziming Weng, Keli Liu, James M. Ford, Arend Sidow
Published 2019-06-01

SHRiMP: accurate mapping of short color-space reads.

by Stephen M Rumble, Phil Lacroute, Adrian V Dalca, Marc Fiume, Arend Sidow, Michael Brudno
Published 2009-05-01

Constraint and divergence of global gene expression in the mammalian embryo

by Noah Spies, Cheryl L Smith, Jesse M Rodriguez, Julie C Baker, Serafim Batzoglou, Arend Sidow
Published 2015-04-01

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

by Eugene V Davydov, David L Goode, Marina Sirota, Gregory M Cooper, Arend Sidow, Serafim Batzoglou
Published 2010-12-01

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

by Lorenzo Mella, Avantika Lal, Fabrizio Angaroni, Davide Maspero, Rocco Piazza, Arend Sidow, Marco Antoniotti, Alex Graudenzi, Daniele Ramazzotti
Published 2022-09-01

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

by Andrew H Beck, Ziming Weng, Daniela M Witten, Shirley Zhu, Joseph W Foley, Phil Lacroute, Cheryl L Smith, Robert Tibshirani, Matt van de Rijn, Arend Sidow, Robert B West
Published 2010-01-01

Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis

by Zou, Lihua, Sriswasdi, Sira, Ross, Brian D, Missiuro, Patrycja V., Liu, Jun, Ge, Hui, Sidow, Arend
Published 2010

Extensive sequencing of seven human genomes to characterize benchmark reference materials

by Zook, Justin M., Catoe, David, McDaniel, Jennifer, Vang, Lindsay, Spies, Noah, Sidow, Arend, Weng, Ziming, Liu, Yuling, Mason, Christopher E., Alexander, Noah, Henaff, Elizabeth, McIntyre, Alexa B.R., Chandramohan, Dhruva, Chen, Feng, Jaeger, Erich, Moshrefi, Ali, Pham, Khoa, Stedman, William, Liang, Tiffany, Saghbini, Michael, Dzakula, Zeljko, Hastie, Alex, Cao, Han, Deikus, Gintaras, Schadt, Eric, Sebra, Robert, Bashir, Ali, Truty, Rebecca M., Chang, Christopher C., Gulbahce, Natali, Zhao, Keyan, Ghosh, Srinka, Hyland, Fiona, Fu, Yutao, Chaisson, Mark, Xiao, Chunlin, Trow, Jonathan, Sherry, Stephen T., Zaranek, Alexander W., Ball, Madeleine, Bobe, Jason, Estep, Preston Wayne, Church, George McDonald, Marks, Patrick, Kyriazopoulou-Panagiotopoulou, Sofia, Zheng, Grace X.Y., Schnall-Levin, Michael, Ordonez, Heather S., Mudivarti, Patrice A., Giorda, Kristina, Sheng, Ying, Rypdal, Karoline Bjarnesdatter, Salit, Marc
Published 2016