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Michael Brudno

TitleSenior Scientist
InstitutionThe Hospital for Sick Children
DepartmentGenetics and Genome Biology
Address555 University Avenue
Toronto ON M5G 1X8
Phone416-813-1500
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    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Guerreiro Stucklin AS, Ryall S, Fukuoka K, Zapotocky M, Lassaletta A, Li C, Bridge T, Kim B, Arnoldo A, Kowalski PE, Zhong Y, Johnson M, Li C, Ramani AK, Siddaway R, Nobre LF, de Antonellis P, Dunham C, Cheng S, Boué DR, Finlay JL, Coven SL, de Prada I, Perez-Somarriba M, Faria CC, Grotzer MA, Rushing E, Sumerauer D, Zamecnik J, Krskova L, Garcia Ariza M, Cruz O, Morales La Madrid A, Solano P, Terashima K, Nakano Y, Ichimura K, Nagane M, Sakamoto H, Gil-da-Costa MJ, Silva R, Johnston DL, Michaud J, Wilson B, van Landeghem FKH, Oviedo A, McNeely PD, Crooks B, Fried I, Zhukova N, Hansford JR, Nageswararao A, Garzia L, Shago M, Brudno M, Irwin MS, Bartels U, Ramaswamy V, Bouffet E, Taylor MD, Tabori U, Hawkins C. Alterations in ALK/ROS1/NTRK/MET drive a group of infantile hemispheric gliomas. Nat Commun. 2019 Sep 25; 10(1):4343. PMID: 31554817.
      View in: PubMed
    2. Pienkowska M, Choufani S, Turinsky AL, Guha T, Merino DM, Novokmet A, Brudno M, Weksberg R, Shlien A, Hawkins C, Bouffet E, Tabori U, Gilbertson R, Finlay JL, Jabado N, Thomas C, Sill M, Capper D, Hasselblatt M, Malkin D. DNA methylation signature is prognostic of choroid plexus tumor aggressiveness. Clin Epigenetics. 2019 Aug 13; 11(1):117. PMID: 31409384.
      View in: PubMed
    3. 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, Ferlaino M, Fieggen K, Firth HV, FitzPatrick DR, Gration D, Groza T, Haendel M, Hallowell N, Hamosh A, Hehir-Kwa J, Hitz MP, Hughes M, Kini U, Kleefstra T, Kooy RF, Krawitz P, Küry S, Lees M, Lyon GJ, Lyonnet S, Marcadier JL, Meyn S, Moslerová V, Politei JM, Poulton CC, Raymond FL, Reijnders MRF, Robinson PN, Romano C, Rose CM, Sainsbury DCG, Schofield L, Sutton VR, Turnovec M, Van Dijck A, Van Esch H, Wilkie AOM. Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative. Front Genet. 2019; 10:611. PMID: 31417602.
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    4. 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, Weksberg R. Functional DNA methylation signatures for autism spectrum disorder genomic risk loci: 16p11.2 deletions and CHD8 variants. Clin Epigenetics. 2019 Jul 16; 11(1):103. PMID: 31311581.
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    5. 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, Perrin L, Safina N, Townshend S, Scherer SW, Anagnostou E, Piton A, Deardorff M, Brudno M, Chitayat D, Weksberg R. New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome. BMC Med Genomics. 2019 07 09; 12(1):105. PMID: 31288860.
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    6. Hoang JA, Mashouri P, Dai R, Brydges MG, Dubeau A, Lépine C, Yin X, Kowalik K, DeLorenzo S, Upton JEM, Moraes TJ, Amin R, Narang I, Boutis K, Schuh S, Maksym GN, Brudno M, Ramani A, Subbarao P, Eiwegger T. Extract and component-specific sensitization patterns in Canadian moderate-to-severe preschool asthmatics. Allergy. 2019 May 24. PMID: 31125434.
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    7. Arbabi A, Adams DR, Fidler S, Brudno M. Identifying Clinical Terms in Medical Text Using Ontology-Guided Machine Learning. JMIR Med Inform. 2019 May 10; 7(2):e12596. PMID: 31094361.
      View in: PubMed
    8. 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, Cohn RD, Brudno M, Dowling JJ. Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease. Am J Hum Genet. 2019 May 02; 104(5):1007. PMID: 31051109.
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    9. Turinsky AL, Butcher DT, Choufani S, Weksberg R, Brudno M. Don't brush off buccal data heterogeneity. Epigenetics. 2019 Feb; 14(2):109-117. PMID: 30821575.
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    10. 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, Cohn RD, Brudno M, Dowling JJ. Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease. Am J Hum Genet. 2019 Mar 07; 104(3):466-483. PMID: 30827497.
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    11. Choufani S, Turinsky AL, Melamed N, Greenblatt E, Brudno M, Bérard A, Fraser WD, Weksberg R, Trasler J, Monnier P. Impact of assisted reproduction, infertility, sex and paternal factors on the placental DNA methylome. Hum Mol Genet. 2019 02 01; 28(3):372-385. PMID: 30239726.
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    12. 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, Baynam G, Palmer R, Gratian D, Dawkins H, Segal M, Jansen AC, Muaz A, Chang WH, Bergerson J, Laulederkind SJF, Yüksel Z, Beltran S, Freeman AF, Sergouniotis PI, Durkin D, Storm AL, Hanauer M, Brudno M, Bello SM, Sincan M, Rageth K, Wheeler MT, Oegema R, Lourghi H, Della Rocca MG, Thompson R, Castellanos F, Priest J, Cunningham-Rundles C, Hegde A, Lovering RC, Hajek C, Olry A, Notarangelo L, Similuk M, Zhang XA, Gómez-Andrés D, Lochmüller H, Dollfus H, Rosenzweig S, Marwaha S, Rath A, Sullivan K, Smith C, Milner JD, Leroux D, Boerkoel CF, Klion A, Carter MC, Groza T, Smedley D, Haendel MA, Mungall C, Robinson PN. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 2019 Jan 08; 47(D1):D1018-D1027. PMID: 30476213.
      View in: PubMed
    13. Maani N, Sabha N, Rezai K, Ramani A, Groom L, Eltayeb N, Mavandadnejad F, Pang A, Russo G, Brudno M, Haucke V, Dirksen RT, Dowling JJ. Tamoxifen therapy in a murine model of myotubular myopathy. Nat Commun. 2018 11 19; 9(1):4849. PMID: 30451841.
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    14. Sultanum N, Singh D, Brudno M, Chevalier F. Doccurate: A Curation-Based Approach for Clinical Text Visualization. IEEE Trans Vis Comput Graph. 2018 Aug 20. PMID: 30136959.
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    15. 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, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, Flicek P. Registered access: authorizing data access. Eur J Hum Genet. 2018 12; 26(12):1721-1731. PMID: 30069064.
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    16. 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. Eur J Med Genet. 2018 Nov; 61(11):706-714. PMID: 29425702.
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    17. 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, Cohn RD, Scherer SW, Ungar WJ. Care and cost consequences of pediatric whole genome sequencing compared to chromosome microarray. Eur J Hum Genet. 2017 12; 25(12):1303-1312. PMID: 29158552.
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    18. 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 Trans Vis Comput Graph. 2018 01; 24(1):371-381. PMID: 28866570.
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    19. Dyke SOM, Knoppers BM, Hamosh A, Firth HV, Hurles M, Brudno M, Boycott KM, Philippakis AA, Rehm HL. "Matching" consent to purpose: The example of the Matchmaker Exchange. Hum Mutat. 2017 10; 38(10):1281-1285. PMID: 28699299.
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    20. 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, Liu X, Crocker S, Davies GA, Brudno M, Armour CM. Noninvasive Prenatal Detection of Trisomy 21 by Targeted Semiconductor Sequencing: A Technical Feasibility Study. Fetal Diagn Ther. 2017; 42(4):302-310. PMID: 28511174.
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    21. Boycott KM, Rath A, Chong JX, Hartley T, Alkuraya FS, Baynam G, Brookes AJ, Brudno M, Carracedo A, den Dunnen JT, Dyke SOM, Estivill X, Goldblatt J, Gonthier C, Groft SC, Gut I, Hamosh A, Hieter P, Höhn S, Hurles ME, Kaufmann P, Knoppers BM, Krischer JP, Macek M, Matthijs G, Olry A, Parker S, Paschall J, Philippakis AA, Rehm HL, Robinson PN, Sham PC, Stefanov R, Taruscio D, Unni D, Vanstone MR, Zhang F, Brunner H, Bamshad MJ, Lochmüller H. International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases. Am J Hum Genet. 2017 May 04; 100(5):695-705. PMID: 28475856.
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    22. 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, Bilan F, Milunsky JM, Basran R, Papsin B, Stockley TL, Scherer SW, Choufani S, Brudno M, Weksberg R. CHARGE and Kabuki Syndromes: Gene-Specific DNA Methylation Signatures Identify Epigenetic Mechanisms Linking These Clinically Overlapping Conditions. Am J Hum Genet. 2017 May 04; 100(5):773-788. PMID: 28475860.
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    23. 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, Kiraly-Borri C, Vasudevan A, Hawkins A, Broley S, Schofield L, Verhoef H, Groza T, Zankl A, Robinson PN, Haendel M, Brudno M, Mattick JS, Dinger ME, Roscioli T, Cowley MJ, Olry A, Hanauer M, Alkuraya FS, Taruscio D, Posada de la Paz M, Lochmüller H, Bushby K, Thompson R, Hedley V, Lasko P, Mina K, Beilby J, Tifft C, Davis M, Laing NG, Julkowska D, Le Cam Y, Terry SF, Kaufmann P, Eerola I, Norstedt I, Rath A, Suematsu M, Groft SC, Austin CP, Draghia-Akli R, Weeramanthri TS, Molster C, Dawkins HJS. Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework. Adv Exp Med Biol. 2017; 1031:55-94. PMID: 29214566.
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    24. 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, Planello AC, Zeller C, Barsyte-Lovejoy D, Lafay-Cousin L, Letourneau L, Bourgey M, Yu M, Gendoo DMA, Dzamba M, Barszczyk M, Medina T, Riemenschneider AN, Morrissy AS, Ra YS, Ramaswamy V, Remke M, Dunham CP, Yip S, Ng HK, Lu JQ, Mehta V, Albrecht S, Pimentel J, Chan JA, Somers GR, Faria CC, Roque L, Fouladi M, Hoffman LM, Moore AS, Wang Y, Choi SA, Hansford JR, Catchpoole D, Birks DK, Foreman NK, Strother D, Klekner A, Bognár L, Garami M, Hauser P, Hortobágyi T, Wilson B, Hukin J, Carret AS, Van Meter TE, Hwang EI, Gajjar A, Chiou SH, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheinemann K, Fleming AJ, Johnston DL, Michaud J, Zelcer S, Hammond R, Afzal S, Ramsay DA, Sirachainan N, Hongeng S, Larbcharoensub N, Grundy RG, Lulla RR, Fangusaro JR, Druker H, Bartels U, Grant R, Malkin D, McGlade CJ, Nicolaides T, Tihan T, Phillips J, Majewski J, Montpetit A, Bourque G, Bader GD, Reddy AT, Gillespie GY, Warmuth-Metz M, Rutkowski S, Tabori U, Lupien M, Brudno M, Schüller U, Pietsch T, Judkins AR, Hawkins CE, Bouffet E, Kim SK, Dirks PB, Taylor MD, Erdreich-Epstein A, Arrowsmith CH, De Carvalho DD, Rutka JT, Jabado N, Huang A. Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors. Cancer Cell. 2016 Dec 12; 30(6):891-908. PMID: 27960086.
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    25. 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, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MW, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JO, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN. The Human Phenotype Ontology in 2017. Nucleic Acids Res. 2017 01 04; 45(D1):D865-D876. PMID: 27899602.
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    26. Dzamba M, Ramani AK, Buczkowicz P, Jiang Y, Yu M, Hawkins C, Brudno M. Identification of complex genomic rearrangements in cancers using CouGaR. Genome Res. 2017 01; 27(1):107-117. PMID: 27986820.
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    27. Miscevic F, Foong J, Schmitt B, Blaser S, Brudno M, Schulze A. An MRspec database query and visualization engine with applications as a clinical diagnostic and research tool. Mol Genet Metab. 2016 12; 119(4):300-306. PMID: 27847299.
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    28. Links AE, Draper D, Lee E, Guzman J, Valivullah Z, Maduro V, Lebedev V, Didenko M, Tomlin G, Brudno M, Girdea M, Dumitriu S, Haendel MA, Mungall CJ, Smedley D, Hochheiser H, Arnold AM, Coessens B, Verhoeven S, Bone W, Adams D, Boerkoel CF, Gahl WA, Sincan M. Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience. Front Med (Lausanne). 2016; 3:39. PMID: 27785453.
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    29. Glueck M, Gvozdik A, Chevalier F, Khan A, Brudno M, Wigdor D. PhenoStacks: Cross-Sectional Cohort Phenotype Comparison Visualizations. IEEE Trans Vis Comput Graph. 2017 01; 23(1):191-200. PMID: 27514055.
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    30. Liu B, Guo H, Brudno M, Wang Y. deBGA: read alignment with de Bruijn graph-based seed and extension. Bioinformatics. 2016 11 01; 32(21):3224-3232. PMID: 27378303.
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    31. Roifman M, Choufani S, Turinsky AL, Drewlo S, Keating S, Brudno M, Kingdom J, Weksberg R. Genome-wide placental DNA methylation analysis of severely growth-discordant monochorionic twins reveals novel epigenetic targets for intrauterine growth restriction. Clin Epigenetics. 2016; 8:70. PMID: 27330572.
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    32. Labrie V, Buske OJ, Oh E, Jeremian R, Ptak C, Gasiunas G, Maleckas A, Petereit R, Žvirbliene A, Adamonis K, Kriukiene E, Koncevicius K, Gordevicius J, Nair A, Zhang A, Ebrahimi S, Oh G, Šikšnys V, Kupcinskas L, Brudno M, Petronis A. Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging. Nat Struct Mol Biol. 2016 06; 23(6):566-73. PMID: 27159559.
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    33. 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. 2016 Apr 05; 17:277. PMID: 27044312.
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    34. Arbabi A, Rampášek L, Brudno M. Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction. Bioinformatics. 2016 06 01; 32(11):1662-9. PMID: 27153615.
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    35. 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, Lu QR, Jones B, Witte D, Aronow B, Hawkins CE, Fouladi M. Erratum: Spatial genomic heterogeneity in diffuse intrinsic pontine and midline high-grade glioma: implications for diagnostic biopsy and targeted therapeutics. Acta Neuropathol Commun. 2016 Feb 09; 4:13. PMID: 26860432.
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    36. 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, Fiume M, Sherry ST. Consent Codes: Upholding Standard Data Use Conditions. PLoS Genet. 2016 Jan; 12(1):e1005772. PMID: 26796797.
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    37. 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, Alipanahi B, Ahmed S, Babul-Hirji R, Porras RB, Carter MT, Chad L, Chaudhry A, Chitayat D, Doust SJ, Cytrynbaum C, Dupuis L, Ejaz R, Fishman L, Guerin A, Hashemi B, Helal M, Hewson S, Inbar-Feigenberg M, Kannu P, Karp N, Kim R, Kronick J, Liston E, MacDonald H, Mercimek-Mahmutoglu S, Mendoza-Londono R, Nasr E, Nimmo G, Parkinson N, Quercia N, Raiman J, Roifman M, Schulze A, Shugar A, Shuman C, Sinajon P, Siriwardena K, Weksberg R, Yoon G, Carew C, Erickson R, Leach RA, Klein R, Ray PN, Meyn MS, Scherer SW, Cohn RD, Marshall CR. Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine. NPJ Genom Med. 2016 Jan 13; 1. PMID: 28567303.
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    38. Hoffman LM, DeWire M, Ryall S, Buczkowicz P, Leach J, Miles L, Ramani A, Brudno M, Kumar SS, Drissi R, Dexheimer P, Salloum R, Chow L, Hummel T, Stevenson C, Lu QR, Jones B, Witte D, Aronow B, Hawkins CE, Fouladi M. Spatial genomic heterogeneity in diffuse intrinsic pontine and midline high-grade glioma: implications for diagnostic biopsy and targeted therapeutics. Acta Neuropathol Commun. 2016 Jan 04; 4:1. PMID: 26727948.
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    39. Glueck M, Hamilton P, Chevalier F, Breslav S, Khan A, Wigdor D, Brudno M. PhenoBlocks: Phenotype Comparison Visualizations. IEEE Trans Vis Comput Graph. 2016 Jan; 22(1):101-10. PMID: 26529691.
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    40. 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, Reardon W, Mendoza-Londono R, Brudno M, Gibson WT, Chitayat D, Weksberg R. NSD1 mutations generate a genome-wide DNA methylation signature. Nat Commun. 2015 Dec 22; 6:10207. PMID: 26690673.
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    41. 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, Markello TC, Mungall CJ, Nehrebecky M, Robinson PN, Sincan M, Soldatos AG, Tifft CJ, Toro C, Trang H, Valkanas E, Vasilevsky N, Wahl C, Wolfe LA, Boerkoel CF, Brudno M, Haendel MA, Gahl WA, Smedley D. Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genet Med. 2016 06; 18(6):608-17. PMID: 26562225.
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    42. Foong J, Girdea M, Stavropoulos J, Brudno M. Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data. PLoS One. 2015; 10(10):e0139656. PMID: 26437450.
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    43. 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, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat. 2015 Oct; 36(10):915-21. PMID: 26295439.
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    44. 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. Hum Mutat. 2015 Oct; 36(10):922-7. PMID: 26255989.
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    45. 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, Adams D, Gahl WA, Boycott KM, Brudno M. PhenomeCentral: a portal for phenotypic and genotypic matchmaking of patients with rare genetic diseases. Hum Mutat. 2015 Oct; 36(10):931-40. PMID: 26251998.
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    46. Krawitz P, Buske O, Zhu N, Brudno M, Robinson PN. The genomic birthday paradox: how much is enough? Hum Mutat. 2015 Oct; 36(10):989-97. PMID: 26239817.
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    47. 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 Res. 2015 Sep 03; 43(15):7217-28. PMID: 26130710.
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    48. Mustafa H, David M, Brudno M. Assembly and characterization of novel Alu inserts detected from next-generation sequencing data. Mob Genet Elements. 2014 Oct; 4(5):1-7. PMID: 26442170.
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    49. Buske OJ, Manickaraj A, Mital S, Ray PN, Brudno M. Identification of deleterious synonymous variants in human genomes. Bioinformatics. 2015 Mar 01; 31(5):799. PMID: 25488928.
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    50. 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, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Res. 2014 Dec; 24(12):2077-89. PMID: 25273068.
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    51. 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. J Paediatr Child Health. 2015 Apr; 51(4):381-6. PMID: 25109851.
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    52. Rampášek L, Arbabi A, Brudno M. Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing. Bioinformatics. 2014 Jun 15; 30(12):i212-8. PMID: 24931986.
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    53. 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, Rousseau F, Marshall C, Wintle RF, Shen Y, Scherer SW, Friedman JM, Michaud JL, Boycott KM. FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project. Am J Hum Genet. 2014 Jun 05; 94(6):809-17. PMID: 24906018.
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    54. Poliakov A, Foong J, Brudno M, Dubchak I. GenomeVISTA--an integrated software package for whole-genome alignment and visualization. Bioinformatics. 2014 Sep 15; 30(18):2654-5. PMID: 24860159.
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    55. 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, Bourgey M, Bourque G, Montpetit A, Cordero F, Castelo-Branco P, Mangerel J, Tabori U, Ho KC, Huang A, Taylor KR, Mackay A, Bendel AE, Nazarian J, Fangusaro JR, Karajannis MA, Zagzag D, Foreman NK, Donson A, Hegert JV, Smith A, Chan J, Lafay-Cousin L, Dunn S, Hukin J, Dunham C, Scheinemann K, Michaud J, Zelcer S, Ramsay D, Cain J, Brennan C, Souweidane MM, Jones C, Allis CD, Brudno M, Becher O, Hawkins C. Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations. Nat Genet. 2014 May; 46(5):451-6. PMID: 24705254.
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    56. 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. Nat Methods. 2014 Mar; 11(3):333-7. PMID: 24464287.
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    57. 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, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014 Jan; 42(Database issue):D966-74. PMID: 24217912.
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    58. David M, Mustafa H, Brudno M. Detecting Alu insertions from high-throughput sequencing data. Nucleic Acids Res. 2013 Sep; 41(17):e169. PMID: 23921633.
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    59. Buske OJ, Manickaraj A, Mital S, Ray PN, Brudno M. Identification of deleterious synonymous variants in human genomes. Bioinformatics. 2013 Aug 01; 29(15):1843-50. PMID: 23736532.
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    60. 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. Hum Mutat. 2013 Aug; 34(8):1057-65. PMID: 23636887.
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    61. Donmez N, Brudno M. SCARPA: scaffolding reads with practical algorithms. Bioinformatics. 2013 Feb 15; 29(4):428-34. PMID: 23274213.
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    62. 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 Res. 2013 Mar; 23(3):519-29. PMID: 23204306.
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    63. 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. 2012 Oct 15; 28(20):2576-83. PMID: 22851530.
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    64. 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 Res. 2012 Jul; 40(Web Server issue):W615-21. PMID: 22638571.
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    65. Warde-Farley D, Brudno M, Morris Q, Goldenberg A. Mixture model for sub-phenotyping in GWAS. Pac Symp Biocomput. 2012; 363-74. PMID: 22174291.
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    66. 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. J Virol. 2011 Dec; 85(24):12995-3009. PMID: 21994460.
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    67. David M, Dzamba M, Lister D, Ilie L, Brudno M. SHRiMP2: sensitive yet practical SHort Read Mapping. Bioinformatics. 2011 Apr 01; 27(7):1011-2. PMID: 21278192.
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    68. Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M. Detecting copy number variation with mated short reads. Genome Res. 2010 Nov; 20(11):1613-22. PMID: 20805290.
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    69. Fiume M, Williams V, Brook A, Brudno M. Savant: genome browser for high-throughput sequencing data. Bioinformatics. 2010 Aug 15; 26(16):1938-44. PMID: 20562449.
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    70. Dalca AV, Rumble SM, Levy S, Brudno M. VARiD: a variation detection framework for color-space and letter-space platforms. Bioinformatics. 2010 Jun 15; 26(12):i343-9. PMID: 20529926.
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    71. 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, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C. The genetic landscape of a cell. Science. 2010 Jan 22; 327(5964):425-31. PMID: 20093466.
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    72. Dalca AV, Brudno M. Genome variation discovery with high-throughput sequencing data. Brief Bioinform. 2010 Jan; 11(1):3-14. PMID: 20053733.
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    73. Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat Methods. 2009 Nov; 6(11 Suppl):S13-20. PMID: 19844226.
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    74. 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. 2009 Nov 01; 25(21):2863-4. PMID: 19783529.
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    75. Medvedev P, Brudno M. Maximum likelihood genome assembly. J Comput Biol. 2009 Aug; 16(8):1101-16. PMID: 19645596.
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    76. Lee S, Hormozdiari F, Alkan C, Brudno M. MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat Methods. 2009 Jul; 6(7):473-4. PMID: 19483690.
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    77. Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol. 2009 May; 5(5):e1000386. PMID: 19461883.
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    78. 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. J Biol. 2009; 8(3):33. PMID: 19371447.
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    79. Dubchak I, Poliakov A, Kislyuk A, Brudno M. Multiple whole-genome alignments without a reference organism. Genome Res. 2009 Apr; 19(4):682-9. PMID: 19176791.
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    80. Donmez N, Bazykin GA, Brudno M, Kondrashov AS. Polymorphism due to multiple amino acid substitutions at a codon site within Ciona savignyi. Genetics. 2009 Feb; 181(2):685-90. PMID: 19087959.
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    81. Lee S, Cheran E, Brudno M. A robust framework for detecting structural variations in a genome. Bioinformatics. 2008 Jul 01; 24(13):i59-67. PMID: 18586745.
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    82. Dalca AV, Brudno M. FRESCO: flexible alignment with rectangle scoring schemes. Pac Symp Biocomput. 2008; 3-14. PMID: 18229672.
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    83. Bazykin GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS. Extensive parallelism in protein evolution. Biol Direct. 2007 Aug 16; 2:20. PMID: 17705846.
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    84. Brudno M, Poliakov A, Minovitsky S, Ratnere I, Dubchak I. Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W669-74. PMID: 17488840.
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    85. Small KS, Brudno M, Hill MM, Sidow A. Extreme genomic variation in a natural population. Proc Natl Acad Sci U S A. 2007 Mar 27; 104(13):5698-703. PMID: 17372217.
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    86. Small KS, Brudno M, Hill MM, Sidow A. A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol. 2007; 8(3):R41. PMID: 17374142.
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    87. Brudno M. An introduction to the Lagan alignment toolkit. Methods Mol Biol. 2007; 395:205-20. PMID: 17993676.
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    88. 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. J Bioinform Comput Biol. 2006 Oct; 4(5):981-98. PMID: 17099937.
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    89. Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 2005 Feb; 15(2):330-40. PMID: 15687296.
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    90. Brudno M, Steinkamp R, Morgenstern B. The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W41-4. PMID: 15215346.
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    91. 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, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 01; 428(6982):493-521. PMID: 15057822.
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    92. 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 Res. 2004 Apr; 14(4):685-92. PMID: 15060011.
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    93. Cooper GM, Brudno M, Stone EA, Dubchak I, Batzoglou S, Sidow A. Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Res. 2004 Apr; 14(4):539-48. PMID: 15059994.
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    94. 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. 2004 Mar 22; 20(5):636-43. PMID: 15033870.
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    95. Brudno M, Chapman M, Göttgens B, Batzoglou S, Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics. 2003 Dec 23; 4:66. PMID: 14693042.
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    96. Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, Morgenstern B. AGenDA: homology-based gene prediction. Bioinformatics. 2003 Aug 12; 19(12):1575-7. PMID: 12912840.
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    97. Cooper GM, Brudno M, Green ED, Batzoglou S, Sidow A. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res. 2003 May; 13(5):813-20. PMID: 12727901.
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    98. 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 Res. 2003 Apr; 13(4):721-31. PMID: 12654723.
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    99. Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S. Glocal alignment: finding rearrangements during alignment. Bioinformatics. 2003; 19 Suppl 1:i54-62. PMID: 12855437.
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    100. Brudno M, Morgenstern B. Fast and sensitive alignment of large genomic sequences. Proc IEEE Comput Soc Bioinform Conf. 2002; 1:138-47. PMID: 15838131.
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    101. 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 Res. 2001 Jun 01; 29(11):2338-48. PMID: 11376152.
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    102. 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. 2000 Nov; 16(11):1046-7. PMID: 11159318.
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    103. 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 Res. 2000 Sep; 10(9):1304-6. PMID: 10984448.
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    104. Dralyuk I, Brudno M, Gelfand MS, Zorn M, Dubchak I. ASDB: database of alternatively spliced genes. Nucleic Acids Res. 2000 Jan 01; 28(1):296-7. PMID: 10592252.
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