| Year |
Citation |
Score |
| 2023 |
Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, ... Batzoglou S, et al. The landscape of tolerated genetic variation in humans and primates. Science (New York, N.Y.). 380: eabn8153. PMID 37262156 DOI: 10.1126/science.abn8197 |
0.333 |
|
| 2023 |
Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, ... Batzoglou S, et al. The landscape of tolerated genetic variation in humans and primates. Biorxiv : the Preprint Server For Biology. PMID 37205491 DOI: 10.1101/2023.05.01.538953 |
0.333 |
|
| 2020 |
Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, ... ... Batzoglou S, et al. The DNA methylation landscape of advanced prostate cancer. Nature Genetics. PMID 32661416 DOI: 10.1038/S41588-020-0648-8 |
0.407 |
|
| 2020 |
Roodgar M, Babveyh A, Nguyen LH, Zhou W, Sinha R, Lee H, Hanks JB, Avula M, Jiang L, Jian R, Lee H, Song G, Chaib H, Weissman IL, Batzoglou S, et al. Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding. Gigascience. 9. PMID 32649757 DOI: 10.1093/Gigascience/Giaa069 |
0.465 |
|
| 2020 |
Zlitni S, Bishara A, Moss EL, Tkachenko E, Kang JB, Culver RN, Andermann TM, Weng Z, Wood C, Handy C, Ji HP, Batzoglou S, Bhatt AS. Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale. Genome Medicine. 12: 50. PMID 32471482 DOI: 10.1186/S13073-020-00747-0 |
0.399 |
|
| 2019 |
Ricketts C, Seidman D, Popic V, Hormozdiari F, Batzoglou S, Hajirasouliha I. Meltos: Multi-Sample Tumor Phylogeny Reconstruction for Structural Variants. Bioinformatics (Oxford, England). PMID 31584621 DOI: 10.1093/Bioinformatics/Btz737 |
0.386 |
|
| 2019 |
Kuleshov V, Ding J, Vo C, Hancock B, Ratner A, Li Y, Ré C, Batzoglou S, Snyder M. A machine-compiled database of genome-wide association studies. Nature Communications. 10: 3341. PMID 31350405 DOI: 10.1038/S41467-019-11026-X |
0.326 |
|
| 2019 |
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, et al. Predicting Splicing from Primary Sequence with Deep Learning. Cell. PMID 30661751 DOI: 10.1016/J.Cell.2018.12.015 |
0.325 |
|
| 2018 |
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, ... ... Batzoglou S, et al. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell. 175: 889. PMID 30340047 DOI: 10.1016/J.Cell.2018.10.019 |
0.317 |
|
| 2018 |
Bishara A, Moss EL, Kolmogorov M, Parada AE, Weng Z, Sidow A, Dekas AE, Batzoglou S, Bhatt AS. High-quality genome sequences of uncultured microbes by assembly of read clouds. Nature Biotechnology. PMID 30320765 DOI: 10.1038/Nbt.4266 |
0.49 |
|
| 2018 |
Wang B, Pourshafeie A, Zitnik M, Zhu J, Bustamante CD, Batzoglou S, Leskovec J. Network enhancement as a general method to denoise weighted biological networks. Nature Communications. 9: 3108. PMID 30082777 DOI: 10.1038/S41467-018-05469-X |
0.325 |
|
| 2018 |
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, ... ... Batzoglou S, et al. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell. PMID 30033370 DOI: 10.1016/J.Cell.2018.06.039 |
0.357 |
|
| 2018 |
Zhou X, Batzoglou S, Sidow A, Zhang L. HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data. Bmc Genomics. 19: 467. PMID 29914369 DOI: 10.1186/S12864-018-4867-7 |
0.412 |
|
| 2018 |
Popic V, Kuleshov V, Snyder M, Batzoglou S. Fast Metagenomic Binning via Hashing and Bayesian Clustering. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 29658784 DOI: 10.1089/Cmb.2017.0250 |
0.337 |
|
| 2017 |
Wang B, Huang L, Zhu Y, Kundaje A, Batzoglou S, Goldenberg A. Vicus: Exploiting local structures to improve network-based analysis of biological data. Plos Computational Biology. 13: e1005621. PMID 29023470 DOI: 10.1371/Journal.Pcbi.1005621 |
0.566 |
|
| 2017 |
Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou S, Sidow A. Genome-wide reconstruction of complex structural variants using read clouds. Nature Methods. PMID 28714986 DOI: 10.1038/Nmeth.4366 |
0.494 |
|
| 2017 |
Popic V, Batzoglou S. A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy. Nature Communications. 8: 15311. PMID 28508884 DOI: 10.1038/Ncomms15311 |
0.413 |
|
| 2017 |
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, et al. Microbial Typing by Machine Learned DNA Melt Signatures. Scientific Reports. 7: 42097. PMID 28165067 DOI: 10.1038/Srep42097 |
0.336 |
|
| 2016 |
Kuleshov V, Snyder MP, Batzoglou S. Genome assembly from synthetic long read clouds. Bioinformatics (Oxford, England). 32: i216-i224. PMID 27307620 DOI: 10.1093/Bioinformatics/Btw267 |
0.416 |
|
| 2015 |
Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nature Biotechnology. PMID 26655498 DOI: 10.1038/Nbt.3416 |
0.432 |
|
| 2015 |
Huang L, Wang B, Chen R, Bercovici S, Batzoglou S. Reveel: large-scale population genotyping using low-coverage sequencing data. Bioinformatics (Oxford, England). PMID 26353840 DOI: 10.1093/Bioinformatics/Btv530 |
0.49 |
|
| 2015 |
Bishara A, Liu Y, Weng Z, Kashef-Haghighi D, Newburger DE, West R, Sidow A, Batzoglou S. Read clouds uncover variation in complex regions of the human genome. Genome Research. 25: 1570-80. PMID 26286554 DOI: 10.1101/Gr.191189.115 |
0.53 |
|
| 2015 |
Popic V, Salari R, Hajirasouliha I, Kashef-Haghighi D, West RB, Batzoglou S. Fast and scalable inference of multi-sample cancer lineages. Genome Biology. 16: 91. PMID 25944252 DOI: 10.1186/S13059-015-0647-8 |
0.314 |
|
| 2015 |
Rodriguez JM, Bercovici S, Huang L, Frostig R, Batzoglou S. Parente2: a fast and accurate method for detecting identity by descent. Genome Research. 25: 280-9. PMID 25273070 DOI: 10.1101/Gr.173641.114 |
0.451 |
|
| 2015 |
Bishara A, Liu Y, Kashef-Haghighi D, Weng Z, Newburger DE, West R, Sidow A, Batzoglou S. Read clouds uncover variation in complex regions of the human genome Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9029: 30-31. DOI: 10.1007/978-3-319-16706-0_5 |
0.321 |
|
| 2014 |
Huang L, Bercovici S, Rodriguez JM, Batzoglou S. An effective filter for IBD detection in large data sets. Plos One. 9: e92713. PMID 24667521 DOI: 10.1371/Journal.Pone.0092713 |
0.356 |
|
| 2013 |
Salari R, Saleh SS, Kashef-Haghighi D, Khavari D, Newburger DE, West RB, Sidow A, Batzoglou S. Inference of tumor phylogenies with improved somatic mutation discovery. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 933-44. PMID 24195709 DOI: 10.1089/cmb.2013.0106 |
0.309 |
|
| 2013 |
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, ... ... Batzoglou S, et al. Extensive variation in chromatin states across humans. Science (New York, N.Y.). 342: 750-2. PMID 24136358 DOI: 10.1126/Science.1242510 |
0.574 |
|
| 2013 |
Huang L, Popic V, Batzoglou S. Short read alignment with populations of genomes. Bioinformatics (Oxford, England). 29: i361-70. PMID 23813006 DOI: 10.1093/Bioinformatics/Btt215 |
0.534 |
|
| 2013 |
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 evolution during progression to breast cancer. Genome Research. 23: 1097-108. PMID 23568837 DOI: 10.1101/Gr.151670.112 |
0.368 |
|
| 2012 |
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, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111 |
0.62 |
|
| 2012 |
Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Research. 22: 1748-59. PMID 22955986 DOI: 10.1101/gr.136127.111 |
0.535 |
|
| 2012 |
Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Research. 22: 1735-47. PMID 22955985 DOI: 10.1101/Gr.136366.111 |
0.579 |
|
| 2012 |
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, ... ... Batzoglou S, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 489: 91-100. PMID 22955619 DOI: 10.1038/Nature11245 |
0.63 |
|
| 2012 |
Newburger DE, Natsoulis G, Grimes S, Bell JM, Davis RW, Batzoglou S, Ji HP. The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome. Nucleic Acids Research. 40: D1137-43. PMID 22102592 DOI: 10.1093/Nar/Gkr973 |
0.525 |
|
| 2010 |
Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. Plos Computational Biology. 6: e1001025. PMID 21152010 DOI: 10.1371/Journal.Pcbi.1001025 |
0.513 |
|
| 2010 |
Goode DL, Cooper GM, Schmutz J, Dickson M, Gonzales E, Tsai M, Karra K, Davydov E, Batzoglou S, Myers RM, Sidow A. Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. Genome Research. 20: 301-10. PMID 20067941 DOI: 10.1101/Gr.102210.109 |
0.493 |
|
| 2009 |
Flannick J, Novak A, Do CB, Srinivasan BS, Batzoglou S. Automatic parameter learning for multiple local network alignment. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1001-22. PMID 19645599 DOI: 10.1089/Cmb.2009.0099 |
0.617 |
|
| 2009 |
Deshpande O, Batzoglou S, Feldman MW, Cavalli-Sforza LL. A serial founder effect model for human settlement out of Africa. Proceedings. Biological Sciences / the Royal Society. 276: 291-300. PMID 18796400 DOI: 10.1098/Rspb.2008.0750 |
0.747 |
|
| 2008 |
Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods. 5: 829-34. PMID 19160518 DOI: 10.1038/Nmeth.1246 |
0.446 |
|
| 2008 |
Boutte CC, Srinivasan BS, Flannick JA, Novak AF, Martens AT, Batzoglou S, Viollier PH, Crosson S. Genetic and computational identification of a conserved bacterial metabolic module. Plos Genetics. 4: e1000310. PMID 19096521 DOI: 10.1371/Journal.Pgen.1000310 |
0.653 |
|
| 2008 |
Flannick J, Novak A, Do CB, Srinivasan BS, Batzoglou S. Automatic parameter learning for multiple network alignment Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4955: 214-231. DOI: 10.1007/978-3-540-78839-3_19 |
0.545 |
|
| 2007 |
Gross SS, Do CB, Sirota M, Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biology. 8: R269. PMID 18096039 DOI: 10.1186/Gb-2007-8-12-R269 |
0.332 |
|
| 2007 |
Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, Pullen KM, El-Sayed YY, Taslimi MM, Batzoglou S, Ronaghi M. Bacterial flora-typing with targeted, chip-based Pyrosequencing. Bmc Microbiology. 7: 108. PMID 18047683 DOI: 10.1186/1471-2180-7-108 |
0.393 |
|
| 2007 |
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Batzoglou S, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341 |
0.508 |
|
| 2007 |
Srinivasan BS, Shah NH, Flannick JA, Abeliuk E, Novak AF, Batzoglou S. Current progress in network research: toward reference networks for key model organisms. Briefings in Bioinformatics. 8: 318-32. PMID 17728341 DOI: 10.1093/Bib/Bbm038 |
0.648 |
|
| 2007 |
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Batzoglou S, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874 |
0.799 |
|
| 2007 |
Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Batzoglou S, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307 |
0.805 |
|
| 2007 |
Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. Whole-genome sequencing and assembly with high-throughput, short-read technologies. Plos One. 2: e484. PMID 17534434 DOI: 10.1371/Journal.Pone.0000484 |
0.489 |
|
| 2006 |
Phuong TM, Do CB, Edgar RC, Batzoglou S. Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Research. 34: 5932-42. PMID 17068081 DOI: 10.1093/Nar/Gkl511 |
0.435 |
|
| 2006 |
Naughton BT, Fratkin E, Batzoglou S, Brutlag DL. A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. Nucleic Acids Research. 34: 5730-9. PMID 17041233 DOI: 10.1093/Nar/Gkl585 |
0.3 |
|
| 2006 |
Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S. Graemlin: general and robust alignment of multiple large interaction networks. Genome Research. 16: 1169-81. PMID 16899655 DOI: 10.1101/Gr.5235706 |
0.628 |
|
| 2006 |
Fratkin E, Naughton BT, Brutlag DL, Batzoglou S. MotifCut: regulatory motifs finding with maximum density subgraphs. Bioinformatics (Oxford, England). 22: e150-7. PMID 16873465 DOI: 10.1093/Bioinformatics/Btl243 |
0.324 |
|
| 2006 |
Edgar RC, Batzoglou S. Multiple sequence alignment. Current Opinion in Structural Biology. 16: 368-73. PMID 16679011 DOI: 10.1016/J.Sbi.2006.04.004 |
0.44 |
|
| 2006 |
Davydov E, Batzoglou S. A computational model for RNA multiple structural alignment Theoretical Computer Science. 368: 205-216. DOI: 10.1016/J.Tcs.2006.09.013 |
0.321 |
|
| 2006 |
Do CB, Gross SS, Batzoglou S. CONTRAlign: Discriminative training for protein sequence alignment Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 160-174. DOI: 10.1007/11732990_15 |
0.317 |
|
| 2006 |
Srinivasan BS, Novak AF, Flannick JA, Batzoglou S, McAdams HH. Integrated protein interaction networks for 11 microbes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 1-14. |
0.548 |
|
| 2005 |
Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature. 438: 1105-15. PMID 16372000 DOI: 10.1038/Nature04341 |
0.543 |
|
| 2005 |
Flannick J, Batzoglou S. Using multiple alignments to improve seeded local alignment algorithms. Nucleic Acids Research. 33: 4563-77. PMID 16100379 DOI: 10.1093/Nar/Gki767 |
0.668 |
|
| 2005 |
Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Research. 15: 901-13. PMID 15965027 DOI: 10.1101/Gr.3577405 |
0.797 |
|
| 2005 |
Batzoglou S. The many faces of sequence alignment. Briefings in Bioinformatics. 6: 6-22. PMID 15826353 DOI: 10.1093/Bib/6.1.6 |
0.523 |
|
| 2005 |
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Research. 15: 330-40. PMID 15687296 DOI: 10.1101/Gr.2821705 |
0.664 |
|
| 2004 |
Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Batzoglou S, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/Science.1105136 |
0.779 |
|
| 2004 |
Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS. A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Research. 32: W204-7. PMID 15215381 DOI: 10.1093/Nar/Gkh461 |
0.594 |
|
| 2004 |
Brudno M, Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, Dubchak I. Automated whole-genome multiple alignment of rat, mouse, and human. Genome Research. 14: 685-92. PMID 15060011 DOI: 10.1101/Gr.2067704 |
0.675 |
|
| 2004 |
Cooper GM, Brudno M, Stone EA, Dubchak I, Batzoglou S, Sidow A. Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Research. 14: 539-48. PMID 15059994 DOI: 10.1101/Gr.2034704 |
0.656 |
|
| 2004 |
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Batzoglou S, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426 |
0.703 |
|
| 2004 |
Shah N, Couronne O, Pennacchio LA, Brudno M, Batzoglou S, Bethel EW, Rubin EM, Hamann B, Dubchak I. Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics (Oxford, England). 20: 636-43. PMID 15033870 DOI: 10.1093/Bioinformatics/Btg459 |
0.639 |
|
| 2004 |
Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S. Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Research. 14: 451-8. PMID 14993210 DOI: 10.1101/Gr.1327604 |
0.676 |
|
| 2004 |
Do CB, Brudno M, Batzoglou S. PROBCONS: Probabilistic consistency-based multiple alignment of amino acid sequences Proceedings of the National Conference On Artificial Intelligence. 703-708. |
0.625 |
|
| 2004 |
Sundararajan M, Brudno M, Small K, Sidow A, Batzoglou S. Chaining algorithms for alignment of draft sequence Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3240: 326-337. |
0.64 |
|
| 2003 |
Brudno M, Chapman M, Göttgens B, Batzoglou S, Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. Bmc Bioinformatics. 4: 66. PMID 14693042 DOI: 10.1186/1471-2105-4-66 |
0.717 |
|
| 2003 |
Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, Morgenstern B. AGenDA: homology-based gene prediction. Bioinformatics (Oxford, England). 19: 1575-7. PMID 12912840 DOI: 10.1093/Bioinformatics/Btg181 |
0.677 |
|
| 2003 |
Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S. Glocal alignment: finding rearrangements during alignment. Bioinformatics (Oxford, England). 19: i54-62. PMID 12855437 DOI: 10.1093/Bioinformatics/Btg1005 |
0.693 |
|
| 2003 |
Khambata-Ford S, Liu Y, Gleason C, Dickson M, Altman RB, Batzoglou S, Myers RM. Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay. Genome Research. 13: 1765-74. PMID 12805274 DOI: 10.1101/Gr.529803 |
0.686 |
|
| 2003 |
Cooper GM, Brudno M, Green ED, Batzoglou S, Sidow A. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Research. 13: 813-20. PMID 12727901 DOI: 10.1101/Gr.1064503 |
0.72 |
|
| 2003 |
Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Research. 13: 721-31. PMID 12654723 DOI: 10.1101/Gr.926603 |
0.718 |
|
| 2002 |
Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: a whole-genome shotgun assembler. Genome Research. 12: 177-89. PMID 11779843 DOI: 10.1101/gr.208902 |
0.341 |
|
| 2001 |
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Batzoglou S, et al. Initial sequencing and analysis of the human genome. Nature. 409: 860-921. PMID 11237011 DOI: 10.1038/35057062 |
0.542 |
|
| 2001 |
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Batzoglou S, et al. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature. 412: 565-566. DOI: 10.1038/35087627 |
0.539 |
|
| 2000 |
Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Research. 10: 950-8. PMID 10899144 DOI: 10.1101/Gr.10.7.950 |
0.44 |
|
| 1999 |
Batzoglou S, Berger B, Mesirov J, Lander ES. Sequencing a genome by walking with clone-end sequences: a mathematical analysis. Genome Research. 9: 1163-74. PMID 10613838 DOI: 10.1101/Gr.9.12.1163 |
0.537 |
|
| 1999 |
Pachter L, Batzoglou S, Spitkovsky VI, Banks E, Lander ES, Kleitman DJ, Berger B. A dictionary-based approach for gene annotation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 419-30. PMID 10582576 DOI: 10.1089/106652799318364 |
0.432 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2008 |
Sundquist A, Fratkin E, Do CB, Batzoglou S. Effect of genetic divergence in identifying ancestral origin using HAPAA. Genome Research. 18: 676-82. PMID 18353807 DOI: 10.1101/Gr.072850.107 |
0.299 |
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| 1999 |
Pachter L, Batzoglou S, Spitkovsky VI, Beebee WS, Lander ES, Berger B, Kleitman DJ. Dictionary based approach for gene annotation Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 285-294. |
0.297 |
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| 2018 |
Ramazzotti D, Lal A, Wang B, Batzoglou S, Sidow A. Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival. Nature Communications. 9: 4453. PMID 30367051 DOI: 10.1038/S41467-018-06921-8 |
0.294 |
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| 2017 |
Wang B, Ramazzotti D, De Sano L, Zhu J, Pierson E, Batzoglou S. SIMLR: A Tool for Large-Scale Genomic Analyses by Multi-Kernel Learning. Proteomics. PMID 29265724 DOI: 10.1002/Pmic.201700232 |
0.293 |
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| 2006 |
Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics (Oxford, England). 22: e90-8. PMID 16873527 DOI: 10.1093/Bioinformatics/Btl246 |
0.289 |
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| 2017 |
Wang B, Zhu J, Pierson E, Ramazzotti D, Batzoglou S. Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. Nature Methods. PMID 28263960 DOI: 10.1038/Nmeth.4207 |
0.281 |
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| 2013 |
Aerni SJ, Liu X, Do CB, Gross SS, Nguyen A, Guo SD, Long F, Peng H, Kim SS, Batzoglou S. Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans. Bioinformatics (Oxford, England). 29: i18-26. PMID 23812982 DOI: 10.1093/Bioinformatics/Btt223 |
0.279 |
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| 1997 |
Agarwala R, Batzoglou S, Dancík V, Decatur SE, Hannenhalli S, Farach M, Muthukrishnan S, Skiena S. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 4: 275-96. PMID 9278060 DOI: 10.1089/Cmb.1997.4.275 |
0.279 |
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| 2005 |
Manohar A, Batzoglou S. TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 111-9. PMID 16447969 DOI: 10.1109/CSB.2005.53 |
0.276 |
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| 2003 |
Lee SI, Batzoglou S. Application of independent component analysis to microarrays. Genome Biology. 4: R76. PMID 14611662 DOI: 10.1186/Gb-2003-4-11-R76 |
0.273 |
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| 2009 |
Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. Autoimmune disease classification by inverse association with SNP alleles. Plos Genetics. 5: e1000792. PMID 20041220 DOI: 10.1371/Journal.Pgen.1000792 |
0.273 |
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| 2013 |
Rodriguez JM, Bercovici S, Elmore M, Batzoglou S. Ancestry inference in complex admixtures via variable-length Markov chain linkage models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 199-211. PMID 23421795 DOI: 10.1089/Cmb.2012.0088 |
0.273 |
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| 2009 |
Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S. A Classifier-based approach to identify genetic similarities between diseases. Bioinformatics (Oxford, England). 25: i21-9. PMID 19477990 DOI: 10.1093/Bioinformatics/Btp226 |
0.269 |
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| 2009 |
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. Analysis of cell fate from single-cell gene expression profiles in C. elegans. Cell. 139: 623-33. PMID 19879847 DOI: 10.1016/J.Cell.2009.08.044 |
0.267 |
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| 2015 |
Spies N, Smith CL, Rodriguez JM, Baker JC, Batzoglou S, Sidow A. Constraint and divergence of global gene expression in the mammalian embryo. Elife. 4: e05538. PMID 25871848 DOI: 10.7554/Elife.05538 |
0.256 |
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| 2018 |
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. Author Correction: Predicting the clinical impact of human mutation with deep neural networks. Nature Genetics. PMID 30559491 DOI: 10.1038/S41588-018-0329-Z |
0.255 |
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| 2014 |
Batzoglou S, Schwartz R. Computational biology and bioinformatics. Bioinformatics (Oxford, England). 30: i1-2. PMID 24931972 DOI: 10.1093/Bioinformatics/Btu304 |
0.251 |
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| 2008 |
Do CB, Batzoglou S. What is the expectation maximization algorithm? Nature Biotechnology. 26: 897-9. PMID 18688245 DOI: 10.1038/Nbt1406 |
0.248 |
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| 2015 |
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, et al. Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proceedings of the National Academy of Sciences of the United States of America. 112: E1116-25. PMID 25713363 DOI: 10.1073/Pnas.1501199112 |
0.248 |
|
| 2006 |
Srinivasan BS, Do CB, Batzoglou S. Evidence for intelligent (algorithm) design. Genome Biology. 7: 322. PMID 16879725 DOI: 10.1186/Gb-2006-7-7-322 |
0.237 |
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| 2015 |
Spies N, Smith CL, Rodriguez JM, Baker JC, Batzoglou S, Sidow A. Author response: Constraint and divergence of global gene expression in the mammalian embryo Elife. DOI: 10.7554/Elife.05538.014 |
0.237 |
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| 2015 |
Weng Z, Spies N, Zhu SX, Newburger DE, Kashef-Haghighi D, Batzoglou S, Sidow A, West RB. Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia. Genome Medicine. 7: 28. PMID 25918554 DOI: 10.1186/S13073-015-0146-2 |
0.226 |
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| 2010 |
Batzoglou S. RECOMB Main Conference 2009. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 201. PMID 20377440 DOI: 10.1089/Cmb.2010.Pr01 |
0.223 |
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| 2013 |
Rodriguez JM, Batzoglou S, Bercovici S. An accurate method for inferring relatedness in large datasets of unphased genotypes via an embedded likelihood-ratio test Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7821: 212-229. DOI: 10.1007/978-3-642-37195-0_18 |
0.216 |
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| 2008 |
Sundquist A, Fratkin E, Do CB, Batzoglou S. Effects of genetic divergence in identifying ancestral origin using HAPAA Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4955: 423. DOI: 10.1007/978-3-540-78839-3_36 |
0.205 |
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| 2008 |
Do CB, Foo CS, Batzoglou S. A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics (Oxford, England). 24: i68-76. PMID 18586747 DOI: 10.1093/bioinformatics/btn177 |
0.187 |
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| 2004 |
Lee SI, Batzoglou S. ICA-based clustering of genes from microarray expression data Advances in Neural Information Processing Systems. |
0.18 |
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| 2024 |
Suhre K, Venkataraman GR, Guturu H, Halama A, Stephan N, Thareja G, Sarwath H, Motamedchaboki K, Donovan MKR, Siddiqui A, Batzoglou S, Schmidt F. Nanoparticle enrichment mass-spectrometry proteomics identifies protein-altering variants for precise pQTL mapping. Nature Communications. 15: 989. PMID 38307861 DOI: 10.1038/s41467-024-45233-y |
0.155 |
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| 2022 |
Ferdosi S, Tangeysh B, Brown TR, Everley PA, Figa M, McLean M, Elgierari EM, Zhao X, Garcia VJ, Wang T, Chang MEK, Riedesel K, Chu J, Mahoney M, Xia H, ... ... Batzoglou S, et al. Engineered nanoparticles enable deep proteomics studies at scale by leveraging tunable nano-bio interactions. Proceedings of the National Academy of Sciences of the United States of America. 119: e2106053119. PMID 35275789 DOI: 10.1073/pnas.2106053119 |
0.139 |
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| 2011 |
Kyriazopoulou-Panagiotopoulou S, Kashef Haghighi D, Aerni SJ, Sundquist A, Bercovici S, Batzoglou S. Reconstruction of genealogical relationships with applications to Phase III of HapMap. Bioinformatics (Oxford, England). 27: i333-41. PMID 21685089 DOI: 10.1093/bioinformatics/btr243 |
0.114 |
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| 2023 |
Huang T, Wang J, Stukalov A, Donovan MKR, Ferdosi S, Williamson L, Just S, Castro G, Cantrell LS, Elgierari E, Benz RW, Huang Y, Motamedchaboki K, Hakimi A, Arrey T, ... ... Batzoglou S, et al. Protein Coronas on Functionalized Nanoparticles Enable Quantitative and Precise Large-Scale Deep Plasma Proteomics. Biorxiv : the Preprint Server For Biology. PMID 37693476 DOI: 10.1101/2023.08.28.555225 |
0.104 |
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| 1999 |
Batzoglou S, Istrail S. Physical mapping with repeated probes: The hypergraph superstring problem Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1645: 66-77. DOI: 10.1007/3-540-48452-3_5 |
0.1 |
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| 2023 |
Donovan MKR, Huang Y, Blume JE, Wang J, Hornburg D, Ferdosi S, Mohtashemi I, Kim S, Ko M, Benz RW, Platt TL, Batzoglou S, Diaz LA, Farokhzad OC, Siddiqui A. Functionally distinct BMP1 isoforms show an opposite pattern of abundance in plasma from non-small cell lung cancer subjects and controls. Plos One. 18: e0282821. PMID 36989217 DOI: 10.1371/journal.pone.0282821 |
0.098 |
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| 2024 |
Lacar B, Ferdosi S, Alavi A, Stukalov A, Venkataraman GR, de Geus M, Dodge H, Wu CY, Kivisakk P, Das S, Guturu H, Hyman B, Batzoglou S, Arnold SE, Siddiqui A. Identification of Novel Biomarkers for Alzheimer's Disease and Related Dementias Using Unbiased Plasma Proteomics. Biorxiv : the Preprint Server For Biology. PMID 38260620 DOI: 10.1101/2024.01.05.574446 |
0.096 |
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| 2022 |
Hornburg D, Ferdosi S, Stukalov A, Hasan M, Tangeysh B, Brown TR, Wang T, Elgierari EM, Zhao X, Huang Y, Alavi A, Lee-McMullen B, Chu J, Figa M, Tao W, ... ... Batzoglou S, et al. Enhanced competition at the nano-bio interface enables comprehensive characterization of protein corona dynamics and deep coverage of proteomes. Advanced Materials (Deerfield Beach, Fla.). e2206008. PMID 35986672 DOI: 10.1002/adma.202206008 |
0.081 |
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| 2007 |
Gross SS, Russakovsky O, Do CB, Batzoglou S. Training conditional random fields for maximum labelwise accuracy Advances in Neural Information Processing Systems. 529-536. |
0.075 |
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| 1997 |
Agarwala R, Batzoglou S, Dancik V, Decatur SE, Farach M, Hannenhalli S, Muthukrishnan S, Skiena S. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model Proceedings of Thr Annual International Conference On Computational Molecular Biology, Recomb. 1-2. |
0.068 |
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| 2009 |
Batzoglou S. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5541: XI. |
0.063 |
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| Hide low-probability matches. |