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Items: 1 to 50 of 92

1.

A machine-compiled database of genome-wide association studies.

Kuleshov V, Ding J, Vo C, Hancock B, Ratner A, Li Y, Ré C, Batzoglou S, Snyder M.

Nat Commun. 2019 Jul 26;10(1):3341. doi: 10.1038/s41467-019-11026-x.

2.

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
3.

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
4.

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.

5.

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.

6.

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]

7.

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.

8.

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.

9.

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.

10.

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.

11.

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
12.

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
13.

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.

14.

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.

15.

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.

16.

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
17.

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.

18.

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.

19.

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.

20.

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
21.

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.

22.

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.

23.

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.

24.

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.

25.

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-Dueñas 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.

26.

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.

27.

Computational biology and bioinformatics.

Batzoglou S, Schwartz R.

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

28.

An effective filter for IBD detection in large data sets.

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

PLoS One. 2014 Mar 25;9(3):e92713. doi: 10.1371/journal.pone.0092713. eCollection 2014.

29.

Inference of tumor phylogenies with improved somatic mutation discovery.

Salari R, Saleh SS, Kashef-Haghighi D, Khavari D, Newburger DE, West RB, Sidow A, Batzoglou S.

J Comput Biol. 2013 Nov;20(11):933-44. doi: 10.1089/cmb.2013.0106.

30.

Extensive variation in chromatin states across humans.

Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M.

Science. 2013 Nov 8;342(6159):750-2. doi: 10.1126/science.1242510. Epub 2013 Oct 17.

31.

Short read alignment with populations of genomes.

Huang L, Popic V, Batzoglou S.

Bioinformatics. 2013 Jul 1;29(13):i361-70. doi: 10.1093/bioinformatics/btt215.

32.

Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans.

Aerni SJ, Liu X, Do CB, Gross SS, Nguyen A, Guo SD, Long F, Peng H, Kim SS, Batzoglou S.

Bioinformatics. 2013 Jul 1;29(13):i18-26. doi: 10.1093/bioinformatics/btt223.

33.

Genome evolution during progression to breast cancer.

Newburger DE, Kashef-Haghighi D, Weng Z, Salari R, Sweeney RT, Brunner AL, Zhu SX, Guo X, Varma S, Troxell ML, West RB, Batzoglou S, Sidow A.

Genome Res. 2013 Jul;23(7):1097-108. doi: 10.1101/gr.151670.112. Epub 2013 Apr 8.

34.

Ancestry inference in complex admixtures via variable-length Markov chain linkage models.

Rodriguez JM, Bercovici S, Elmore M, Batzoglou S.

J Comput Biol. 2013 Mar;20(3):199-211. doi: 10.1089/cmb.2012.0088. Epub 2013 Feb 19.

35.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

36.

Linking disease associations with regulatory information in the human genome.

Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M.

Genome Res. 2012 Sep;22(9):1748-59. doi: 10.1101/gr.136127.111.

37.

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.

Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A.

Genome Res. 2012 Sep;22(9):1735-47. doi: 10.1101/gr.136366.111.

38.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

39.

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome.

Newburger DE, Natsoulis G, Grimes S, Bell JM, Davis RW, Batzoglou S, Ji HP.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1137-43. doi: 10.1093/nar/gkr973. Epub 2011 Nov 18.

40.

Reconstruction of genealogical relationships with applications to Phase III of HapMap.

Kyriazopoulou-Panagiotopoulou S, Kashef Haghighi D, Aerni SJ, Sundquist A, Bercovici S, Batzoglou S.

Bioinformatics. 2011 Jul 1;27(13):i333-41. doi: 10.1093/bioinformatics/btr243.

41.

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

Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S.

PLoS Comput Biol. 2010 Dec 2;6(12):e1001025. doi: 10.1371/journal.pcbi.1001025.

42.

RECOMB Main Conference 2009.

Batzoglou S.

J Comput Biol. 2010 Mar;17(3):201. doi: 10.1089/cmb.2010.Pr01. No abstract available.

PMID:
20377440
43.

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

Goode DL, Cooper GM, Schmutz J, Dickson M, Gonzales E, Tsai M, Karra K, Davydov E, Batzoglou S, Myers RM, Sidow A.

Genome Res. 2010 Mar;20(3):301-10. doi: 10.1101/gr.102210.109. Epub 2010 Jan 12.

44.

Autoimmune disease classification by inverse association with SNP alleles.

Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ.

PLoS Genet. 2009 Dec;5(12):e1000792. doi: 10.1371/journal.pgen.1000792. Epub 2009 Dec 24.

45.

Analysis of cell fate from single-cell gene expression profiles in C. elegans.

Liu X, Long F, Peng H, Aerni SJ, Jiang M, Sánchez-Blanco A, Murray JI, Preston E, Mericle B, Batzoglou S, Myers EW, Kim SK.

Cell. 2009 Oct 30;139(3):623-33. doi: 10.1016/j.cell.2009.08.044.

46.

Automatic parameter learning for multiple local network alignment.

Flannick J, Novak A, Do CB, Srinivasan BS, Batzoglou S.

J Comput Biol. 2009 Aug;16(8):1001-22. doi: 10.1089/cmb.2009.0099.

47.

A Classifier-based approach to identify genetic similarities between diseases.

Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S.

Bioinformatics. 2009 Jun 15;25(12):i21-9. doi: 10.1093/bioinformatics/btp226.

48.

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.

Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A.

Nat Methods. 2008 Sep;5(9):829-34. doi: 10.1038/nmeth.1246.

49.

Genetic and computational identification of a conserved bacterial metabolic module.

Boutte CC, Srinivasan BS, Flannick JA, Novak AF, Martens AT, Batzoglou S, Viollier PH, Crosson S.

PLoS Genet. 2008 Dec;4(12):e1000310. doi: 10.1371/journal.pgen.1000310. Epub 2008 Dec 19.

50.

A serial founder effect model for human settlement out of Africa.

Deshpande O, Batzoglou S, Feldman MW, Cavalli-Sforza LL.

Proc Biol Sci. 2009 Jan 22;276(1655):291-300. doi: 10.1098/rspb.2008.0750.

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