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Items: 1 to 20 of 93

1.

Predicting Splicing from Primary Sequence with Deep Learning.

Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, Kosmicki JA, Arbelaez J, Cui W, Schwartz GB, Chow ED, Kanterakis E, Gao H, Kia A, Batzoglou S, Sanders SJ, Farh KK.

Cell. 2019 Jan 24;176(3):535-548.e24. doi: 10.1016/j.cell.2018.12.015. Epub 2019 Jan 17.

PMID:
30661751
2.

Author Correction: Predicting the clinical impact of human mutation with deep neural networks.

Sundaram L, Gao H, Padigepati SR, McRae JF, Li Y, Kosmicki JA, Fritzilas N, Hakenberg J, Dutta A, Shon J, Xu J, Batzoglou S, Li X, Farh KK.

Nat Genet. 2019 Feb;51(2):364. doi: 10.1038/s41588-018-0329-z.

PMID:
30559491
3.

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

Ramazzotti D, Lal A, Wang B, Batzoglou S, Sidow A.

Nat Commun. 2018 Oct 26;9(1):4453. doi: 10.1038/s41467-018-06921-8.

4.

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 Oct 18;175(3):889. doi: 10.1016/j.cell.2018.10.019. No abstract available.

5.

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

Bishara A, Moss EL, Kolmogorov M, Parada AE, Weng Z, Sidow A, Dekas AE, Batzoglou S, Bhatt AS.

Nat Biotechnol. 2018 Oct 15. doi: 10.1038/nbt.4266. [Epub ahead of print]

6.

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.

7.

Predicting the clinical impact of human mutation with deep neural networks.

Sundaram L, Gao H, Padigepati SR, McRae JF, Li Y, Kosmicki JA, Fritzilas N, Hakenberg J, Dutta A, Shon J, Xu J, Batzoglou S, Li X, Farh KK.

Nat Genet. 2018 Aug;50(8):1161-1170. doi: 10.1038/s41588-018-0167-z. Epub 2018 Jul 23. Erratum in: Nat Genet. 2019 Feb;51(2):364.

8.

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. Erratum in: Cell. 2018 Oct 18;175(3):889.

9.

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.

10.

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.

PMID:
29658784
11.

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.

PMID:
29265724
12.

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.

13.

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.

14.

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.

15.

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.

PMID:
28263960
16.

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.

17.

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.

18.

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.

19.

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.

PMID:
26353840
20.

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.

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