Michael Brudno, Ph.D. - Publications

Affiliations: 
2004 Stanford University, Palo Alto, CA 

98 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Labrie V, Buske OJ, Oh E, Jeremian R, Ptak C, Gasiūnas G, Maleckas A, Petereit R, Žvirbliene A, Adamonis K, Kriukienė E, Koncevičius K, Gordevičius J, Nair A, Zhang A, ... ... Brudno M, et al. Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging. Nature Structural & Molecular Biology. PMID 27159559 DOI: 10.1038/nsmb.3227  0.8
2016 Dyke SO, Philippakis AA, Rambla De Argila J, Paltoo DN, Luetkemeier ES, Knoppers BM, Brookes AJ, Spalding JD, Thompson M, Roos M, Boycott KM, Brudno M, Hurles M, Rehm HL, Matern A, et al. Consent Codes: Upholding Standard Data Use Conditions. Plos Genetics. 12: e1005772. PMID 26796797 DOI: 10.1371/journal.pgen.1005772  0.8
2016 Glueck M, Hamilton P, Chevalier F, Breslav S, Khan A, Wigdor D, Brudno M. PhenoBlocks: Phenotype Comparison Visualizations. Ieee Transactions On Visualization and Computer Graphics. 22: 101-10. PMID 26529691 DOI: 10.1109/TVCG.2015.2467733  0.8
2015 Hood RL, McGillivray G, Hunter MF, Roberston SP, Bulman DE, Boycott KM, Stark Z. Severe connective tissue laxity including aortic dilatation in Sotos syndrome. American Journal of Medical Genetics. Part A. PMID 26613968 DOI: 10.1002/ajmg.a.37402  0.8
2015 Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, Köhler S, Lee EM, Links AE, ... ... Brudno M, et al. Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 26562225 DOI: 10.1038/gim.2015.137  0.8
2015 Foong J, Girdea M, Stavropoulos J, Brudno M. Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data. Plos One. 10: e0139656. PMID 26437450 DOI: 10.1371/journal.pone.0139656  0.8
2015 Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, et al. The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery. Human Mutation. 36: 915-21. PMID 26295439 DOI: 10.1002/humu.22858  0.8
2015 Buske OJ, Schiettecatte F, Hutton B, Dumitriu S, Misyura A, Huang L, Hartley T, Girdea M, Sobreira N, Mungall C, Brudno M. The Matchmaker Exchange API: Automating Patient Matching Through the Exchange of Structured Phenotypic and Genotypic Profiles. Human Mutation. 36: 922-7. PMID 26255989 DOI: 10.1002/humu.22850  0.8
2015 Buske OJ, Girdea M, Dumitriu S, Gallinger B, Hartley T, Trang H, Misyura A, Friedman T, Beaulieu C, Bone WP, Links AE, Washington NL, Haendel MA, Robinson PN, Boerkoel CF, ... ... Brudno M, et al. PhenomeCentral: A Portal for Phenotypic and Genotypic Matchmaking of Patients with Rare Genetic Diseases. Human Mutation. PMID 26251998 DOI: 10.1002/humu.22851  0.8
2015 Krawitz P, Buske O, Zhu N, Brudno M, Robinson PN. The Genomic Birthday Paradox: How Much Is Enough? Human Mutation. 36: 989-97. PMID 26239817 DOI: 10.1002/humu.22848  0.8
2015 Jiang Y, Turinsky AL, Brudno M. The missing indels: an estimate of indel variation in a human genome and analysis of factors that impede detection. Nucleic Acids Research. 43: 7217-28. PMID 26130710 DOI: 10.1093/nar/gkv677  0.8
2015 Sawyer SL, Cheuk-Him Ng A, Innes AM, Wagner JD, Dyment DA, Tetreault M, Majewski J, Boycott KM, Screaton RA, Nicholson G. Homozygous mutations in MFN2 cause multiple symmetric lipomatosis associated with neuropathy. Human Molecular Genetics. PMID 26085578 DOI: 10.1093/hmg/ddv229  0.8
2015 Liu H, Sawyer SL, Gos M, Grynspan D, Issa K, Ramphal R, Rotaru C, Consortium FC, Majewski J, Boycott KM, Graham G, Bromwich M. Atypical fibrodysplasia ossificans progressiva diagnosed by whole-exome sequencing. American Journal of Medical Genetics. Part A. 167: 1337-41. PMID 25899773 DOI: 10.1002/ajmg.a.36969  0.8
2015 Rousseau-Nepton I, Okubo M, Grabs R, Mitchell J, Polychronakos C, Rodd C. A founder AGL mutation causing glycogen storage disease type IIIa in Inuit identified through whole-exome sequencing: a case series. Cmaj : Canadian Medical Association Journal = Journal De L'Association Medicale Canadienne. 187: E68-73. PMID 25602008 DOI: 10.1503/cmaj.140840  0.8
2015 Chardon JW, Smith AC, Woulfe J, Pena E, Rakhra K, Dennie C, Beaulieu C, Huang L, Schwartzentruber J, Hawkins C, Harms MB, Dojeiji S, Zhang M, Majewski J, et al. LIMS2 mutations are associated with a novel muscular dystrophy, severe cardiomyopathy and triangular tongues. Clinical Genetics. PMID 25589244 DOI: 10.1111/cge.12561  0.8
2015 Kmoch S, Majewski J, Ramamurthy V, Cao S, Fahiminiya S, Ren H, MacDonald IM, Lopez I, Sun V, Keser V, Khan A, Stránecký V, Hartmannová H, P?istoupilová A, Hoda?ová K, et al. Mutations in PNPLA6 are linked to photoreceptor degeneration and various forms of childhood blindness. Nature Communications. 6: 5614. PMID 25574898 DOI: 10.1038/ncomms6614  0.8
2015 Sawyer SL, Tian L, Kähkönen M, Schwartzentruber J, Kircher M, Majewski J, Dyment DA, Innes AM, Boycott KM, Moreau LA, Moilanen JS, Greenberg RA. Biallelic mutations in BRCA1 cause a new Fanconi anemia subtype. Cancer Discovery. 5: 135-42. PMID 25472942 DOI: 10.1158/2159-8290.CD-14-1156  0.8
2015 Baynam G, Walters M, Claes P, Kung S, LeSouef P, Dawkins H, Bellgard M, Girdea M, Brudno M, Robinson P, Zankl A, Groza T, Gillett D, Goldblatt J. Phenotyping: targeting genotype's rich cousin for diagnosis. Journal of Paediatrics and Child Health. 51: 381-6. PMID 25109851 DOI: 10.1111/jpc.12705  0.8
2015 Frosk P, Chodirker B, Simard L, El-Matary W, Hanlon-Dearman A, Schwartzentruber J, Majewski J, Boycott K, Friedman J, Michaud J, Bernier F, Brudno M, Fernandez B, Knoppers B, Samuels M, et al. A novel CCBE1 mutation leading to a mild form of hennekam syndrome: Case report and review of the literature Bmc Medical Genetics. 16. DOI: 10.1186/s12881-015-0175-0  0.8
2014 Vincent A, Forster N, Maynes JT, Paton TA, Billingsley G, Roslin NM, Ali A, Sutherland J, Wright T, Westall CA, Paterson AD, Marshall CR, Héon E. OTX2 mutations cause autosomal dominant pattern dystrophy of the retinal pigment epithelium. Journal of Medical Genetics. 51: 797-805. PMID 25293953 DOI: 10.1136/jmedgenet-2014-102620  0.8
2014 Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, ... ... Brudno M, et al. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Research. 24: 2077-89. PMID 25273068 DOI: 10.1101/gr.174920.114  0.8
2014 Schwartzentruber J, Buhas D, Majewski J, Sasarman F, Papillon-Cavanagh S, Thiffault I, Thiffaut I, Sheldon KM, Massicotte C, Patry L, Simon M, Zare AS, McKernan KJ, Michaud J, et al. Mutation in the nuclear-encoded mitochondrial isoleucyl-tRNA synthetase IARS2 in patients with cataracts, growth hormone deficiency with short stature, partial sensorineural deafness, and peripheral neuropathy or with Leigh syndrome. Human Mutation. 35: 1285-9. PMID 25130867 DOI: 10.1002/humu.22629  0.8
2014 Farhan SM, Murphy LM, Robinson JF, Wang J, Siu VM, Rupar CA, Prasad AN, Hegele RA. Linkage analysis and exome sequencing identify a novel mutation in KCTD7 in patients with progressive myoclonus epilepsy with ataxia. Epilepsia. 55: e106-11. PMID 25060828 DOI: 10.1111/epi.12730  0.8
2014 Lynch DC, Revil T, Schwartzentruber J, Bhoj EJ, Innes AM, Lamont RE, Lemire EG, Chodirker BN, Taylor JP, Zackai EH, McLeod DR, Kirk EP, Hoover-Fong J, Fleming L, Savarirayan R, et al. Disrupted auto-regulation of the spliceosomal gene SNRPB causes cerebro-costo-mandibular syndrome. Nature Communications. 5: 4483. PMID 25047197 DOI: 10.1038/ncomms5483  0.8
2014 Rampášek L, Arbabi A, Brudno M. Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing. Bioinformatics (Oxford, England). 30: i212-8. PMID 24931986 DOI: 10.1093/bioinformatics/btu292  0.8
2014 Beaulieu CL, Majewski J, Schwartzentruber J, Samuels ME, Fernandez BA, Bernier FP, Brudno M, Knoppers B, Marcadier J, Dyment D, Adam S, Bulman DE, Jones SJ, Avard D, Nguyen MT, et al. FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project. American Journal of Human Genetics. 94: 809-17. PMID 24906018 DOI: 10.1016/j.ajhg.2014.05.003  0.8
2014 Poliakov A, Foong J, Brudno M, Dubchak I. GenomeVISTA--an integrated software package for whole-genome alignment and visualization. Bioinformatics (Oxford, England). 30: 2654-5. PMID 24860159 DOI: 10.1093/bioinformatics/btu355  0.8
2014 Buczkowicz P, Hoeman C, Rakopoulos P, Pajovic S, Letourneau L, Dzamba M, Morrison A, Lewis P, Bouffet E, Bartels U, Zuccaro J, Agnihotri S, Ryall S, Barszczyk M, Chornenkyy Y, ... ... Brudno M, et al. Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations. Nature Genetics. 46: 451-6. PMID 24705254 DOI: 10.1038/ng.2936  0.8
2014 Mirzaa GM, Parry DA, Fry AE, Giamanco KA, Schwartzentruber J, Vanstone M, Logan CV, Roberts N, Johnson CA, Singh S, Kholmanskikh SS, Adams C, Hodge RD, Hevner RF, Bonthron DT, et al. De novo CCND2 mutations leading to stabilization of cyclin D2 cause megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome. Nature Genetics. 46: 510-5. PMID 24705253 DOI: 10.1038/ng.2948  0.8
2014 Wang B, Mezlini AM, Demir F, Fiume M, Tu Z, Brudno M, Haibe-Kains B, Goldenberg A. Similarity network fusion for aggregating data types on a genomic scale. Nature Methods. 11: 333-7. PMID 24464287 DOI: 10.1038/nmeth.2810  0.8
2014 Greenway SC, McLeod R, Hume S, Roslin NM, Alvarez N, Giuffre M, Zhan SH, Shen Y, Preuss C, Andelfinger G, Jones SJ, Gerull B. Exome sequencing identifies a novel variant in ACTC1 associated with familial atrial septal defect. The Canadian Journal of Cardiology. 30: 181-7. PMID 24461919 DOI: 10.1016/j.cjca.2013.12.003  0.8
2014 Au PY, Racher HE, Graham JM, Kramer N, Lowry RB, Parboosingh JS, Innes AM. De novo exon 1 missense mutations of SKI and Shprintzen-Goldberg syndrome: two new cases and a clinical review. American Journal of Medical Genetics. Part A. 164: 676-84. PMID 24357594 DOI: 10.1002/ajmg.a.36340  0.8
2014 Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Research. 42: D966-74. PMID 24217912 DOI: 10.1093/nar/gkt1026  0.8
2014 McKenzie ED, Sharma PN, Parboosingh JS, Suchowersky O, Boycott K, Friedman J, Michaud J, Bernier F, Brudno M, Fernandez B, Knoppers B, Samuels M, Scherer S. Novel SACS mutation deviates from the French Canadian ARSACS phenotype Canadian Journal of Neurological Sciences. 41: 88-89.  0.8
2013 Rastas P, Paulin L, Hanski I, Lehtonen R, Auvinen P. Lep-MAP: fast and accurate linkage map construction for large SNP datasets. Bioinformatics (Oxford, England). 29: 3128-34. PMID 24078685 DOI: 10.1093/bioinformatics/btt563  0.8
2013 Marschall T, Hajirasouliha I, Schönhuth A. MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. Bioinformatics (Oxford, England). 29: 3143-50. PMID 24072733 DOI: 10.1093/bioinformatics/btt556  0.8
2013 David M, Mustafa H, Brudno M. Detecting Alu insertions from high-throughput sequencing data. Nucleic Acids Research. 41: e169. PMID 23921633 DOI: 10.1093/nar/gkt612  0.8
2013 Buske OJ, Manickaraj A, Mital S, Ray PN, Brudno M. Identification of deleterious synonymous variants in human genomes. Bioinformatics (Oxford, England). 29: 1843-50. PMID 23736532 DOI: 10.1093/bioinformatics/btt308  0.8
2013 Girdea M, Dumitriu S, Fiume M, Bowdin S, Boycott KM, Chénier S, Chitayat D, Faghfoury H, Meyn MS, Ray PN, So J, Stavropoulos DJ, Brudno M. PhenoTips: patient phenotyping software for clinical and research use. Human Mutation. 34: 1057-65. PMID 23636887 DOI: 10.1002/humu.22347  0.8
2013 Donmez N, Brudno M. SCARPA: scaffolding reads with practical algorithms. Bioinformatics (Oxford, England). 29: 428-34. PMID 23274213 DOI: 10.1093/bioinformatics/bts716  0.8
2013 Mezlini AM, Smith EJ, Fiume M, Buske O, Savich GL, Shah S, Aparicio S, Chiang DY, Goldenberg A, Brudno M. iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Research. 23: 519-29. PMID 23204306 DOI: 10.1101/gr.142232.112  0.8
2012 Jiang Y, Wang Y, Brudno M. PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics (Oxford, England). 28: 2576-83. PMID 22851530 DOI: 10.1093/bioinformatics/bts484  0.8
2012 Fiume M, Smith EJ, Brook A, Strbenac D, Turner B, Mezlini AM, Robinson MD, Wodak SJ, Brudno M. Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Research. 40: W615-21. PMID 22638571 DOI: 10.1093/nar/gks427  0.8
2012 Warde-Farley D, Brudno M, Morris Q, Goldenberg A. Mixture model for sub-phenotyping in GWAS. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 363-74. PMID 22174291  0.8
2011 Marsh AK, Willer DO, Ambagala AP, Dzamba M, Chan JK, Pilon R, Fournier J, Sandstrom P, Brudno M, MacDonald KS. Genomic sequencing and characterization of cynomolgus macaque cytomegalovirus. Journal of Virology. 85: 12995-3009. PMID 21994460 DOI: 10.1128/JVI.05840-11  0.8
2011 David M, Dzamba M, Lister D, Ilie L, Brudno M. SHRiMP2: sensitive yet practical SHort Read Mapping. Bioinformatics (Oxford, England). 27: 1011-2. PMID 21278192 DOI: 10.1093/bioinformatics/btr046  0.8
2011 Lagar-Cavilla HA, Whitney JA, Bryant R, Patchin P, Brudno M, De Lara E, Rumble SM, Satyanarayanan M, Scannell A. SnowFlock: Virtual machine cloning as a first-class cloud primitive Acm Transactions On Computer Systems. 29. DOI: 10.1145/1925109.1925111  0.8
2011 Whitney J, Koh J, Costanzo M, Brown G, Boone C, Brudno M. Clustering with overlap for genetic interaction networks via local search optimization Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6833: 326-338. DOI: 10.1007/978-3-642-23038-7_27  0.8
2011 Donmez N, Brudno M. Hapsembler: An assembler for highly polymorphic genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6577: 38-52. DOI: 10.1007/978-3-642-20036-6_5  0.8
2010 Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M. Detecting copy number variation with mated short reads. Genome Research. 20: 1613-22. PMID 20805290 DOI: 10.1101/gr.106344.110  0.8
2010 Fiume M, Williams V, Brook A, Brudno M. Savant: genome browser for high-throughput sequencing data. Bioinformatics (Oxford, England). 26: 1938-44. PMID 20562449 DOI: 10.1093/bioinformatics/btq332  0.8
2010 Dalca AV, Rumble SM, Levy S, Brudno M. VARiD: a variation detection framework for color-space and letter-space platforms. Bioinformatics (Oxford, England). 26: i343-9. PMID 20529926 DOI: 10.1093/bioinformatics/btq184  0.8
2010 Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, ... ... Brudno M, et al. The genetic landscape of a cell. Science (New York, N.Y.). 327: 425-31. PMID 20093466 DOI: 10.1126/science.1180823  0.8
2010 Dalca AV, Brudno M. Genome variation discovery with high-throughput sequencing data. Briefings in Bioinformatics. 11: 3-14. PMID 20053733 DOI: 10.1093/bib/bbp058  0.8
2010 Lee S, Xing E, Brudno M. MoGUL: Detecting common insertions and deletions in a population Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6044: 357-368. DOI: 10.1007/978-3-642-12683-3_23  0.8
2010 Alkan C, Brudno M, Eichler EE, Kann MG, Sahinalp SC. Personal genomics Pacific Symposium On Biocomputing 2010, Psb 2010. 302-304.  0.8
2009 Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nature Methods. 6: S13-20. PMID 19844226 DOI: 10.1038/nmeth.1374  0.8
2009 Brudno M, Medvedev P, Stoye J, De La Vega FM. A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinformatics (Oxford, England). 25: 2863-4. PMID 19783529 DOI: 10.1093/bioinformatics/btp525  0.8
2009 Medvedev P, Brudno M. Maximum likelihood genome assembly. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1101-16. PMID 19645596 DOI: 10.1089/cmb.2009.0047  0.8
2009 Lee S, Hormozdiari F, Alkan C, Brudno M. MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nature Methods. 6: 473-4. PMID 19483690 DOI: 10.1038/nmeth.f.256  0.8
2009 Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. SHRiMP: accurate mapping of short color-space reads. Plos Computational Biology. 5: e1000386. PMID 19461883 DOI: 10.1371/journal.pcbi.1000386  0.8
2009 Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe MJ, Wilde A, Brudno M, Morris QD, Hughes TR. Conservation of core gene expression in vertebrate tissues. Journal of Biology. 8: 33. PMID 19371447 DOI: 10.1186/jbiol130  0.8
2009 Dubchak I, Poliakov A, Kislyuk A, Brudno M. Multiple whole-genome alignments without a reference organism. Genome Research. 19: 682-9. PMID 19176791 DOI: 10.1101/gr.081778.108  0.8
2009 Donmez N, Bazykin GA, Brudno M, Kondrashov AS. Polymorphism due to multiple amino acid substitutions at a codon site within Ciona savignyi. Genetics. 181: 685-90. PMID 19087959 DOI: 10.1534/genetics.108.097535  0.8
2009 Patchin P, Lagar-Cavilla HA, De Lara E, Brudno M. Adding the easy button to the cloud with SnowFlock and MPI Proceedings of the 3rd Acm Workshop On System-Level Virtualization For High Performance Computing, Hpcvirt'09. 1-8. DOI: 10.1145/1519138.1519139  0.8
2009 Lagar-Cavilla HA, Whitney JA, Scannell A, Patchin P, Rumble SM, De Lara E, Brudno M, Satyanarayanan M. SnowFlock: Rapid virtual Machine cloning for cloud computing Proceedings of the 4th Acm European Conference On Computer Systems, Eurosys'09. 1-12. DOI: 10.1145/1519065.1519067  0.8
2009 Quon G, Teh YW, Chan E, Hughes T, Brudno M, Morris Q. A mixture model for the evolution of gene expression in non-homogeneous datasets Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference. 1297-1304.  0.8
2008 Lee S, Cheran E, Brudno M. A robust framework for detecting structural variations in a genome. Bioinformatics (Oxford, England). 24: i59-67. PMID 18586745 DOI: 10.1093/bioinformatics/btn176  0.8
2008 Dalca AV, Brudno M. Fresco: Flexible alignment with rectangle scoring schemes Pacific Symposium On Biocomputing 2008, Psb 2008. 3-14. PMID 18229672  0.8
2008 Yanovsky V, Rumble SM, Brudno M. Read mapping algorithms for single molecule sequencing data Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5251: 38-49. DOI: 10.1007/978-3-540-87361-7_4  0.8
2008 Medvedev P, Brudno M. Ab initio whole genome shotgun assembly with mated short reads Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4955: 50-64. DOI: 10.1007/978-3-540-78839-3_5  0.8
2008 Brudno M, Moret B, Linder R, Warnow T. Beyond gap models: Reconstructing alignments and phylogenies under genomic-scale events Pacific Symposium On Biocomputing 2008, Psb 2008. 1-2.  0.8
2007 Brudno M. An introduction to the Lagan alignment toolkit. Methods in Molecular Biology (Clifton, N.J.). 395: 205-20. PMID 17993676 DOI: 10.1385/1-59745-514-8:205  0.8
2007 Bazykin GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS. Extensive parallelism in protein evolution. Biology Direct. 2: 20. PMID 17705846 DOI: 10.1186/1745-6150-2-20  0.8
2007 Brudno M, Poliakov A, Minovitsky S, Ratnere I, Dubchak I. Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Research. 35: W669-74. PMID 17488840 DOI: 10.1093/nar/gkm279  0.8
2007 Small KS, Brudno M, Hill MM, Sidow A. A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biology. 8: R41. PMID 17374142 DOI: 10.1186/gb-2007-8-3-r41  0.8
2007 Small KS, Brudno M, Hill MM, Sidow A. Extreme genomic variation in a natural population. Proceedings of the National Academy of Sciences of the United States of America. 104: 5698-703. PMID 17372217 DOI: 10.1073/pnas.0700890104  0.8
2007 Medvedev P, Georgiou K, Myers G, Brudno M. Computability of models for sequence assembly Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4645: 289-301.  0.8
2006 Kovaleva GY, Bazykin GA, Brudno M, Gelfand MS. Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter. Journal of Bioinformatics and Computational Biology. 4: 981-98. PMID 17099937 DOI: 10.1142/S0219720006002284  0.8
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  0.8
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, ... ... Brudno M, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/science.1105136  0.8
2004 Brudno M, Steinkamp R, Morgenstern B. The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. Nucleic Acids Research. 32: W41-4. PMID 15215346 DOI: 10.1093/nar/gkh361  0.8
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  0.8
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  0.8
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, ... ... Brudno M, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/nature02426  0.8
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  0.8
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.  0.8
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.  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
2002 Brudno M, Morgenstern B. Fast and sensitive alignment of large genomic sequences. Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference. 1: 138-47. PMID 15838131 DOI: 10.1109/CSB.2002.1039337  0.8
2001 Brudno M, Gelfand MS, Spengler S, Zorn M, Dubchak I, Conboy JG. Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing Nucleic Acids Research. 29: 2338-2348. PMID 11376152  0.8
2000 Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I. VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics (Oxford, England). 16: 1046-7. PMID 11159318  0.8
2000 Dubchak I, Brudno M, Loots GG, Pachter L, Mayor C, Rubin EM, Frazer KA. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Research. 10: 1304-6. PMID 10984448 DOI: 10.1101/gr.142200  0.8
2000 Dralyuk I, Brudno M, Gelfand MS, Zorn M, Dubchak I. ASDB: Database of alternatively spliced genes Nucleic Acids Research. 28: 296-297. PMID 10592252  0.8
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