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Items: 1 to 20 of 85


Network enhancement as a general method to denoise weighted biological networks.

Wang B, Pourshafeie A, Zitnik M, Zhu J, Bustamante CD, Batzoglou S, Leskovec J.

Nat Commun. 2018 Aug 6;9(1):3108. doi: 10.1038/s41467-018-05469-x.


Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.

Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Ryan CJ, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H, Gilbert LA, Lara PN Jr, Evans CP, Goldstein TC, Stuart JM, Tomlins SA, Spratt DE, Cheetham RK, Cheng DT, Farh K, Gehring JS, Hakenberg J, Liao A, Febbo PG, Shon J, Sickler B, Batzoglou S, Knudsen KE, He HH, Huang J, Wyatt AW, Dehm SM, Ashworth A, Chinnaiyan AM, Maher CA, Small EJ, Feng FY.

Cell. 2018 Jul 26;174(3):758-769.e9. doi: 10.1016/j.cell.2018.06.039. Epub 2018 Jul 19.


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

Zhou X, Batzoglou S, Sidow A, Zhang L.

BMC Genomics. 2018 Jun 18;19(1):467. doi: 10.1186/s12864-018-4867-7.


Fast Metagenomic Binning via Hashing and Bayesian Clustering.

Popic V, Kuleshov V, Snyder M, Batzoglou S.

J Comput Biol. 2018 Jul;25(7):677-688. doi: 10.1089/cmb.2017.0250. Epub 2018 Apr 16.


SIMLR: A Tool for Large-Scale Genomic Analyses by Multi-Kernel Learning.

Wang B, Ramazzotti D, De Sano L, Zhu J, Pierson E, Batzoglou S.

Proteomics. 2018 Jan;18(2). doi: 10.1002/pmic.201700232.


Vicus: Exploiting local structures to improve network-based analysis of biological data.

Wang B, Huang L, Zhu Y, Kundaje A, Batzoglou S, Goldenberg A.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005621. doi: 10.1371/journal.pcbi.1005621. eCollection 2017 Oct.


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

Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou S, Sidow A.

Nat Methods. 2017 Sep;14(9):915-920. doi: 10.1038/nmeth.4366. Epub 2017 Jul 17.


A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy.

Popic V, Batzoglou S.

Nat Commun. 2017 May 16;8:15311. doi: 10.1038/ncomms15311.


Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning.

Wang B, Zhu J, Pierson E, Ramazzotti D, Batzoglou S.

Nat Methods. 2017 Apr;14(4):414-416. doi: 10.1038/nmeth.4207. Epub 2017 Mar 6.


Microbial Typing by Machine Learned DNA Melt Signatures.

Andini N, Wang B, Athamanolap P, Hardick J, Masek BJ, Thair S, Hu A, Avornu G, Peterson S, Cogill S, Rothman RE, Carroll KC, Gaydos CA, Wang JT, Batzoglou S, Yang S.

Sci Rep. 2017 Feb 6;7:42097. doi: 10.1038/srep42097.


Genome assembly from synthetic long read clouds.

Kuleshov V, Snyder MP, Batzoglou S.

Bioinformatics. 2016 Jun 15;32(12):i216-i224. doi: 10.1093/bioinformatics/btw267.


Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome.

Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M.

Nat Biotechnol. 2016 Jan;34(1):64-9. doi: 10.1038/nbt.3416. Epub 2015 Dec 14.


Reveel: large-scale population genotyping using low-coverage sequencing data.

Huang L, Wang B, Chen R, Bercovici S, Batzoglou S.

Bioinformatics. 2016 Jun 1;32(11):1686-96. doi: 10.1093/bioinformatics/btv530. Epub 2015 Sep 9.


Read clouds uncover variation in complex regions of the human genome.

Bishara A, Liu Y, Weng Z, Kashef-Haghighi D, Newburger DE, West R, Sidow A, Batzoglou S.

Genome Res. 2015 Oct;25(10):1570-80. doi: 10.1101/gr.191189.115. Epub 2015 Aug 18.


Fast and scalable inference of multi-sample cancer lineages.

Popic V, Salari R, Hajirasouliha I, Kashef-Haghighi D, West RB, Batzoglou S.

Genome Biol. 2015 May 6;16:91. doi: 10.1186/s13059-015-0647-8.


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

Weng Z, Spies N, Zhu SX, Newburger DE, Kashef-Haghighi D, Batzoglou S, Sidow A, West RB.

Genome Med. 2015 Apr 9;7(1):28. doi: 10.1186/s13073-015-0146-2. eCollection 2015.


Constraint and divergence of global gene expression in the mammalian embryo.

Spies N, Smith CL, Rodriguez JM, Baker JC, Batzoglou S, Sidow A.

Elife. 2015 Apr 14;4:e05538. doi: 10.7554/eLife.05538.


Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation.

Green MR, Kihira S, Liu CL, Nair RV, Salari R, Gentles AJ, Irish J, Stehr H, Vicente-DueƱas C, Romero-Camarero I, Sanchez-Garcia I, Plevritis SK, Arber DA, Batzoglou S, Levy R, Alizadeh AA.

Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1116-25. doi: 10.1073/pnas.1501199112. Epub 2015 Feb 23.


Parente2: a fast and accurate method for detecting identity by descent.

Rodriguez JM, Bercovici S, Huang L, Frostig R, Batzoglou S.

Genome Res. 2015 Feb;25(2):280-9. doi: 10.1101/gr.173641.114. Epub 2014 Oct 1.


Computational biology and bioinformatics.

Batzoglou S, Schwartz R.

Bioinformatics. 2014 Jun 15;30(12):i1-2. doi: 10.1093/bioinformatics/btu304. No abstract available.

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