Institute for Clinical and Translational Research

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ALEKSANDAR MILOSAVLJEVIC

TitleProfessor
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular & Human Genetics
DivisionMolecular & Human Genetics
AddressOne Baylor Plaza, 400D
Houston TX 77030
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    Collapse Overview 
    Collapse keywords
    Epigenome
    Epigenetics
    Genome
    Genomics
    Bioinformatics
    cancer genomics
    clinical genomics
    computational biology


    Collapse Bibliographic 
    Collapse selected publications
    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. Milosavljevic A, Stavropoulos A, Descroix V, Götrick B. A questionnaire-based study evaluating differences between dental students in Paris (F) and Malmö (SE) regarding diagnosis and treatment decisions of patients with different severity levels of periodontal diseases. Eur J Dent Educ. 2018 Jan 08. PMID: 29316064.
      View in: PubMed
    2. Li Z, Milosavljevic AR, Carmichael I, Ptasinska S. Characterization of Neutral Radicals from a Dissociative Electron Attachment Process. Phys Rev Lett. 2017 Aug 04; 119(5):053402. PMID: 28949760.
      View in: PubMed
    3. Milosavljevi? AR, Rousseau P, Domaracka A, Huber BA, Giuliani A. Multiple electron capture from isolated protein poly-anions in collision with slow highly charged ions. Phys Chem Chem Phys. 2017 May 19. PMID: 28524199.
      View in: PubMed
    4. 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 Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants. Genome Med. 2017 Jan 12; 9(1):3. PMID: 28081714.
      View in: PubMed
    5. 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 Nov 15; 17(8):2075-2086. PMID: 27851969.
      View in: PubMed
    6. 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; 7(3):817-31. PMID: 27579472.
      View in: PubMed
    7. Rackwitz J, Kopyra J, D?bkowska I, Ebel K, Rankovi? MLj, Milosavljevi? AR, Bald I. Sensitizing DNA Towards Low-Energy Electrons with 2-Fluoroadenine. Angew Chem Int Ed Engl. 2016 Aug 22; 55(35):10248-52. PMID: 27481662.
      View in: PubMed
    8. 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 Jul 07; 99(1):247. PMID: 27392081.
      View in: PubMed
    9. Milosavljevi? AR, Huang W, Sadhu S, Ptasinska S. Low-Energy Electron-Induced Transformations in Organolead Halide Perovskite. Angew Chem Int Ed Engl. 2016 Aug 16; 55(34):10083-7. PMID: 27355420.
      View in: PubMed
    10. 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 Jun 2; 98(6):1067-76. PMID: 27181684; PMCID: PMC4908185 [Available on 12/02/16].
      View in: PubMed, PubMed Central
    11. 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, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC. Extending gene ontology in the context of extracellular RNA and vesicle communication. J Biomed Semantics. 2016; 7:19. PMID: 27076901; PMCID: PMC4830068.
      View in: PubMed, PubMed Central
    12. Doj?ilovi? R, Pajovi? JD, Božani? DK, Vodnik VV, Dimitrijevi?-Brankovi? S, Milosavljevi? AR, Kaš?àkovà S, Réfrégiers M, Djokovi? V. 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 7; 141(6):1988-96. PMID: 26858997.
      View in: PubMed
    13. Milosavljevic A, Götrick B, Hallström H, Stavropoulos A, Knutsson K. Assessment of Prognosis and Periodontal Treatment Goals Among General Dental Practitioners and Dental Hygienists. Oral Health Prev Dent. 2016; 14(5):433-441. PMID: 27351737.
      View in: PubMed
    14. Milosavljevic A, Westerberg J, Hellén-Halme K. Diagnostic accuracy of carious lesions in digital radiographs at a public dental clinic - can it be improved by optimizing viewing conditions and further education?. Swed Dent J. 2016; 40(2):235-242. PMID: 28853795.
      View in: PubMed
    15. Rankovi? MLj, Canon F, Nahon L, Giuliani A, Milosavljevi? AR. 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.
      View in: PubMed
    16. 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 [Available on 02/01/17].
      View in: PubMed, PubMed Central
    17. Vogel S, Rackwitz J, Schürman R, Prinz J, Milosavljevi? AR, Réfrégiers M, Giuliani A, Bald I. 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.
      View in: PubMed
    18. Canon F, Milosavljevi? AR, Nahon L, Giuliani A. Action spectroscopy of a protonated peptide in the ultraviolet range. Phys Chem Chem Phys. 2015 Oct 21; 17(39):25725-33. PMID: 25586594.
      View in: PubMed
    19. 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.
      View in: PubMed
    20. Pajovi? JD, Doj?ilovi? R, Božani? DK, Kaš?áková S, Réfrégiers M, Dimitrijevi?-Brankovi? S, Vodnik VV, Milosavljevi? AR, Piscopiello E, Luyt AS, Djokovi? V. Tryptophan-functionalized gold nanoparticles for deep UV imaging of microbial cells. Colloids Surf B Biointerfaces. 2015 Nov 1; 135:742-50. PMID: 26340364.
      View in: PubMed
    21. 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.
      View in: PubMed, PubMed Central
    22. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563; PMCID: PMC4530010.
      View in: PubMed, PubMed Central
    23. 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; 6:6370. PMID: 25691256; PMCID: PMC4335353.
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    24. 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; 6:6363. PMID: 25691127; PMCID: PMC4333717.
      View in: PubMed, PubMed Central
    25. 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.
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    26. Milosavljevi? AR, Cerovski VZ, Canon F, Rankovi? MLj, Škoro 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 5; 5(11):1994-9. PMID: 26273885.
      View in: PubMed
    27. 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; 15:257. PMID: 24694284; PMCID: PMC4234434.
      View in: PubMed, PubMed Central
    28. 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.
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    29. 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.
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    30. Giuliani A, Milosavljevi? AR, Canon F, Nahon L. Contribution of synchrotron radiation to photoactivation studies of biomolecular ions in the gas phase. Mass Spectrom Rev. 2014 Nov-Dec; 33(6):424-41. PMID: 24375654.
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    31. 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.
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    32. Milosavljevic A, Götrick B, Hallström H, Jansson H, Knutsson K. Different treatment strategies are applied to patients with the same periodontal status in general dentistry. Acta Odontol Scand. 2014 May; 72(4):290-7. PMID: 24053366.
      View in: PubMed
    33. Dittwald P, Gambin T, Szafranski P, Li J, Amato S, Divon MY, Rodríguez Rojas LX, 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. 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.
      View in: PubMed, PubMed Central
    34. Wu CC, Kannan K, Lin S, Yen L, Milosavljevic A. Identification of cancer fusion drivers using network fusion centrality. Bioinformatics. 2013 May 1; 29(9):1174-81. PMID: 23505294; PMCID: PMC3634186.
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    35. 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.
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    36. 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.
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    37. 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.
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    38. 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.
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    39. 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.
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    40. 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; 13(6):R43. PMID: 22703893; PMCID: PMC3446315.
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    41. 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.
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    42. 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.
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    43. 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.
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    44. Milosavljevi? AR, Canon F, Nicolas C, Miron C, Nahon L, Giuliani A. Gas-Phase Protein Inner-Shell Spectroscopy by Coupling an Ion Trap with a Soft X-ray Beamline. J Phys Chem Lett. 2012 May 3; 3(9):1191-6. PMID: 26288054.
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    45. 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; 13:8. PMID: 22239737; PMCID: PMC3292476.
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    46. 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.
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    47. 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.
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    48. Milosavljevi? AR, Nicolas C, Lemaire J, Dehon C, Thissen R, Bizau JM, Réfrégiers M, Nahon L, Giuliani A. Photoionization of a protein isolated in vacuo. Phys Chem Chem Phys. 2011 Sep 14; 13(34):15432-6. PMID: 21766124.
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    49. 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.
      View in: PubMed, PubMed Central
    50. 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; 12:311. PMID: 21668978; PMCID: PMC3141668.
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    51. 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; 12(1):277. PMID: 21627805; PMCID: PMC3118218.
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    52. Milosavljevic A. Emerging patterns of epigenomic variation. Trends Genet. 2011 Jun; 27(6):242-50. PMID: 21507501; PMCID: PMC3104125.
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    53. 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 1; 71(11):3841-51. PMID: 21498633.
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    54. 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; 4:34. PMID: 21489305; PMCID: PMC3102606.
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    55. 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; 6(1):e16327. PMID: 21305028; PMCID: PMC3031566.
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    56. Buchold GM, Coarfa C, Kim J, Milosavljevic A, Gunaratne PH, Matzuk MM. Analysis of microRNA expression in the prepubertal testis. PLoS One. 2010; 5(12):e15317. PMID: 21206922; PMCID: PMC3012074.
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    57. 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; 11:572. PMID: 21092284; PMCID: PMC3001746.
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    58. 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.
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    59. Milosavljevic A. Putting epigenome comparison into practice. Nat Biotechnol. 2010 Oct; 28(10):1053-6. PMID: 20944597; PMCID: PMC4144442.
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    60. 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.
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    61. 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.
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    62. 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.
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    63. 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.
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    64. 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.
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    65. 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.
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    66. Velicki L, Milosavljevi? A, Majin M, Vujin B, Kovacevi? P. Postpartal right ventricular thrombosis. Herz. 2008 Nov; 33(7):532-4. PMID: 19066750.
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    72. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13; 316(5822):222-34. PMID: 17431167.
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    74. The genome of the sea urchin Strongylocentrotus purpuratus. Science. 2006 Nov 10; 314(5801):941-52. PMID: 17095691; PMCID: PMC3159423.
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    75. 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):706-10. PMID: 17010566.
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    78. 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.
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    79. 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.
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    80. 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. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1; 428(6982):493-521. PMID: 15057822.
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    81. Csurös M, Milosavljevic A. Pooled Genomic Indexing (PGI): analysis and design of experiments. J Comput Biol. 2004; 11(5):1001-21. PMID: 15700414.
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    82. Csürös M, Li B, Milosavljevic A. Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments. Genome Inform. 2003; 14:186-95. PMID: 15706533.
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    83. Milosavljevic A. The economic value of bioinformation. Bioinformatics. 2000 Jul; 16(7):571-2. PMID: 11038327.
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    84. Paunesku T, Chang-Liu CM, Shearin-Jones P, Watson C, Milton J, Oryhon J, Salbego D, Milosavljevic A, Woloschak GE. Identification of genes regulated by UV/salicylic acid. Int J Radiat Biol. 2000 Feb; 76(2):189-98. PMID: 10716640.
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    85. Milosavljevi? A, Savkovi? S, Crkvenjakov R, Salbego D, Serrato H, Kreuzer H, Gemmell A, Batus S, Gruji? D, Carnahan S, Paunesku T, Tepavcevi? J. DNA sequence recognition by hybridization to short oligomers: experimental verification of the method on the E. coli genome. Genomics. 1996 Oct 1; 37(1):77-86. PMID: 8921373.
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    87. Milosavljevi? A, Savkovi? S, Crkvenjakov R, Salbego D, Serrato H, Kreuzer H, Gemmell A, Batus S, Gruji? D, Carnahan S, Tepavcevi? J. Genome-scale DNA sequence recognition by hybridization to short oligomers. Proc Int Conf Intell Syst Mol Biol. 1996; 4:176-81. PMID: 8877517.
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    88. Milosavljevi? A, Strezoska Z, Zeremski M, Gruji? D, Paunesku T, Crkvenjakov R. Clone clustering by hybridization. Genomics. 1995 May 1; 27(1):83-9. PMID: 7665186.
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    89. Milosavljevi? A. DNA sequence recognition by hybridization to short oligomers. J Comput Biol. 1995; 2(2):355-70. PMID: 7497133.
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    90. Milosavljevi? A. Sequence comparisons via algorithmic mutual information. Proc Int Conf Intell Syst Mol Biol. 1994; 2:303-9. PMID: 7584405.
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    91. Milosavljevi? A, Jurka J. Discovering simple DNA sequences by the algorithmic significance method. Comput Appl Biosci. 1993 Aug; 9(4):407-11. PMID: 8402207.
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    92. 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.
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    93. Milosavljevi? A. Discovering sequence similarity by the algorithmic significance method. Proc Int Conf Intell Syst Mol Biol. 1993; 1:284-91. PMID: 7584347.
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