| Year |
Citation |
Score |
| 2022 |
Boycott KM, Hartley T, Kernohan KD, Dyment DA, Howley H, Innes AM, Bernier FP, Brudno M. Care4Rare Canada: Outcomes from a decade of network science for rare disease gene discovery. American Journal of Human Genetics. 109: 1947-1959. PMID 36332610 DOI: 10.1016/j.ajhg.2022.10.002 |
0.366 |
|
| 2022 |
Osmond M, Hartley T, Johnstone B, Andjic S, Girdea M, Gillespie M, Buske O, Dumitriu S, Koltunova V, Ramani A, Boycott KM, Brudno M. PhenomeCentral: 7 years of rare disease matchmaking. Human Mutation. PMID 35165961 DOI: 10.1002/humu.24348 |
0.323 |
|
| 2022 |
Thorogood A, Rehm HL, Goodhand P, Page AJH, Joly Y, Baudis M, Rambla J, Navarro A, Nyronen TH, Linden M, Dove ES, Fiume M, Brudno M, Cline MS, Bimey E. International federation of genomic medicine databases using GA4GH standards. Cell Genomics. 1. PMID 35128509 DOI: 10.1016/j.xgen.2021.100032 |
0.328 |
|
| 2021 |
Dursi LJ, Bozoky Z, de Borja R, Li H, Bujold D, Lipski A, Rashid SF, Sethi A, Memon N, Naidoo D, Coral-Sasso F, Wong M, Quirion PO, Lu Z, Agarwal S, ... ... Brudno M, et al. CanDIG: Federated network across Canada for multi-omic and health data discovery and analysis. Cell Genomics. 1: 100033. PMID 36778585 DOI: 10.1016/j.xgen.2021.100033 |
0.303 |
|
| 2021 |
Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, ... ... Brudno M, et al. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genomics. 1. PMID 35072136 DOI: 10.1016/j.xgen.2021.100029 |
0.389 |
|
| 2020 |
Turinsky AL, Choufani S, Lu K, Liu D, Mashouri P, Min D, Weksberg R, Brudno M. EpigenCentral: Portal for DNA methylation data analysis and classification in rare diseases. Human Mutation. PMID 32623772 DOI: 10.1002/Humu.24076 |
0.312 |
|
| 2020 |
Mohanraj S, Díaz-Mejía JJ, Pham MD, Elrick H, Husić M, Rashid S, Luo P, Bal P, Lu K, Patel S, Mahalanabis A, Naidas A, Christensen E, Croucher D, Richards LM, ... ... Brudno M, et al. CReSCENT: CanceR Single Cell ExpressioN Toolkit. Nucleic Acids Research. PMID 32479601 DOI: 10.1093/Nar/Gkaa437 |
0.308 |
|
| 2020 |
Choufani S, Gibson WT, Turinsky AL, Chung BHY, Wang T, Garg K, Vitriolo A, Cohen ASA, Cyrus S, Goodman S, Chater-Diehl E, Brzezinski J, Brudno M, Ming LH, White SM, et al. DNA Methylation Signature for EZH2 Functionally Classifies Sequence Variants in Three PRC2 Complex Genes. American Journal of Human Genetics. PMID 32243864 DOI: 10.1016/J.Ajhg.2020.03.008 |
0.444 |
|
| 2019 |
Nellåker C, Alkuraya FS, Baynam G, Bernier RA, Bernier FPJ, Boulanger V, Brudno M, Brunner HG, Clayton-Smith J, Cogné B, Dawkins HJS, deVries BBA, Douzgou S, Dudding-Byth T, Eichler EE, et al. Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative. Frontiers in Genetics. 10: 611. PMID 31417602 DOI: 10.3389/Fgene.2019.00611 |
0.345 |
|
| 2019 |
Siu MT, Butcher DT, Turinsky AL, Cytrynbaum C, Stavropoulos DJ, Walker S, Caluseriu O, Carter M, Lou Y, Nicolson R, Georgiades S, Szatmari P, Anagnostou E, Scherer SW, Choufani S, ... Brudno M, et al. Functional DNA methylation signatures for autism spectrum disorder genomic risk loci: 16p11.2 deletions and CHD8 variants. Clinical Epigenetics. 11: 103. PMID 31311581 DOI: 10.1186/S13148-019-0684-3 |
0.346 |
|
| 2019 |
Chater-Diehl E, Ejaz R, Cytrynbaum C, Siu MT, Turinsky A, Choufani S, Goodman SJ, Abdul-Rahman O, Bedford M, Dorrani N, Engleman K, Flores-Daboub J, Genevieve D, Mendoza-Londono R, Meschino W, ... ... Brudno M, et al. New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome. Bmc Medical Genomics. 12: 105. PMID 31288860 DOI: 10.1186/S12920-019-0555-Y |
0.387 |
|
| 2019 |
Gonorazky HD, Naumenko S, Ramani AK, Nelakuditi V, Mashouri P, Wang P, Kao D, Ohri K, Viththiyapaskaran S, Tarnopolsky MA, Mathews KD, Moore SA, Osorio AN, Villanova D, Kemaladewi DU, ... ... Brudno M, et al. Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease. American Journal of Human Genetics. PMID 30827497 DOI: 10.1016/J.Ajhg.2019.01.012 |
0.369 |
|
| 2018 |
Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Osumi-Sutherland D, Cipriani V, Balhoff JP, Conlin T, Blau H, ... ... Brudno M, et al. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Research. PMID 30476213 DOI: 10.1093/Nar/Gky1105 |
0.409 |
|
| 2018 |
Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, ... ... Brudno M, et al. Registered access: authorizing data access. European Journal of Human Genetics : Ejhg. PMID 30069064 DOI: 10.1038/S41431-018-0219-Y |
0.342 |
|
| 2018 |
Maiella S, Olry A, Hanauer M, Lanneau V, Lourghi H, Donadille B, Rodwell C, Köhler S, Seelow D, Jupp S, Parkinson H, Groza T, Brudno M, Robinson PN, Rath A. Harmonising phenomics information for a better interoperability in the rare disease field. European Journal of Medical Genetics. PMID 29425702 DOI: 10.1016/J.Ejmg.2018.01.013 |
0.409 |
|
| 2017 |
Baynam G, Bowman F, Lister K, Walker CE, Pachter N, Goldblatt J, Boycott KM, Gahl WA, Kosaki K, Adachi T, Ishii K, Mahede T, McKenzie F, Townshend S, Slee J, ... ... Brudno M, et al. Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework. Advances in Experimental Medicine and Biology. 1031: 55-94. PMID 29214566 DOI: 10.1007/978-3-319-67144-4_4 |
0.309 |
|
| 2017 |
Hayeems RZ, Bhawra J, Tsiplova K, Meyn MS, Monfared N, Bowdin S, Stavropoulos DJ, Marshall CR, Basran R, Shuman C, Ito S, Cohn I, Hum C, Girdea M, Brudno M, et al. Care and cost consequences of pediatric whole genome sequencing compared to chromosome microarray. European Journal of Human Genetics : Ejhg. PMID 29158552 DOI: 10.1038/S41431-017-0020-3 |
0.311 |
|
| 2017 |
Glueck M, Naeini MP, Doshi-Velez F, Chevalier F, Khan A, Wigdor D, Brudno M. PhenoLines: Phenotype Comparison Visualizations for Disease Subtyping via Topic Models. Ieee Transactions On Visualization and Computer Graphics. PMID 28866570 DOI: 10.1109/Tvcg.2017.2745118 |
0.31 |
|
| 2017 |
Xi Y, Arbabi A, McNaughton AJM, Hamilton A, Hull D, Perras H, Chiu T, Morrison S, Goldsmith C, Creede E, Anger GJ, Honeywell C, Cloutier M, Macchio N, Kiss C, ... ... Brudno M, et al. Noninvasive Prenatal Detection of Trisomy 21 by Targeted Semiconductor Sequencing: A Technical Feasibility Study. Fetal Diagnosis and Therapy. PMID 28511174 DOI: 10.1159/000460248 |
0.365 |
|
| 2017 |
Butcher DT, Cytrynbaum C, Turinsky AL, Siu MT, Inbar-Feigenberg M, Mendoza-Londono R, Chitayat D, Walker S, Machado J, Caluseriu O, Dupuis L, Grafodatskaya D, Reardon W, Gilbert-Dussardier B, Verloes A, ... ... Brudno M, et al. CHARGE and Kabuki Syndromes: Gene-Specific DNA Methylation Signatures Identify Epigenetic Mechanisms Linking These Clinically Overlapping Conditions. American Journal of Human Genetics. 100: 773-788. PMID 28475860 DOI: 10.1016/J.Ajhg.2017.04.004 |
0.306 |
|
| 2016 |
Stavropoulos DJ, Merico D, Jobling R, Bowdin S, Monfared N, Thiruvahindrapuram B, Nalpathamkalam T, Pellecchia G, Yuen RKC, Szego MJ, Hayeems RZ, Shaul RZ, Brudno M, Girdea M, Frey B, et al. Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine. Npj Genomic Medicine. 1. PMID 28567303 DOI: 10.1038/Npjgenmed.2015.12 |
0.409 |
|
| 2016 |
Dzamba M, Ramani AK, Buczkowicz P, Jiang Y, Yu M, Hawkins C, Brudno M. Identification of complex genomic rearrangements in cancers using CouGaR. Genome Research. PMID 27986820 DOI: 10.1101/Gr.211201.116 |
0.448 |
|
| 2016 |
Torchia J, Golbourn B, Feng S, Ho KC, Sin-Chan P, Vasiljevic A, Norman JD, Guilhamon P, Garzia L, Agamez NR, Lu M, Chan TS, Picard D, de Antonellis P, Khuong-Quang DA, ... ... Brudno M, et al. Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors. Cancer Cell. 30: 891-908. PMID 27960086 DOI: 10.1016/J.Ccell.2016.11.003 |
0.381 |
|
| 2016 |
Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, et al. The Human Phenotype Ontology in 2017. Nucleic Acids Research. PMID 27899602 DOI: 10.1093/Nar/Gkw1039 |
0.38 |
|
| 2016 |
Liu B, Guo H, Brudno M, Wang Y. deBGA: read alignment with de Bruijn Graph-based seed and extension. Bioinformatics (Oxford, England). PMID 27378303 DOI: 10.1093/Bioinformatics/Btw371 |
0.396 |
|
| 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 |
0.313 |
|
| 2016 |
Arbabi A, Rampášek L, Brudno M. Cell Free DNA Fragment-Size Distribution Analysis (FSDA) for Non-Invasive Prenatal CNV Prediction. Bioinformatics (Oxford, England). PMID 27153615 DOI: 10.1093/Bioinformatics/Btw178 |
0.408 |
|
| 2016 |
Russell JN, Marsh AK, Willer DO, Ambagala AP, Dzamba M, Chan JK, Pilon R, Fournier J, Brudno M, Antony JM, Sandstrom P, Evans BJ, MacDonald KS. A novel strain of cynomolgus macaque cytomegalovirus: implications for host-virus co-evolution. Bmc Genomics. 17: 277. PMID 27044312 DOI: 10.1186/S12864-016-2588-3 |
0.37 |
|
| 2016 |
Hoffman LM, DeWire M, Ryall S, Buczkowicz P, Leach J, Miles L, Ramani AK, Brudno M, Kumar SS, Drissi R, Dexheimer P, Salloum R, Chow L, Hummel T, Stevenson C, et al. Erratum: Spatial genomic heterogeneity in diffuse intrinsic pontine and midline high-grade glioma: implications for diagnostic biopsy and targeted therapeutics. Acta Neuropathologica Communications. 4: 13. PMID 26860432 DOI: 10.1186/s40478-016-0283-x |
0.36 |
|
| 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 |
0.356 |
|
| 2015 |
Choufani S, Cytrynbaum C, Chung BH, Turinsky AL, Grafodatskaya D, Chen YA, Cohen AS, Dupuis L, Butcher DT, Siu MT, Luk HM, Lo IF, Lam ST, Caluseriu O, Stavropoulos DJ, ... ... Brudno M, et al. NSD1 mutations generate a genome-wide DNA methylation signature. Nature Communications. 6: 10207. PMID 26690673 DOI: 10.1038/Ncomms10207 |
0.405 |
|
| 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 |
0.409 |
|
| 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 |
0.349 |
|
| 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 |
0.357 |
|
| 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 |
0.367 |
|
| 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 |
0.333 |
|
| 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 |
0.46 |
|
| 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 |
0.488 |
|
| 2015 |
Buske OJ, Manickaraj A, Mital S, Ray PN, Brudno M. Identification of deleterious synonymous variants in human genomes. Bioinformatics (Oxford, England). 31: 799. PMID 25488928 DOI: 10.1093/bioinformatics/btu765 |
0.365 |
|
| 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 |
0.373 |
|
| 2015 |
Meyn M, Monfared N, Marshall CR, Merico D, Stavropoulos DJ, Hayeems RZ, Szego M, Jobling R, Girdea M, Bader GD, Brudno M, Cohn RD, Scherer SW, Shaul RZ, Shuman C, et al. MG-108 Beyond the ACMG 56: Parental choices and initial results from a comprehensive whole genome sequencing-based search for predictive genomic variants in children Journal of Medical Genetics. 52: A3.2-A4. DOI: 10.1136/Jmedgenet-2015-103578.8 |
0.454 |
|
| 2015 |
Marshall CR, Stavropoulos DJ, Jobling R, Merico D, Bowdin S, Monfared N, Meyn M, Szego M, Shaul RZ, Thiruvahindrapuram B, Pellecchia G, Nalpathamkalam T, Brudno M, Girdea M, Hayeems RZ, et al. MG-132 Diagnostic utility of whole genome sequencing in paediatric medicine Journal of Medical Genetics. 52: A12.1-A12. DOI: 10.1136/Jmedgenet-2015-103578.31 |
0.427 |
|
| 2014 |
Mustafa H, David M, Brudno M. Assembly and characterization of novel Alu inserts detected from next-generation sequencing data. Mobile Genetic Elements. 4: 1-7. PMID 26442170 DOI: 10.4161/21592543.2014.969584 |
0.531 |
|
| 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 |
0.446 |
|
| 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 |
0.424 |
|
| 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 |
0.325 |
|
| 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 |
0.492 |
|
| 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 |
0.346 |
|
| 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 |
0.333 |
|
| 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 |
0.355 |
|
| 2014 |
Torchia J, Picard D, Kwang DA, Dzamba M, Ho KC, Kim S, Louterneau L, Lafay-Cousin L, Chan TS, Golbourn B, Morrissy S, Birks D, Faria C, Foreman N, Fan X, ... ... Brudno M, et al. Integrative Genomic Analyses of Atypical Teratoid Rhabdoid Tumours (ATRTs) Cancer Genetics. 207: 447-448. DOI: 10.1016/J.Cancergen.2014.09.013 |
0.434 |
|
| 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 |
0.502 |
|
| 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 |
0.426 |
|
| 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 |
0.308 |
|
| 2013 |
Donmez N, Brudno M. SCARPA: scaffolding reads with practical algorithms. Bioinformatics (Oxford, England). 29: 428-34. PMID 23274213 DOI: 10.1093/Bioinformatics/Bts716 |
0.34 |
|
| 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 |
0.314 |
|
| 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 |
0.363 |
|
| 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 |
0.405 |
|
| 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 |
0.473 |
|
| 2011 |
Buske O, Dzamba M, Foong J, Lau L, Fiume M, Marshall C, Walker S, Prasad A, Brudno M. Variant detection and the Autism sequencing project Bmc Bioinformatics. 12. DOI: 10.1186/1471-2105-12-S11-A4 |
0.359 |
|
| 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 |
0.402 |
|
| 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 |
0.503 |
|
| 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 |
0.523 |
|
| 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 |
0.389 |
|
| 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 |
0.475 |
|
| 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 |
0.396 |
|
| 2010 |
Alkan C, Brudno M, Eichler EE, Kann MG, Sahinalp SC. Personal genomics Pacific Symposium On Biocomputing 2010, Psb 2010. 302-304. |
0.31 |
|
| 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 |
0.513 |
|
| 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 |
0.46 |
|
| 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 |
0.461 |
|
| 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 |
0.375 |
|
| 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 |
0.438 |
|
| 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 |
0.328 |
|
| 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 |
0.527 |
|
| 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 |
0.41 |
|
| 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 |
0.314 |
|
| 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 |
0.364 |
|
| 2007 |
Brudno M. An introduction to the Lagan alignment toolkit. Methods in Molecular Biology (Clifton, N.J.). 395: 205-20. PMID 17993676 DOI: 10.1007/978-1-59745-514-5_13 |
0.474 |
|
| 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 |
0.536 |
|
| 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 |
0.52 |
|
| 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 |
0.428 |
|
| 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 |
0.673 |
|
| 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 |
0.73 |
|
| 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 |
0.544 |
|
| 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 |
0.69 |
|
| 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, ... ... 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 |
0.709 |
|
| 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 |
0.66 |
|
| 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. |
0.638 |
|
| 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. |
0.655 |
|
| 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 |
0.721 |
|
| 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 |
0.681 |
|
| 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 |
0.696 |
|
| 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 |
0.721 |
|
| 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 |
0.435 |
|
| 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 DOI: 10.1093/Nar/29.11.2338 |
0.386 |
|
| 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 DOI: 10.1093/Bioinformatics/16.11.1046 |
0.38 |
|
| 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 |
0.508 |
|
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