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ALEKSANDAR MILOSAVLJEVIC

TitleProfessor
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular & Human Genetics
AddressOne Baylor Plaza
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    OT2OD038054     (MILOSAVLJEVIC, ALEKSANDAR)Sep 8, 2025 - Sep 7, 2026
    NIH
    Multimodal AI for Precise Clinical and Genetic Diagnosis of Congenital Heart Disease
    Role: Principal Investigator
    U24HG012108     (SESTAN, NENAD)Sep 22, 2021 - Jun 30, 2026
    NIH
    Laboratory, Data Analysis, and Coordinating Center (LDACC) for the Developmental Human Genotype-Tissue Expression Project
    Role: Co-Principal Investigator
    U01AG072439     (SHULMAN, JOSHUA M)Jul 1, 2021 - Jun 30, 2026
    NIH
    Functional Genomic Dissection of Alzheimer's Disease in Humans and Drosophila Models
    Role: Co-Principal Investigator
    OT2OD030547     (MILOSAVLJEVIC, ALEKSANDAR)Sep 24, 2020 - Sep 23, 2025
    NIH
    GENOMIC INDEXING OF COMMON FUND DATASETS
    Role: Principal Investigator
    U54OD030165     (HEANEY, JASON D.)Sep 15, 2020 - Aug 31, 2030
    NIH
    BCM CENTER FOR PRECISION MEDICINE MODELS
    Role: Co-Principal Investigator
    UH3TR002881     (GHIRAN, IONITA CALIN ;JONES, JENNIFER ;MILOSAVLJEVIC, ALEKSANDAR)Sep 16, 2019 - Jun 30, 2023
    NIH
    Integrative, multi-parametric characterization of the EV surface protein and nucleic acid landscape by nano-flow and sorting cytometry
    Role: Co-Principal Investigator
    UG3TR002881     (GHIRAN, IONITA CALIN)Sep 16, 2019 - Jun 30, 2021
    NIH
    Integrative, multi-parametric characterization of the EV surface protein and nucleic acid landscape by nano-flow and sorting cytometry
    Role: Co-Principal Investigator
    U54DA049098     (GALAS, DAVID J.;GERSTEIN, MARK BENDER;MILOSAVLJEVIC, ALEKSANDAR)Aug 15, 2019 - Jul 31, 2023
    NIH
    DATA MANAGEMENT AND RESOURCE REPOSITORY FOR THE exRNA ATLAS PHASE II
    Role: Principal Investigator
    U24HG009649     (PLON, SHARON E.)Sep 12, 2017 - Jun 30, 2026
    NIH
    Baylor College of Medicine/Stanford University Clinical Genome Resource (CLINGEN)
    Role: Co-Principal Investigator
    R13ES025509     (STAMATOYANNOPOULOS, JOHN A)May 1, 2015 - Jun 30, 2016
    NIH
    Epigenomics 2015: A Roadmap to the Living Genome
    Role: Co-Principal Investigator
    U54DA036134     (MILOSAVLJEVIC, ALEKSANDAR)Aug 1, 2013 - Jul 31, 2019
    NIH
    DATA MANAGEMENT AND RESOURCE REPOSITORY FOR THE exRNA ATLAS
    Role: Principal Investigator
    R01CA163849     (JUSTICE, MONICA J.)Jul 23, 2013 - May 31, 2019
    NIH
    The pluripotency regulator Prdm14 initiates cancer by epigenetic mechanisms
    Role: Co-Principal Investigator
    U01DA025956     (MILOSAVLJEVIC, ALEKSANDAR)Sep 20, 2008 - Jul 31, 2015
    NIH
    Epigenomics Data Analysis and Coordination Center at Baylor College of Medicine
    Role: Principal Investigator
    R21HG004554     (MILOSAVLJEVIC, ALEKSANDAR)Jul 1, 2007 - Jun 30, 2010
    NIH
    Comprehensive High-throughput Mapping of Cancer Genomes
    Role: Principal Investigator
    R33CA114151     (MILOSAVLJEVIC, ALEKSANDAR)May 1, 2007 - Apr 30, 2011
    NIH
    Multiplexed Methods for the Study of Chromosomal Aberrations in Cancer
    Role: Principal Investigator
    R01HG004009     (MILOSAVLJEVIC, ALEKSANDAR)Aug 15, 2006 - Mar 31, 2010
    NIH
    Genboree System for Translational Studies of Genome Variation
    Role: Principal Investigator
    U01RR018464     (MILOSAVLJEVIC, ALEKSANDAR)Sep 30, 2002 - Aug 31, 2005
    NIH
    Clone Pooling Methods for Physical Mapping
    Role: Principal Investigator
    R01HG002583     (MILOSAVLJEVIC, ALEKSANDAR)Jul 19, 2002 - Mar 31, 2006
    NIH
    Clone-Array Pooled Shotgun Indexing
    Role: Principal Investigator

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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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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Ahooyi TM, Stear B, Simmons JA, Metzger VT, Kumar P, Evangelista JE, Clarke DJB, Xie Z, Kim H, Jenkins SL, Maurya MR, Ramachandran S, Fahy E, Gillespie TH, Imam FT, Kokash N, Roth ME, Fullem R, Jevtic D, Mihajlovic A, Tiemeyer M, Bakker C, Schroeder AJ, Markowski J, Nedzel J, Hill DD, Terry J, Nemarich C, Boline J, Park PJ, Ardlie KG, Vora J, Mazumder R, Ranzinger R, de Bono B, Subramaniam S, Grethe JS, Yang JJ, Lambert CG, Resnick A, Milosavljevic A, Ma'ayan A, Silverstein JC, Taylor DM. The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data. bioRxiv. 2025 Sep 04. PMID: 40832351; PMCID: PMC12363844.
      Citations:    
    2. Persson P, Bladh M, Teleka S, Milosavljevic A, Gustafsson N, J?ghagen EL, Klinge B, De Silva K, V?h?sarja N, Buhlin K, Nilsson P, Orho-Melander M, Melander O, Naimi-Akbar A, J?nsson D. Using Dental Register Information and Questionnaire Data to Assess Periodontitis in Large Cohort Studies. J Clin Periodontol. 2025 Aug 19. PMID: 40827525.
      Citations:    Fields:    
    3. Milisavljevic F, Bogdanovic I, Miljkovic A, Milin-Lazovic J, Milosavljevic A, Lazic I, Ilic R, Grujicic D. Supracerebellar highway-fast and safe road to pediatric pineal tumor resection. Childs Nerv Syst. 2025 Aug 13; 41(1):260. PMID: 40802062.
      Citations:    Fields:    Translation:Humans
    4. Omo-Lamai S, Wang Y, Patel MN, Milosavljevic A, Zuschlag D, Poddar S, Wu J, Wang L, Dong F, Espy C, Majumder A, Essien EO, Shen M, Channer B, Papp TE, Tobin M, Maheshwari R, Jeong S, Patel S, Shah A, Murali S, Chase LS, Zamora ME, Arral ML, Marcos-Contreras OA, Myerson JW, Hunter CA, Discher D, Gaskill PJ, Tsourkas A, Muzykantov VR, Brodsky I, Shin S, Whitehead KA, Parhiz H, Katzen J, Miner JJ, Trauner D, Brenner JS. Limiting endosomal damage sensing reduces inflammation triggered by lipid nanoparticle endosomal escape. Nat Nanotechnol. 2025 Sep; 20(9):1285-1297. PMID: 40789922; PMCID: PMC12352612.
      Citations:    Fields:    Translation:HumansAnimalsCells
    5. Jonjev ?, Bjeljac I, Milosavljevic A, Todic M, Mrvic S, Kalinic N. Bilateral skeletonized IMAs used as "in situ" grafts for different coronary territories: long-term propensity matching study. Indian J Thorac Cardiovasc Surg. 2025 Sep; 41(9):1144-1152. PMID: 40860409; PMCID: PMC12373614.
      Citations:    
    6. Milo?evic D, Milosavljevic A, Simovic P, Trajkovic A, Medeiros A, Savic-Zdravkovic D, Stojanovic K, Kostic T, Predic B. Unsupervised deep clustering as a tool for the?identification of dark taxa in biomonitoring. Environ Monit Assess. 2025 Jul 04; 197(8):858. PMID: 40613928.
      Citations:    Fields:    Translation:AnimalsPHPublic Health
    7. Arbesfeld JA, Da EY, Stevenson JS, Kuzma K, Paul A, Farris T, Capodanno BJ, Grindstaff SB, Riehle K, Saraiva-Agostinho N, Safer JF, Casper J, Haeussler M, Milosavljevic A, Foreman J, Firth HV, Hunt SE, Iqbal S, Cline MS, Rubin AF, Wagner AH. Mapping MAVE data for use in human genomics applications. Genome Biol. 2025 Jun 25; 26(1):179. PMID: 40563119; PMCID: PMC12188674.
      Citations:    Fields:    Translation:Humans
    8. Clarke DJB, Evangelista JE, Xie Z, Marino GB, Byrd AI, Maurya MR, Srinivasan S, Yu K, Petrosyan V, Roth ME, Milinkov M, King CH, Vora JK, Keeney J, Nemarich C, Khan W, Lachmann A, Ahmed N, Agris A, Pan J, Ramachandran S, Fahy E, Esquivel E, Mihajlovic A, Jevtic B, Milinovic V, Kim S, McNeely P, Wang T, Wenger E, Brown MA, Sickler A, Zhu Y, Jenkins SL, Blood PD, Taylor DM, Resnick AC, Mazumder R, Milosavljevic A, Subramaniam S, Ma'ayan A. Playbook workflow builder: Interactive construction of bioinformatics workflows. PLoS Comput Biol. 2025 Apr; 21(4):e1012901. PMID: 40179105; PMCID: PMC11967941.
      Citations: 1     Fields:    Translation:Humans
    9. Yao Z, Ayoub A, Srinivasan V, Wu J, Tang C, Duan R, Milosavljevic A, Xing L, Ebetino FH, Frontier AJ, Boyce BF. Hydroxychloroquine and a low antiresorptive activity bisphosphonate conjugate prevent and reverse ovariectomy-induced bone loss in mice through dual antiresorptive and anabolic effects. Bone Res. 2024 Sep 05; 12(1):52. PMID: 39231935; PMCID: PMC11375055.
      Citations:    
    10. Wright MW, Thaxton CL, Nelson T, DiStefano MT, Savatt JM, Brush MH, Cheung G, Mandell ME, Wulf B, Ward TJ, Goehringer S, O'Neill T, Weller P, Preston CG, Keseler IM, Goldstein JL, Strande NT, McGlaughon J, Azzariti DR, Cordova I, Dziadzio H, Babb L, Riehle K, Milosavljevic A, Martin CL, Rehm HL, Plon SE, Berg JS, Riggs ER, Klein TE, Wright MW, Thaxton CL, Nelson T, DiStefano MT, Savatt JM, Brush MH, Cheung G, Mandell ME, Wulf B, Ward TJ, Goehringer S, O'Neill T, Weller P, Preston CG, Keseler IM, Goldstein JL, Strande NT, McGlaughon J, Azzariti DR, Cordova I, Dziadzio H, Babb L, Riehle K, Milosavljevic A, Martin CL, Rehm HL, Plon SE, Berg JS, Riggs ER, Klein TE. Generating Clinical-Grade Gene-Disease Validity Classifications Through the ClinGen Data Platforms. Annu Rev Biomed Data Sci. 2024 08; 7(1):31-50. PMID: 38663031; PMCID: PMC12001867.
      Citations: 3     Fields:    Translation:Humans
    11. Danilovic D, Nahon L, Garcia GA, Milosavljevic AR, Vukmirovic N, Dojcilovic R, To?ic D, Djokovic V, Bo?anic DK. Velocity Map Imaging Photoelectron Spectroscopy of Silver Iodide Aerosol Particles. Chemphyschem. 2024 Sep 02; 25(17):e202400328. PMID: 38804589.
      Citations:    
    12. Arbesfeld JA, Da EY, Stevenson JS, Kuzma K, Paul A, Farris T, Capodanno BJ, Grindstaff SB, Riehle K, Saraiva-Agostinho N, Safer JF, Milosavljevic A, Foreman J, Firth HV, Hunt SE, Iqbal S, Cline MS, Rubin AF, Wagner AH, Arbesfeld JA, Da EY, Stevenson JS, Kuzma K, Paul A, Farris T, Capodanno BJ, Grindstaff SB, Riehle K, Saraiva-Agostinho N, Safer JF, Milosavljevic A, Foreman J, Firth HV, Hunt SE, Iqbal S, Cline MS, Rubin AF, Wagner AH. Mapping MAVE data for use in human genomics applications. bioRxiv. 2024 Jun 30. PMID: 38979347; PMCID: PMC11230167.
      Citations:    
    13. Mart?nez-Fern?ndez L, Rankovic ML, Canon F, Nahon L, Giuliani A, Milosavljevic AR, Martin-Somer A. Photodissociation of leucine-enkephalin protonated peptide: an experimental and theoretical perspective. RSC Adv. 2024 May 22; 14(24):16809-16820. PMID: 38784408; PMCID: PMC11112675.
      Citations:    
    14. Simovic P, Milosavljevic A, Stojanovic K, Radenkovic M, Savic-Zdravkovic D, Predic B, Petrovic A, Bo?anic M, Milo?evic D. Automated identification of aquatic insects: A case study using deep learning and computer vision techniques. Sci Total Environ. 2024 Jul 20; 935:172877. PMID: 38740196.
      Citations:    
    15. Poon CYL, Leung TY, Wang CC, Daljit S, Nicolaides K, Scaglia F, Cheng KYY, Milosavljevic A. Aspirin delays the metabolic clock of gestation in women at risk of preeclampsia: abridged secondary publication. Hong Kong Med J. 2024 Feb; 30 Suppl 1(1):45-46. PMID: 38413214.
      Citations:    Fields:    
    16. Xu W, Billon C, Li H, Wilderman A, Qi L, Graves A, Rideb JRDC, Zhao Y, Hayes M, Yu K, Losby M, Hampton CS, Adeyemi CM, Nasiotis E, Oh TG, Fan W, Downes M, Welch RD, Evans RM, Milosavljevic A, Walker JK, Pei L, Burris T, Zhang L, Hong SJ, Fu C, Jensen BC. Novel Pan-ERR Agonists Ameliorate Heart Failure Through Enhancing Cardiac Fatty Acid Metabolism and Mitochondrial Function. Circulation. 2024 01 16; 149(3):227-250. PMID: 37961903; PMCID: PMC10842599.
      Citations: 1     Fields:    Translation:AnimalsCells
    17. Murillo OD, Petrosyan V, LaPlante EL, Dobrolecki LE, Lewis MT, Milosavljevic A. Deconvolution of cancer cell states by the XDec-SM method. PLoS Comput Biol. 2023 08; 19(8):e1011365. PMID: 37578979; PMCID: PMC10449115.
      Citations:    Fields:    Translation:HumansCells
    18. Arce JE, Welsh JA, Cook S, Tigges J, Ghiran I, Jones JC, Jackson A, Roth M, Milosavljevic A. The NanoFlow Repository. Bioinformatics. 2023 06 01; 39(6). PMID: 37285317; PMCID: PMC10272702.
      Citations: 2     Fields:    
    19. Jonjev ZS, Milosavljevic AM, Kalinic N, Adam A. Clipless skeletonized internal mammary artery harvesting with harmonic technology. Multimed Man Cardiothorac Surg. 2023 May 22; 2023. PMID: 37212423.
      Citations:    
    20. LaPlante EL, St?rchler A, Fullem R, Chen D, Starner AC, Esquivel E, Alsop E, Jackson AR, Ghiran I, Pereira G, Rozowsky J, Chang J, Gerstein MB, Alexander RP, Roth ME, Franklin JL, Coffey RJ, Raffai RL, Mansuy IM, Stavrakis S, deMello AJ, Laurent LC, Wang YT, Tsai CF, Liu T, Jones J, Van Keuren-Jensen K, Van Nostrand E, Mateescu B, Milosavljevic A. exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers. Cell Genom. 2023 May 10; 3(5):100303. PMID: 37228754; PMCID: PMC10203258.
      Citations: 4     
    21. Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, G?rsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guig? R, Gingeras TR, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes?& variant-impact models. Cell. 2023 03 30; 186(7):1493-1511.e40. PMID: 37001506; PMCID: PMC10074325.
      Citations: 2     Fields:    
    22. Cable J, Witwer KW, Coffey RJ, Milosavljevic A, von Lersner AK, Jimenez L, Pucci F, Barr MM, Dekker N, Barman B, Humphrys D, Williams J, de Palma M, Guo W, Bastos N, Hill AF, Levy E, Hantak MP, Crewe C, Aikawa E, Adamczyk AM, Zanotto TM, Ostrowski M, Arab T, Rabe DC, Sheikh A, da Silva DR, Jones JC, Okeoma C, Gaborski T, Zhang Q, Gololobova O. Exosomes, microvesicles, and other extracellular vesicles-a Keystone Symposia report. Ann N Y Acad Sci. 2023 05; 1523(1):24-37. PMID: 36961472; PMCID: PMC10715677.
      Citations:    Fields:    Translation:HumansCells
    23. Licht O, Barreiro-Lage D, Rousseau P, Giuliani A, Milosavljevic AR, Isaak A, Mastai Y, Albeck A, Singh R, Nguyen VTT, Nahon L, Mart?nez-Fern?ndez L, D?az-Tendero S, Toker Y. Peptide Bond Formation in the Protonated Serine Dimer Following Vacuum UV Photon-Induced Excitation. Angew Chem Int Ed Engl. 2023 Apr 03; 62(15):e202218770. PMID: 36789791.
      Citations:    
    24. Krysiak K, Danos AM, Saliba J, McMichael JF, Coffman AC, Kiwala S, Barnell EK, Sheta L, Grisdale CJ, Kujan L, Pema S, Lever J, Ridd S, Spies NC, Andric V, Chiorean A, Rieke DT, Clark KA, Reisle C, Venigalla AC, Evans M, Jani P, Takahashi H, Suda A, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Kesserwan C, Lamping M, Shen H, Marr AR, Hoang MH, Singhal K, Khanfar M, Li BV, Lin WH, Terraf P, Corson LB, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, King I, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith M, Griffith OL. CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. Nucleic Acids Res. 2023 01 06; 51(D1):D1230-D1241. PMID: 36373660; PMCID: PMC9825608.
      Citations: 2     Fields:    Translation:Humans
    25. Petrosyan V, Dobrolecki LE, Thistlethwaite L, Lewis AN, Sallas C, Srinivasan RR, Lei JT, Kovacevic V, Obradovic P, Ellis MJ, Osborne CK, Rimawi MF, Pavlick A, Shafaee MN, Dowst H, Jain A, Saltzman AB, Malovannaya A, Marangoni E, Welm AL, Welm BE, Li S, Wulf GM, Sonzogni O, Huang C, Vasaikar S, Hilsenbeck SG, Zhang B, Milosavljevic A, Lewis MT. Identifying biomarkers of differential chemotherapy response in TNBC patient-derived xenografts with a CTD/WGCNA approach. iScience. 2023 Jan 20; 26(1):105799. PMID: 36619972; PMCID: PMC9813793.
      Citations: 4     
    26. LaPlante EL, Liu D, Petrosyan V, Yao Q, Milosavljevic A. XDec-CHI reveals immunosuppressive interactions in pancreatic ductal adenocarcinoma. iScience. 2022 Oct 21; 25(10):105249. PMID: 36274954; PMCID: PMC9579012.
      Citations: 1     
    27. Obradovic P, Kovacevic V, Li X, Milosavljevic A. An Information-Theoretic Bound on p-Values for Detecting Communities Shared between Weighted Labeled Graphs. Entropy (Basel). 2022 Sep 21; 24(10). PMID: 37420347; PMCID: PMC9601153.
      Citations:    
    28. Wei CH, Allot A, Riehle K, Milosavljevic A, Lu Z. tmVar 3.0: an improved variant concept recognition and normalization tool. Bioinformatics. 2022 09 15; 38(18):4449-4451. PMID: 35904569; PMCID: PMC9477515.
      Citations:    Fields:    
    29. Petrosyan V, Dobrolecki LE, LaPlante EL, Srinivasan RR, Bailey MH, Welm AL, Welm BE, Lewis MT, Milosavljevic A. Immunologically "cold" triple negative breast cancers engraft at a higher rate in patient derived xenografts. NPJ Breast Cancer. 2022 Sep 10; 8(1):104. PMID: 36088362; PMCID: PMC9464188.
      Citations:    
    30. Mateescu B, Jones JC, Alexander RP, Alsop E, An JY, Asghari M, Boomgarden A, Bouchareychas L, Cayota A, Chang HC, Charest A, Chiu DT, Coffey RJ, Das S, De Hoff P, deMello A, D'Souza-Schorey C, Elashoff D, Eliato KR, Franklin JL, Galas DJ, Gerstein MB, Ghiran IH, Go DB, Gould S, Grogan TR, Higginbotham JN, Hladik F, Huang TJ, Huo X, Hutchins E, Jeppesen DK, Jovanovic-Talisman T, Kim BYS, Kim S, Kim KM, Kim Y, Kitchen RR, Knouse V, LaPlante EL, Lebrilla CB, Lee LJ, Lennon KM, Li G, Li F, Li T, Liu T, Liu Z, Maddox AL, McCarthy K, Meechoovet B, Maniya N, Meng Y, Milosavljevic A, Min BH, Morey A, Ng M, Nolan J, De Oliveira Junior GP, Paulaitis ME, Phu TA, Raffai RL, Re?tegui E, Roth ME, Routenberg DA, Rozowsky J, Rufo J, Senapati S, Shachar S, Sharma H, Sood AK, Stavrakis S, St?rchler A, Tewari M, Tosar JP, Tucker-Schwartz AK, Turchinovich A, Valkov N, Van Keuren-Jensen K, Vickers KC, Vojtech L, Vreeland WN, Wang C, Wang K, Wang Z, Welsh JA, Witwer KW, Wong DTW, Xia J, Xie YH, Yang K, Zaborowski MP, Zhang C, Zhang Q, Zivkovic AM, Laurent LC. Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research. iScience. 2022 Aug 19; 25(8):104653. PMID: 35958027; PMCID: PMC9358052.
      Citations:    
    31. Krysiak K, Danos AM, Kiwala S, McMichael JF, Coffman AC, Barnell EK, Sheta L, Saliba J, Grisdale CJ, Kujan L, Pema S, Lever J, Spies NC, Chiorean A, Clark KA, Jani P, Takahashi H, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Marr AR, Li BV, Lin WH, Terraf P, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith OL, Griffith M, Rieke DT, Lamping M. A community approach to the cancer-variant-interpretation bottleneck. Nat Cancer. 2022 05; 3(5):522-525. PMID: 35624339; PMCID: PMC9872366.
      Citations:    Translation:Humans
    32. Thistlethwaite LR, Li X, Burrage LC, Riehle K, Hacia JG, Braverman N, Wangler MF, Miller MJ, Elsea SH, Milosavljevic A. Clinical diagnosis of metabolic disorders using untargeted metabolomic profiling and disease-specific networks learned from profiling data. Sci Rep. 2022 04 21; 12(1):6556. PMID: 35449147; PMCID: PMC9023513.
      Citations:    Fields:    Translation:Humans
    33. Welsh JA, Killingsworth B, Kepley J, Traynor T, Cook S, Savage J, Marte J, Lee MJ, Maeng HM, Pleet ML, Magana S, Merino MJ, Linehan WM, Greten T, Cooks T, Harris CC, Apolo A, Abdel-Mageed A, Ivanov AR, Trepel JB, Roth M, Tkach M, Milosavljevic A, LeBlanc A, Berzofsky JA, Ruppin E, Aldape K, Camphausen K, Gulley JL, Ghiran I, Jacobson S, Jones JC, Gorgens A, Maire CL, Lamszus K, Ricklefs FL, Th?ry C. MPAPASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays. Cell Rep Methods. 2022 01 24; 2(1):100136. PMID: 35474866; PMCID: PMC9017130.
      Citations:    
    34. Ghamrawi R, Velickovic I, Milicevic O, White WM, Thistlethwaite LR, Cunningham JM, Milosavljevic A, Milic NM, Garovic VD. Buffy Coat DNA Methylation Profile Is Representative of Methylation Patterns in White Blood Cell Types in Normal Pregnancy. Front Bioeng Biotechnol. 2021; 9:782843. PMID: 35071203; PMCID: PMC8766967.
      Citations:    
    35. Thistlethwaite LR, Petrosyan V, Li X, Miller MJ, Elsea SH, Milosavljevic A. Correction: CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models. PLoS Comput Biol. 2021 Oct; 17(10):e1009551. PMID: 34695129; PMCID: PMC8544872.
      Citations:    Fields:    
    36. Suvakov S, Ghamrawi R, Cubro H, Tu H, White WM, Tobah YSB, Milic NM, Grande JP, Cunningham JM, Chebib FT, Prata LGPL, Zhu Y, Tchkonia T, Kirkland JL, Nath KA, Milosavljevic A, Garovic VD. Epigenetic and senescence markers indicate an accelerated ageing-like state in women with preeclamptic pregnancies. EBioMedicine. 2021 Aug; 70:103536. PMID: 34391091; PMCID: PMC8365351.
      Citations: 4     Fields:    Translation:HumansCells
    37. Li X, Milosavljevic A, Elsea SH, Wang CC, Scaglia F, Syngelaki A, Nicolaides KH, Poon LC. Effective Aspirin Treatment of Women at Risk for Preeclampsia Delays the Metabolic Clock of Gestation. Hypertension. 2021 11; 78(5):1398-1410. PMID: 34225470.
      Citations: 1     Fields:    Translation:Humans
    38. Webster NJ, Maywald RL, Benton SM, Dawson EP, Murillo OD, LaPlante EL, Milosavljevic A, Lanza DG, Heaney JD. Testicular germ cell tumors arise in the absence of sex-specific differentiation. Development. 2021 05 01; 148(9). PMID: 33912935; PMCID: PMC8126408.
      Citations: 5     Fields:    Translation:AnimalsCells
    39. Thistlethwaite LR, Petrosyan V, Li X, Miller MJ, Elsea SH, Milosavljevic A. CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models. PLoS Comput Biol. 2021 01; 17(1):e1008550. PMID: 33513132; PMCID: PMC7875364.
      Citations: 5     Fields:    Translation:HumansCells
    40. Milosavljevic A, Jancic J, Mircic A, Do?ic A, Boljanovic J, Milisavljevic M, Cetkovic M. Morphological and functional characteristics of satellite glial cells in the peripheral nervous system. Folia Morphol (Warsz). 2021; 80(4):745-755. PMID: 33330971.
      Citations:    
    41. Lurie E, Liu D, LaPlante EL, Thistlethwaite LR, Yao Q, Milosavljevic A. Histoepigenetic analysis of the mesothelin network within pancreatic ductal adenocarcinoma cells reveals regulation of retinoic acid receptor gamma and AKT by mesothelin. Oncogenesis. 2020 Jul 02; 9(7):62. PMID: 32616712; PMCID: PMC7332500.
      Citations: 2     
    42. Lucero R, Zappulli V, Sammarco A, Murillo OD, Cheah PS, Srinivasan S, Tai E, Ting DT, Wei Z, Roth ME, Laurent LC, Krichevsky AM, Breakefield XO, Milosavljevic A. Glioma-Derived miRNA-Containing Extracellular Vesicles Induce Angiogenesis by Reprogramming Brain Endothelial Cells. Cell Rep. 2020 02 18; 30(7):2065-2074.e4. PMID: 32075753; PMCID: PMC7148092.
      Citations: 47     Fields:    Translation:HumansCells
    43. Bacher R, Jost D, Waguet A, HADACA consortium, Houseman EA, Lurie E, Lutsik P, Milosavljevic A, Scherer M, Blum MGB, Richard M, Decamps C, Priv? F. Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software. BMC Bioinformatics. 2020 Jan 13; 21(1):16. PMID: 31931698; PMCID: PMC6958785.
      Citations: 14     Fields:    Translation:HumansCells
    44. Popovic D, Kocic G, Katic V, Zarubica A, Velickovic LJ, Nickovic VP, Jovic A, Veljkovic A, Petrovic V, Rakic V, Jovic Z, Ulrih NP, Sokolovic D, Stojanovic M, Stankovic M, Radenkovic G, Nikolic GR, Lukac ?, Milosavljevic A, Sokolovic D. Anthocyanins Protect Hepatocytes against CCl4-Induced Acute Liver Injury in Rats by Inhibiting Pro-inflammatory mediators, Polyamine Catabolism, Lipocalin-2, and Excessive Proliferation of Kupffer Cells. Antioxidants (Basel). 2019 Oct 04; 8(10). PMID: 31590249; PMCID: PMC6826396.
      Citations:    
    45. Das S, Extracellular RNA Communication Consortium, Ansel KM, Bitzer M, Charest A, Galas DJ, Gerstein MB, Gupta M, Milosavljevic A, McManus MT, Patel T, Raffai RL, Rozowsky J, Roth ME, Saugstad JA, Van Keuren-Jensen K, Weaver AM, Laurent LC, Breakefield XO. The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research. Cell. 2019 04 04; 177(2):231-242. PMID: 30951667; PMCID: PMC6601620.
      Citations: 72     Fields:    Translation:HumansCells
    46. Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A. exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. Cell. 2019 04 04; 177(2):463-477.e15. PMID: 30951672; PMCID: PMC6616370.
      Citations: 94     Fields:    Translation:HumansCells
    47. Rozowsky J, Kitchen RR, Park JJ, Galeev TR, Diao J, Warrell J, Thistlethwaite W, Subramanian SL, Milosavljevic A, Gerstein M. exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling. Cell Syst. 2019 04 24; 8(4):352-357.e3. PMID: 30956140; PMCID: PMC7079576.
      Citations: 38     Fields:    Translation:HumansAnimals
    48. Popovic D, Kocic G, Katic V, Jovic Z, Zarubica A, Jankovic Velickovic L, Nikolic V, Jovic A, Kundalic B, Rakic V, Ulrih NP, Skrt M, Sokolovic D, Dinic L, Stojanovic M, Milosavljevic A, Velickovic F, Sokolovic D. Protective effects of anthocyanins from bilberry extract in rats exposed to nephrotoxic effects of carbon tetrachloride. Chem Biol Interact. 2019 May 01; 304:61-72. PMID: 30825423.
      Citations:    
    49. Burrage LC, Thistlethwaite L, Stroup BM, Sun Q, Miller MJ, Nagamani SCS, Craigen W, Scaglia F, Sutton VR, Graham B, Kennedy AD, Members of the UCDC,, Milosavljevic A, Lee BH, Elsea SH. Untargeted metabolomic profiling reveals multiple pathway perturbations and new clinical biomarkers in urea cycle disorders. Genet Med. 2019 09; 21(9):1977-1986. PMID: 30670878; PMCID: PMC6650380.
      Citations: 16     Fields:    Translation:Humans
    50. Carrero I, Liu HC, Sikora AG, Milosavljevic A. Histoepigenetic analysis of HPV- and tobacco-associated head and neck cancer identifies both subtype-specific and common therapeutic targets despite divergent microenvironments. Oncogene. 2019 05; 38(19):3551-3568. PMID: 30655605; PMCID: PMC6756123.
      Citations: 14     Fields:    Translation:HumansCells
    51. Pawliczek P, Patel RY, Ashmore LR, Jackson AR, Bizon C, Nelson T, Powell B, Freimuth RR, Strande N, Shah N, Paithankar S, Wright MW, Dwight S, Zhen J, Landrum M, McGarvey P, Babb L, Plon SE, Milosavljevic A, Clinical Genome (ClinGen) Resource. ClinGen Allele Registry links information about genetic variants. Hum Mutat. 2018 11; 39(11):1690-1701. PMID: 30311374; PMCID: PMC6519371.
      Citations: 12     Fields:    Translation:Humans
    52. Dolman L, Page A, Babb L, Freimuth RR, Arachchi H, Bizon C, Brush M, Fiume M, Haendel M, Hansen DP, Milosavljevic A, Patel RY, Pawliczek P, Yates AD, Rehm HL. ClinGen advancing genomic data-sharing standards as a GA4GH driver project. Hum Mutat. 2018 11; 39(11):1686-1689. PMID: 30311379; PMCID: PMC6188700.
      Citations: 7     Fields:    Translation:Humans
    53. Webber EM, Hunter JE, Biesecker LG, Buchanan AH, Clarke EV, Currey E, Dagan-Rosenfeld O, Lee K, Lindor NM, Martin CL, Milosavljevic A, Mittendorf KF, Muessig KR, O'Daniel JM, Patel RY, Ramos EM, Rego S, Slavotinek AM, Sobriera NLM, Weaver MA, Williams MS, Evans JP, Goddard KAB, ClinGen Resource. Evidence-based assessments of clinical actionability in the context of secondary findings: Updates from ClinGen's Actionability Working Group. Hum Mutat. 2018 11; 39(11):1677-1685. PMID: 30311382; PMCID: PMC6211797.
      Citations: 12     Fields:    Translation:Humans
    54. Forbes R, De Fanis A, Bomme C, Rolles D, Pratt ST, Powis I, Besley NA, Simon M, Nandi S, Milosavljevic AR, Nicolas C, Bozek JD, Underwood JG, Holland DMP, Bomme C, Simon M. Photoionization of the iodine 3d, 4s, and 4p orbitals in methyl iodide. J Chem Phys. 2018 Oct 14; 149(14):144302. PMID: 30316287.
      Citations:    Fields:    
    55. Forbes R, De Fanis A, Bomme C, Rolles D, Pratt ST, Powis I, Besley NA, Nandi S, Milosavljevic AR, Nicolas C, Bozek JD, Underwood JG, Holland DMP, Bomme C. Auger electron angular distributions following excitation or ionization of the I 3d level in methyl iodide. J Chem Phys. 2018 Sep 07; 149(9):094304. PMID: 30195315.
      Citations:    Fields:    
    56. Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science. 2018 09 28; 361(6409). PMID: 30139913; PMCID: PMC6198826.
      Citations: 32     Fields:    Translation:HumansCells
    57. Milosavljevic AR, Božanic DK, Sadhu S, Vukmirovic N, Dojcilovic R, Sapkota P, Huang W, Bozek J, Nicolas C, Nahon L, Ptasinska S, Bo?anic DK. Electronic Properties of Free-Standing Surfactant-Capped Lead Halide Perovskite Nanocrystals Isolated in Vacuo. J Phys Chem Lett. 2018 Jul 05; 9(13):3604-3611. PMID: 29902010.
      Citations: 3     Fields:    
    58. Milosavljevic A, DJukic L, Toljic B, Mila?in J, D?eletovic B, Brkovic B, Roganovic J. Melatonin levels in human diabetic dental pulp tissue and its effects on dental pulp cells under hyperglycaemic conditions. Int Endod J. 2018 Oct; 51(10):1149-1158. PMID: 29617040.
      Citations:    
    59. Patel RY, Shah N, Jackson AR, Ghosh R, Pawliczek P, Paithankar S, Baker A, Riehle K, Chen H, Milosavljevic S, Bizon C, Rynearson S, Nelson T, Jarvik GP, Rehm HL, Harrison SM, Azzariti D, Powell B, Babb L, Plon SE, Milosavljevic A, ClinGen Resource. ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants. Genome Med. 2017 01 12; 9(1):3. PMID: 28081714; PMCID: PMC5228115.
      Citations: 27     Fields:    Translation:Humans
    60. Onuchic V, Hartmaier RJ, Boone DN, Samuels ML, Patel RY, White WM, Garovic VD, Oesterreich S, Roth ME, Lee AV, Milosavljevic A. Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types. Cell Rep. 2016 11 15; 17(8):2075-2086. PMID: 27851969; PMCID: PMC5115176.
      Citations: 33     Fields:    Translation:HumansCells
    61. Heale BS, Overby CL, Del Fiol G, Rubinstein WS, Maglott DR, Nelson TH, Milosavljevic A, Martin CL, Goehringer SR, Freimuth R, Williams MS. Integrating Genomic Resources with Electronic Health Records using the HL7 Infobutton Standard. Appl Clin Inform. 2016 08 31; 7(3):817-31. PMID: 27579472; PMCID: PMC5052552.
      Citations: 8     Fields:    
    62. Rackwitz J, Kopyra J, D?bkowska I, Ebel K, Rankovi? MLj, Milosavljevi? AR, Bald I, Dabkowska I, Rankovic MLj, Milosavljevic AR. Sensitizing DNA Towards Low-Energy Electrons with 2-Fluoroadenine. Angew Chem Int Ed Engl. 2016 08 22; 55(35):10248-52. PMID: 27481662.
      Citations:    
    63. Amendola LM, Jarvik GP, Leo MC, McLaughlin HM, Akkari Y, Amaral MD, Berg JS, Biswas S, Bowling KM, Conlin LK, Cooper GM, Dorschner MO, Dulik MC, Ghazani AA, Ghosh R, Green RC, Hart R, Horton C, Johnston JJ, Lebo MS, Milosavljevic A, Ou J, Pak CM, Patel RY, Punj S, Richards CS, Salama J, Strande NT, Yang Y, Plon SE, Biesecker LG, Rehm HL. Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium. Am J Hum Genet. 2016 07 07; 99(1):247. PMID: 27392081; PMCID: PMC5005465.
      Citations: 51     Fields:    
    64. Milosavljevi? AR, Huang W, Sadhu S, Ptasinska S, Milosavljevic AR. Low-Energy Electron-Induced Transformations in Organolead Halide Perovskite. Angew Chem Int Ed Engl. 2016 08 16; 55(34):10083-7. PMID: 27355420.
      Citations:    
    65. Amendola LM, Jarvik GP, Leo MC, McLaughlin HM, Akkari Y, Amaral MD, Berg JS, Biswas S, Bowling KM, Conlin LK, Cooper GM, Dorschner MO, Dulik MC, Ghazani AA, Green RC, Hart R, Horton C, Johnston JJ, Lebo MS, Ou J, Pak CM, Punj S, Richards CS, Salama J, Strande NT, Biesecker LG, Rehm HL, Ghosh R, Milosavljevic A, Patel RY, Yang Y, Plon SE. Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium. Am J Hum Genet. 2016 06 02; 98(6):1067-1076. PMID: 27181684; PMCID: PMC4908185.
      Citations: 172     Fields:    Translation:Humans
    66. Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC, L?tvall J, Th?ry C. Extending gene ontology in the context of extracellular RNA and vesicle communication. J Biomed Semantics. 2016; 7:19. PMID: 27076901; PMCID: PMC4830068.
      Citations: 14     Fields:    Translation:HumansCells
    67. Dojcilovic R, Pajovic JD, Božanic DK, Vodnik VV, Dimitrijevic-Brankovic S, Milosavljevic AR, Kašcàkovà S, Réfrégiers M, Djokovic V, Bo?anic DK, Ka?c?kov? S, R?fr?giers M. A fluorescent nanoprobe for single bacterium tracking: functionalization of silver nanoparticles with tryptophan to probe the nanoparticle accumulation with single cell resolution. Analyst. 2016 Mar 21; 141(6):1988-96. PMID: 26858997.
      Citations: 2     Fields:    Translation:Cells
    68. Rankovic MLj, Canon F, Nahon L, Giuliani A, Milosavljevic AR, Canon F. VUV action spectroscopy of protonated leucine-enkephalin peptide in the 6-14 eV range. J Chem Phys. 2015 Dec 28; 143(24):244311. PMID: 26723675.
      Citations: 1     Fields:    Translation:Cells
    69. Overby CL, Heale B, Aronson S, Cherry JM, Dwight S, Milosavljevic A, Nelson T, Niehaus A, Weaver MA, Ramos EM, Williams MS. Providing Access to Genomic Variant Knowledge in a Healthcare Setting: A Vision for the ClinGen Electronic Health Records Workgroup. Clin Pharmacol Ther. 2016 Feb; 99(2):157-60. PMID: 26418054; PMCID: PMC4724305.
      Citations: 6     Fields:    Translation:Humans
    70. Vogel S, Rackwitz J, Schürman R, Prinz J, Milosavljevic AR, Réfrégiers M, Giuliani A, Bald I, Sch?rman R, R?fr?giers M. Using DNA origami nanostructures to determine absolute cross sections for UV photon-induced DNA strand breakage. J Phys Chem Lett. 2015 Nov 19; 6(22):4589-93. PMID: 26536162.
      Citations: 6     Fields:    Translation:Cells
    71. Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A. Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. J Extracell Vesicles. 2015; 4:27497. PMID: 26320941; PMCID: PMC4553261.
      Citations: 28     Fields:    
    72. Pajovic JD, Dojcilovic R, Božanic DK, Kašcáková S, Réfrégiers M, Dimitrijevic-Brankovic S, Vodnik VV, Milosavljevic AR, Piscopiello E, Luyt AS, Djokovic V, Bo?anic DK, Ka?c?kov? S, R?fr?giers M. Tryptophan-functionalized gold nanoparticles for deep UV imaging of microbial cells. Colloids Surf B Biointerfaces. 2015 Nov 01; 135:742-750. PMID: 26340364.
      Citations: 2     Fields:    Translation:Cells
    73. Kannan K, Coarfa C, Chao PW, Luo L, Wang Y, Brinegar AE, Hawkins SM, Milosavljevic A, Matzuk MM, Yen L. Recurrent BCAM-AKT2 fusion gene leads to a constitutively activated AKT2 fusion kinase in high-grade serous ovarian carcinoma. Proc Natl Acad Sci U S A. 2015 Mar 17; 112(11):E1272-7. PMID: 25733895; PMCID: PMC4371965.
      Citations: 17     Fields:    Translation:HumansCells
    74. Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563; PMCID: PMC4530010.
      Citations: 2568     Fields:    Translation:HumansCells
    75. Amin V, Harris RA, Onuchic V, Jackson AR, Charnecki T, Paithankar S, Lakshmi Subramanian S, Riehle K, Coarfa C, Milosavljevic A. Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs. Nat Commun. 2015 Feb 18; 6:6370. PMID: 25691256; PMCID: PMC4335353.
      Citations: 37     Fields:    Translation:HumansCells
    76. Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF. Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun. 2015 Feb 18; 6:6363. PMID: 25691127; PMCID: PMC4333717.
      Citations: 46     Fields:    Translation:HumansAnimalsCells
    77. Coarfa C, Pichot C, Jackson A, Tandon A, Amin V, Raghuraman S, Paithankar S, Lee AV, McGuire SE, Milosavljevic A. Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools. BMC Bioinformatics. 2014; 15 Suppl 7:S2. PMID: 25080362; PMCID: PMC4110728.
      Citations: 10     Fields:    Translation:HumansCells
    78. Milosavljevic AR, Cerovski VZ, Canon F, Rankovic MLj, Škoro N, Nahon L, Giuliani A, Milosavljevic AR, Cerovski VZ, Canon F, Rankovic MLj, ?koro N, Nahon L, Giuliani A. Energy-Dependent UV Photodissociation of Gas-Phase Adenosine Monophosphate Nucleotide Ions: The Role of a Single Solvent Molecule. J Phys Chem Lett. 2014 Jun 05; 5(11):1994-9. PMID: 26273885.
      Citations: 1     Fields:    
    79. Ma J, Coarfa C, Qin X, Bonnen PE, Milosavljevic A, Versalovic J, Aagaard K. mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities. BMC Genomics. 2014 Apr 03; 15:257. PMID: 24694284; PMCID: PMC4234434.
      Citations: 39     Fields:    Translation:Humans
    80. Kannan K, Coarfa C, Rajapakshe K, Hawkins SM, Matzuk MM, Milosavljevic A, Yen L. CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma. PLoS Genet. 2014 Mar; 10(3):e1004216. PMID: 24675677; PMCID: PMC3967933.
      Citations: 26     Fields:    Translation:Humans
    81. Kunde-Ramamoorthy G, Coarfa C, Laritsky E, Kessler NJ, Harris RA, Xu M, Chen R, Shen L, Milosavljevic A, Waterland RA. Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing. Nucleic Acids Res. 2014 Apr; 42(6):e43. PMID: 24391148; PMCID: PMC3973287.
      Citations: 29     Fields:    Translation:HumansCells
    82. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013 Oct; 10(10):949-55. PMID: 24076989.
      Citations: 180     Fields:    Translation:HumansAnimalsCells
    83. Dittwald P, Gambin T, Szafranski P, Li J, Amato S, Divon MY, Elton LE, Scott DA, Schaaf CP, Torres-Martinez W, Stevens AK, Rosenfeld JA, Agadi S, Francis D, Kang SH, Breman A, Lalani SR, Bacino CA, Bi W, Milosavljevic A, Beaudet AL, Patel A, Shaw CA, Lupski JR, Gambin A, Cheung SW, Stankiewicz P, Rodr?guez Rojas LX. NAHR-mediated copy-number variants in a clinical population: mechanistic insights into both genomic disorders and Mendelizing traits. Genome Res. 2013 Sep; 23(9):1395-409. PMID: 23657883; PMCID: PMC3759717.
      Citations: 60     Fields:    Translation:HumansCells
    84. Wu CC, Kannan K, Lin S, Yen L, Milosavljevic A. Identification of cancer fusion drivers using network fusion centrality. Bioinformatics. 2013 May 01; 29(9):1174-81. PMID: 23505294; PMCID: PMC3634186.
      Citations: 16     Fields:    Translation:HumansCells
    85. Harris RA, Shaw C, Li J, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A. Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability. PLoS Genet. 2013; 9(2):e1003333. PMID: 23468659; PMCID: PMC3585018.
      Citations: 1     Fields:    Translation:HumansCells
    86. Evani US, Challis D, Yu J, Jackson AR, Paithankar S, Bainbridge MN, Jakkamsetti A, Pham P, Coarfa C, Milosavljevic A, Yu F. Atlas2 Cloud: a framework for personal genome analysis in the cloud. BMC Genomics. 2012; 13 Suppl 6:S19. PMID: 23134663; PMCID: PMC3481437.
      Citations: 20     Fields:    Translation:Humans
    87. Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ. Spark: a navigational paradigm for genomic data exploration. Genome Res. 2012 Nov; 22(11):2262-9. PMID: 22960372; PMCID: PMC3483555.
      Citations: 20     Fields:    Translation:HumansCells
    88. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31. PMID: 22955991; PMCID: PMC3431496.
      Citations: 881     Fields:    Translation:HumansAnimals
    89. Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, Diaz MA, Shulman R, Aagaard K, Versalovic J, Milosavljevic A. The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences. BMC Bioinformatics. 2012; 13 Suppl 13:S11. PMID: 23320832; PMCID: PMC3426808.
      Citations: 22     Fields:    Translation:Humans
    90. Davies MN, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, Coarfa C, Harris RA, Milosavljevic A, Troakes C, Al-Sarraj S, Dobson R, Schalkwyk LC, Mill J. Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biol. 2012 Jun 15; 13(6):R43. PMID: 22703893; PMCID: PMC3446315.
      Citations: 315     Fields:    Translation:HumansCells
    91. Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic J. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One. 2012; 7(6):e36466. PMID: 22719832; PMCID: PMC3374618.
      Citations: 238     Fields:    Translation:HumansCells
    92. Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A. Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PLoS Genet. 2012; 8(5):e1002692. PMID: 22615578; PMCID: PMC3355074.
      Citations: 43     Fields:    Translation:HumansAnimalsCells
    93. Carbone L, Harris RA, Mootnick AR, Milosavljevic A, Martin DI, Rocchi M, Capozzi O, Archidiacono N, Konkel MK, Walker JA, Batzer MA, de Jong PJ. Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons. Genome Biol Evol. 2012; 4(7):648-58. PMID: 22593550; PMCID: PMC3606032.
      Citations: 29     Fields:    Translation:AnimalsCells
    94. Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F. An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics. 2012 Jan 12; 13:8. PMID: 22239737; PMCID: PMC3292476.
      Citations: 174     Fields:    Translation:Humans
    95. Celestino-Soper PB, Shaw CA, Sanders SJ, Li J, Murtha MT, Ercan-Sencicek AG, Davis L, Thomson S, Gambin T, Chinault AC, Ou Z, German JR, Milosavljevic A, Sutcliffe JS, Cook EH, Stankiewicz P, State MW, Beaudet AL. Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE. Hum Mol Genet. 2011 Nov 15; 20(22):4360-70. PMID: 21865298; PMCID: PMC3196886.
      Citations: 54     Fields:    Translation:Humans
    96. Hampton OA, Koriabine M, Miller CA, Coarfa C, Li J, Den Hollander P, Schoenherr C, Carbone L, Nefedov M, Ten Hallers BF, Lee AV, De Jong PJ, Milosavljevic A. Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines. Cancer Genet. 2011 Aug; 204(8):447-57. PMID: 21962895; PMCID: PMC3185296.
      Citations: 13     Fields:    Translation:HumansCells
    97. Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, Versalovic J. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 2011 Nov; 141(5):1782-91. PMID: 21741921; PMCID: PMC3417828.
      Citations: 248     Fields:    Translation:HumansCells
    98. Fawcett GL, Raveendran M, Deiros DR, Chen D, Yu F, Harris RA, Ren Y, Muzny DM, Reid JG, Wheeler DA, Worley KC, Shelton SE, Kalin NH, Milosavljevic A, Gibbs R, Rogers J. Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta). BMC Genomics. 2011 Jun 13; 12:311. PMID: 21668978; PMCID: PMC3141668.
      Citations: 19     Fields:    Translation:Animals
    99. Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB, Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths-Jones S, Clayton DF. Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. BMC Genomics. 2011 May 31; 12(1):277. PMID: 21627805; PMCID: PMC3118218.
      Citations: 23     Fields:    Translation:Animals
    100. Milosavljevic A. Emerging patterns of epigenomic variation. Trends Genet. 2011 Jun; 27(6):242-50. PMID: 21507501; PMCID: PMC3104125.
      Citations: 16     Fields:    Translation:HumansAnimals
    101. Shohet JM, Ghosh R, Coarfa C, Ludwig A, Benham AL, Chen Z, Patterson DM, Barbieri E, Mestdagh P, Sikorski DN, Milosavljevic A, Kim ES, Gunaratne PH. A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma. Cancer Res. 2011 Jun 01; 71(11):3841-51. PMID: 21498633.
      Citations: 45     Fields:    Translation:HumansAnimalsCells
    102. Miller CA, Settle SH, Sulman EP, Aldape KD, Milosavljevic A. Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors. BMC Med Genomics. 2011 Apr 14; 4:34. PMID: 21489305; PMCID: PMC3102606.
      Citations: 64     Fields:    Translation:HumansCells
    103. Miller CA, Hampton O, Coarfa C, Milosavljevic A. ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One. 2011 Jan 31; 6(1):e16327. PMID: 21305028; PMCID: PMC3031566.
      Citations: 104     Fields:    Translation:Cells
    104. Buchold GM, Coarfa C, Kim J, Milosavljevic A, Gunaratne PH, Matzuk MM. Analysis of microRNA expression in the prepubertal testis. PLoS One. 2010 Dec 29; 5(12):e15317. PMID: 21206922; PMCID: PMC3012074.
      Citations: 37     Fields:    Translation:AnimalsCells
    105. Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, Milosavljevic A. Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. BMC Bioinformatics. 2010 Nov 23; 11:572. PMID: 21092284; PMCID: PMC3001746.
      Citations: 29     Fields:    Translation:Cells
    106. Milosavljevic A. Putting epigenome comparison into practice. Nat Biotechnol. 2010 Oct; 28(10):1053-6. PMID: 20944597; PMCID: PMC4144442.
      Citations: 5     Fields:    Translation:Humans
    107. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010 Oct; 28(10):1045-8. PMID: 20944595; PMCID: PMC3607281.
      Citations: 900     Fields:    Translation:HumansCells
    108. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. PMID: 20852635; PMCID: PMC2955169.
      Citations: 326     Fields:    Translation:HumansCells
    109. Shao L, Kang SH, Li J, Hixson P, Taylor J, Yatsenko SA, Shaw CA, Milosavljevic A, Chang CC, Cheung SW, Patel A. Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics. J Mol Diagn. 2010 Sep; 12(5):670-9. PMID: 20724749; PMCID: PMC2928432.
      Citations: 9     Fields:    Translation:HumansCells
    110. Polikepahad S, Knight JM, Naghavi AO, Oplt T, Creighton CJ, Shaw C, Benham AL, Kim J, Soibam B, Harris RA, Coarfa C, Zariff A, Milosavljevic A, Batts LM, Kheradmand F, Gunaratne PH, Corry DB. Proinflammatory role for let-7 microRNAS in experimental asthma. J Biol Chem. 2010 Sep 24; 285(39):30139-49. PMID: 20630862; PMCID: PMC2943272.
      Citations: 108     Fields:    Translation:HumansAnimals
    111. Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A. MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing. Mol Hum Reprod. 2010 Jul; 16(7):463-71. PMID: 20215419; PMCID: PMC2882868.
      Citations: 62     Fields:    Translation:Animals
    112. Carbone L, Harris RA, Vessere GM, Mootnick AR, Humphray S, Rogers J, Kim SK, Wall JD, Martin D, Jurka J, Milosavljevic A, de Jong PJ. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet. 2009 Jun; 5(6):e1000538. PMID: 19557196; PMCID: PMC2695003.
      Citations: 45     Fields:    Translation:HumansAnimalsCells
    113. Hampton OA, Den Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, Gibbs RA, Lee AV, Milosavljevic A. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res. 2009 Feb; 19(2):167-77. PMID: 19056696; PMCID: PMC2652200.
      Citations: 72     Fields:    Translation:HumansCells
    114. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008 Oct 23; 455(7216):1069-75. PMID: 18948947; PMCID: PMC2694412.
      Citations: 1312     Fields:    Translation:Humans
    115. Raveendran M, Tardif S, Ross CN, Austad SN, Harris RA, Milosavljevic A, Rogers J. Polymorphic microsatellite loci for the common marmoset (Callithrix jacchus) designed using a cost- and time-efficient method. Am J Primatol. 2008 Sep; 70(9):906-10. PMID: 18561252; PMCID: PMC2799112.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    116. Bacolla A, Larson JE, Collins JR, Li J, Milosavljevic A, Stenson PD, Cooper DN, Wells RD. Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties. Genome Res. 2008 Oct; 18(10):1545-53. PMID: 18687880; PMCID: PMC2556271.
      Citations: 48     Fields:    Translation:HumansAnimalsCells
    117. Coarfa C, Milosavljevic A. Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies. Pac Symp Biocomput. 2008; 102-13. PMID: 18229679.
      Citations: 14     Fields:    Translation:HumansAnimals
    118. Harris RA, Rogers J, Milosavljevic A. Human-specific changes of genome structure detected by genomic triangulation. Science. 2007 Apr 13; 316(5822):235-7. PMID: 17431168.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    119. Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS, Cs?r?s M, Pr?fer K. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13; 316(5822):222-34. PMID: 17431167.
      Citations: 677     Fields:    Translation:HumansAnimals
    120. Carbone L, Vessere GM, ten Hallers BF, Zhu B, Osoegawa K, Mootnick A, Kofler A, Wienberg J, Rogers J, Humphray S, Scott C, Harris RA, Milosavljevic A, de Jong PJ. A high-resolution map of synteny disruptions in gibbon and human genomes. PLoS Genet. 2006 Dec 29; 2(12):e223. PMID: 17196042; PMCID: PMC1756914.
      Citations: 23     Fields:    Translation:HumansAnimalsCells
    121. Sea Urchin Genome Sequencing Consortium, Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duloquin L, Flytzanis C, Gache C, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R, Bell? R, Genevi?re AM, Hallb??k F, Duboc V, Lapraz F, R?ttinger E. The genome of the sea urchin Strongylocentrotus purpuratus. Science. 2006 Nov 10; 314(5801):941-52. PMID: 17095691; PMCID: PMC3159423.
      Citations: 405     Fields:    Translation:AnimalsCells
    122. Raveendran M, Harris RA, Milosavljevic A, Johnson Z, Shelledy W, Cameron J, Rogers J. Designing new microsatellite markers for linkage and population genetic analyses in rhesus macaques and other nonhuman primates. Genomics. 2006 Dec; 88(6):706-710. PMID: 17010566.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    123. Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Chen R, Chen Z, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJ, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang J, Wang J, Wang Q, Williams GA, Wong GK, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA. The DNA sequence, annotation and analysis of human chromosome 3. Nature. 2006 Apr 27; 440(7088):1194-8. PMID: 16641997.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    124. Scherer SE, Muzny DM, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Montgomery KT, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Lovering RC, Wheeler DA, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clerc-Blankenburg KP, Davis C, Delgado O, Dinh HH, Draper H, Gonzalez-Garay ML, Havlak P, Jackson LR, Jacob LS, Kelly SH, Li L, Li Z, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Pasternak S, Perez LM, Plopper FJ, Santibanez J, Shen H, Tabor PE, Verduzco D, Waldron L, Wang Q, Williams GA, Zhang J, Zhou J, Allen CC, Amin AG, Anyalebechi V, Bailey M, Barbaria JA, Bimage KE, Bryant NP, Burch PE, Burkett CE, Burrell KL, Calderon E, Cardenas V, Carter K, Casias K, Cavazos I, Cavazos SR, Ceasar H, Chacko J, Chan SN, Chavez D, Christopoulos C, Chu J, Cockrell R, Cox CD, Dang M, Dathorne SR, David R, Davis CM, Davy-Carroll L, Deshazo DR, Donlin JE, D'Souza L, Eaves KA, Emery-Cohen AJ, Escotto M, Flagg N, Forbes LD, Gabisi AM, Garza M, Hamilton C, Henderson N, Hernandez O, Hines S, Hogues ME, Huang M, Idlebird DG, Johnson R, Jolivet A, Jones S, Kagan R, King LM, Leal B, Lebow H, Lee S, LeVan JM, Lewis LC, London P, Lorensuhewa LM, Loulseged H, Lovett DA, Lucier A, Lucier RL, Ma J, Madu RC, Mapua P, Martindale AD, Martinez E, Massey E, Mawhiney S, Meador MG, Mendez S, Mercado C, Mercado IC, Merritt CE, Miner ZL, Minja E, Mitchell T, Mohabbat F, Mohabbat K, Montgomery B, Moore N, Morris S, Munidasa M, Ngo RN, Nguyen NB, Nickerson E, Nwaokelemeh OO, Nwokenkwo S, Obregon M, Oguh M, Oragunye N, Oviedo RJ, Parish BJ, Parker DN, Parrish J, Parks KL, Paul HA, Payton BA, Perez A, Perrin W, Pickens A, Primus EL, Pu LL, Puazo M, Quiles MM, Quiroz JB, Rabata D, Reeves K, Ruiz SJ, Shao H, Sisson I, Sonaike T, Sorelle RP, Sutton AE, Svatek AF, Svetz LA, Tamerisa KS, Taylor TR, Teague B, Thomas N, Thorn RD, Trejos ZY, Trevino BK, Ukegbu ON, Urban JB, Vasquez LI, Vera VA, Villasana DM, Wang L, Ward-Moore S, Warren JT, Wei X, White F, Williamson AL, Wleczyk R, Wooden HS, Wooden SH, Yen J, Yoon L, Yoon V, Zorrilla SE, Nelson D, Kucherlapati R, Weinstock G, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequence Production Team, Simons R. The finished DNA sequence of human chromosome 12. Nature. 2006 03 16; 440(7082):346-51. PMID: 16541075.
      Citations: 18     Fields:    Translation:HumansAnimalsCells
    125. Milosavljevic A, Harris RA, Sodergren EJ, Jackson AR, Kalafus KJ, Hodgson A, Cree A, Dai W, Csuros M, Zhu B, de Jong PJ, Weinstock GM, Gibbs RA. Pooled genomic indexing of rhesus macaque. Genome Res. 2005 Feb; 15(2):292-301. PMID: 15687293; PMCID: PMC546531.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    126. 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, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, 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, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, 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, Payseur BA, Bourque G, 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, Rat Genome Sequencing Project Consortium, Mar Alb? M, H?bner N, L?pez-Ot?n C, Simons R. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 04 01; 428(6982):493-521. PMID: 15057822.
      Citations: 881     Fields:    Translation:HumansAnimalsCells
    127. Kalafus KJ, Jackson AR, Milosavljevic A. Pash: efficient genome-scale sequence anchoring by Positional Hashing. Genome Res. 2004 Apr; 14(4):672-8. PMID: 15060009; PMCID: PMC383312.
      Citations: 13     Fields:    Translation:HumansAnimals
    128. Milosavljevic A, Csur?s M. Pooled Genomic Indexing (PGI): analysis and design of experiments. J Comput Biol. 2004; 11(5):1001-21. PMID: 15700414.
      Citations: 4     Fields:    Translation:AnimalsCells
    129. Li B, Milosavljevic A, Cs?r?s M. Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments. Genome Inform. 2003; 14:186-95. PMID: 15706533.
      Citations: 4     Fields:    Translation:AnimalsCells
    130. Milosavljevic A. The economic value of bioinformation. Bioinformatics. 2000 Jul; 16(7):571-2. PMID: 11038327.
      Citations:    Fields:    Translation:Humans
    131. Milosavljevic A, Zeremski M, Strezoska Z, Grujic D, Dyanov H, Batus S, Salbego D, Paunesku T, Soares MB, Crkvenjakov R. Discovering distinct genes represented in 29,570 clones from infant brain cDNA libraries by applying sequencing by hybridization methodology. Genome Res. 1996 Feb; 6(2):132-41. PMID: 8919692.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    132. Milosavljevic A, Savkovic S, Crkvenjakov R, Salbego D, Serrato H, Kreuzer H, Gemmell A, Batus S, Grujic D, Carnahan S, Tepavcevic J. Genome-scale DNA sequence recognition by hybridization to short oligomers. Proc Int Conf Intell Syst Mol Biol. 1996; 4:176-81. PMID: 8877517.
      Citations:    Fields:    Translation:Cells
    133. Milosavljevic A. DNA sequence recognition by hybridization to short oligomers. J Comput Biol. 1995; 2(2):355-70. PMID: 7497133.
      Citations:    Fields:    Translation:Cells
    134. Milosavljevic A, Jurka J. Discovering simple DNA sequences by the algorithmic significance method. Comput Appl Biosci. 1993 Aug; 9(4):407-11. PMID: 8402207.
      Citations: 10     Fields:    Translation:HumansCells
    135. Jurka J, Kaplan DJ, Duncan CH, Walichiewicz J, Milosavljevic A, Murali G, Solus JF. Identification and characterization of new human medium reiteration frequency repeats. Nucleic Acids Res. 1993 Mar 11; 21(5):1273-9. PMID: 8464711; PMCID: PMC309293.
      Citations: 11     Fields:    Translation:HumansCells
    136. Milosavljevic A. Discovering sequence similarity by the algorithmic significance method. Proc Int Conf Intell Syst Mol Biol. 1993; 1:284-91. PMID: 7584347.
      Citations: 2     Fields:    Translation:HumansCells
    137. Jurka J, Walichiewicz J, Milosavljevic A. Prototypic sequences for human repetitive DNA. J Mol Evol. 1992 Oct; 35(4):286-91. PMID: 1404414.
      Citations: 37     Fields:    Translation:HumansAnimalsCells
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