BRL Publications

ExRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present Across Human Biofluids

Murillo M, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson A, Srinivasan S, Chung A, Laurent C, Kitchen R, Galeev T, Warrell J, Diao J, Welsh J, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah R, Yeri A, Jenkins L, Ahsen M, Cordon-Cardo C, Dogra N, Gifford S, Smith J, Stolovitzky G, Tewari A, Wunsch B, Yadav K, Danielson K, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong D, Zhang X, Balaj L, Gandhi R, Sood A, Alexander R, Wang L, Wu C, Wong D, Galas D, Keuren-Jensen K, Patel T, Jones J, Das S, Cheung KH, Pico A, Su A, Raffai R, Laurent L, Roth M, Gerstein M, Milosavljevic A.

Cell. Doi: 10.1016/j.cell.2019.02.018.

PMID: 30951672

The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research

Das S, Extracellular RNA Communication Consortium, Ansel KM, Bitzer M, Breakefield XO, 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.

Cell. . 2019 4;177(2):231-242. doi: 10.1016/j.cell.2019.03.023.

PMID: 30951667

Evidence-based assessments of clinical actionability in the context of secondary findings: Updates from ClinGen's Actionability Working Group

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.

Hum Mutat. doi: 10.1002/humu.23631 (2018)

PMID: 30311382

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. joural: Science. 2018 361: 6409. Doi: 10:1126/science.aar3146.

Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel R, Rozowsky J, Galeev T, Huang Z, Altshuler R, Zhang Z, Harris R, Coarfa C, Ashmore L, Bertol J, Fakhouri W, Yu F, Kellis M, Gerstein M, and Milosavljevic A.

ClinGen advancing genomic data-sharing standards as a GA4GH driver project

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; Clinical Genome (ClinGen) Resource.

Hum Mutat. doi: 10.1002/humu.23625 (2018)

PMID: 30311379

ClinGen Allele Registry links information about genetic variants

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.

Hum Mutat. doi: 10.1002/humu.23637 (2018)

PMID: 30311374

ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants

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.

Genome Med. doi: 10.1186/s13073-016-0391-z (2017)

PMID: 28081714

Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium

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

Am J Hum Genet. doi: 10.1016/j.ajhg.2016.03.024 (2016)

PMID: 27181684

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

International Human Epigenome Consortium

Cell. doi: 10.1016/j.cell.2016.11.007 (2016)

PMID: 27863232

Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types

Onuchic V, Hartmaier RJ, Boone DN, Samuels ML, Patel RY, White WM, Garovic VD, Oesterreich S, Roth ME, Lee AV, Milosavljevic A.

Cell Rep. doi: 10.1016/j.celrep.2016.10.057 (2016)

PMID: 27851969

Extending gene ontology in the context of extracellular RNA and vesicle communication

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 HMM, Mathivanan S, Milosavljevic A, Laurent LC

Journal of Biomedical Semantics. 2016 7:19. doi: 10.1186/s13326-016-0061-5

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

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.

J Extracell Vesicles. 2015 Aug 28;4:27497. doi: 10.3402/jev.v4.27497. eCollection 2015.

PMID: 26320941

Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs

Amin V, Harris RA, Onuchic V, Jackson A, Charnecki T, Paithankar S, Subramanian S, Riehle K, Coarfa C, Milosavljevic A.

Nat. Commun. 6:6370 doi: 10.1038/ncomms7370 (2015)

PMID: 25691256

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium et. al.

Nature doi: 10.1038/nature14248 (2015)

PMID: 25693563

Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools

Coarfa C, Pichot C, Jackson A, Tandon A, Amin V, Raghuraman S, Paithankar S, Lee AV, McGuire SE, Milosavljevic A.

BMC Bioinformatics. 2014;15 Suppl 7:S2. doi: 10.1186/1471-2105-15-S7-S2. Epub 2014 May 28.

PMID: 25080362

mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities

Ma J, Coarfa C, Qin X, Bonnen PE, Milosavljevic A, Versalovic J, Aagaard K.

BMC Genomics. 2014 Apr 3;15:257. doi: 10.1186/1471-2164-15-257.

PMID: 24694284

Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing

Kunde-Ramamoorthy G, Coarfa C, Laritsky E, Kessler NJ, Harris RA, Xu M, Chen R, Shen L, Milosavljevic A, Waterland RA.

Nucleic Acids Res. 2014 Apr;42(6):e43. doi: 10.1093/nar/gkt1325. Epub 2014 Jan 3.

PMID: 24391148

CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma

Kannan K, Coarfa C, Rajapakshe K, Hawkins SM, Matzuk MM, Milosavljevic A, Yen L.

PLoS Genet. 2014 Mar 27;10(3):e1004216. doi: 10.1371/journal.pgen.1004216. eCollection 2014 Mar.

PMID: 24675677

Recommendations for the design and analysis of epigenome-wide association studies

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.

Nat Methods. 2013 Oct;10(10):949-55. doi: 10.1038/nmeth.2632. Review.

PMID: 24076989

NAHR-mediated copy-number variants in a clinical population: mechanistic insights into both genomic disorders and Mendelizing traits

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.

Genome Res. 2013 Sep;23(9):1395-409. doi: 10.1101/gr.152454.112. Epub 2013 May 8.

PMID: 23657883

Identification of cancer fusion drivers using network fusion centrality

Wu CC, Kannan K, Lin S, Yen L, Milosavljevic A.

Bioinformatics. 2013 May 1;29(9):1174-81. doi: 10.1093/bioinformatics/btt131. Epub 2013 Mar 16.

PMID: 23505294

Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability

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.

PLoS Genet. 2013;9(2):e1003333. doi: 10.1371/journal.pgen.1003333. Epub 2013 Feb 28. No abstract available.

PMID: 23468659

Spark: a navigational paradigm for genomic data exploration

Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ.

Genome Res. 2012 Nov;22(11):2262-9. doi: 10.1101/gr.140665.112. Epub 2012 Sep 7.

PMID: 22960372

Host response to probiotics determined by nutritional status of rotavirus-infected neonatal mice

Preidis GA, Saulnier DM, Blutt SE, Mistretta TA, Riehle KP, Major AM, Venable SF, Barrish JP, Finegold MJ, Petrosino JF, Guerrant RL, Conner ME, Versalovic J.

J Pediatr Gastroenterol Nutr. 2012 Sep;55(3):299-307.

PMID: 22343914

Atlas2 Cloud: a framework for personal genome analysis in the cloud

Evani US, Challis D, Yu J,, Jackson AR,, Paithankar S, Bainbridge MN, Jakkamsetti A, Pham P, Coarfa C, Milosavljevic A, Yu F.

BMC Genomics. 2012;13 Suppl 6:S19. doi: 10.1186/1471-2164-13-S6-S19. Epub 2012 Oct 26.

PMID: 23134663

A framework for human microbiome research

Human Microbiome Project Consortium.

Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209.

PMID: 22699610

Structure, function and diversity of the healthy human microbiome

Human Microbiome Project Consortium.

Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234.

PMID: 22699609

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

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.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

PMID: 22955991

The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences

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.

BMC Bioinformatics. 2012;13 Suppl 13:S11. doi: 10.1186/1471-2105-13-S13-S11. Epub 2012 Aug 24.

PMID: 23320832

Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood

Davies MN, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, Coarfa C, Harris RA, Milosavljevic A, Troakes C, Al-Saraj S, Dobson R, Schalkwyk LC, Mill J.

Genome Biol. 2012 Jun 15;13(6):R43. doi: 10.1186/gb-2012-13-6-r43.

PMID: 22703893

Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine

Preidis GA, Saulnier DM, Blutt SE, Mistretta TA, Riehle KP, Major AM, Venable SF, Finegold MJ, Petrosino JF, Conner ME, Versalovic J.

FASEB J. 2012 May;26(5):1960-9. doi: 10.1096/fj.10-177980. Epub 2012 Jan 20.

PMID: 22267340

A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy

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.

PLoS One. 2012;7(6):e36466. doi: 10.1371/journal.pone.0036466. Epub 2012 Jun 13.

PMID: 22719832

Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons

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.

Genome Biol Evol. 2012;4(7):648-58. doi: 10.1093/gbe/evs048. Epub 2012 May 16.

PMID: 22593550

Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome

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.

PLoS Genet. 2012;8(5):e1002692. doi: 10.1371/journal.pgen.1002692. Epub 2012 May 17.

PMID: 22615578

An integrative variant analysis suite for whole exome next-generation sequencing data

Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F.

BMC Bioinformatics. 2012 Jan 12;13:8. doi: 10.1186/1471-2105-13-8.

PMID: 22239737

Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome

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.

Gastroenterology. 2011 Nov;141(5):1782-91. doi: 10.1053/j.gastro.2011.06.072. Epub 2011 Jul 8.

PMID: 21741921

Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE

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 Jr, Stankiewicz P, State MW, Beaudet AL.

Hum Mol Genet. 2011 Nov 15;20(22):4360-70. doi: 10.1093/hmg/ddr363. Epub 2011 Aug 24.

PMID: 21865298

Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines

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.

Cancer Genet. 2011 Aug;204(8):447-57. doi: 10.1016/j.cancergen.2011.07.009. Erratum in: Cancer Genet. 2011 Dec;204(12):694. Coarfa, Cristian [added];Schoenherr, Caroline [added].

PMID: 21962895

Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta)

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.

BMC Genomics. 2011 Jun 13;12:311. doi: 10.1186/1471-2164-12-311.

PMID: 21668978

Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain

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.

BMC Genomics. 2011 May 31;12(1):277. doi: 10.1186/1471-2164-12-277.

PMID: 21627805

Emerging patterns of epigenomic variation

Milosavljevic A

Trends in Genetics, 2011 Jun;27(6):242-50

PMID: 21507501

A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma

Shohet JM, Ghosh R, Coarfa C, Ludwig A, Benham AL, Chen Z, Patterson DM, Barbieri E, Mestdagh P, Sikorski D, Milosavljevic A, Kim ES, Gunaratne PH

Cancer Res., 2011 Jun 1;71(11):3841-51

PMID: 21498633

Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors

Miller CA, Settle SH, Sulman EP, Aldape KD, Milosavljevic A

BMC Med Genomics, 2011 Apr 14;4(1):34

PMID: 21489305

ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads

Miller CA, Hampton O, Coarfa C, Milosavljevic A

PLoS One, 2011 Jan 31;6(1):e16327

PMID: 21305028

Analysis of MicroRNA Expression in the Prepubertal Testis

Buchold GM, Coarfa C, Kim J, Milosavljevic A, Gunaratne PH, Matzuk MM

PLoS One, 2010 Dec 29;5(12):e15317

PMID: 21206922

Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing

Coarfa C, Fu Y, Miller C, Chen Z, Harris RA, Milosavljevic A

BMC Bioinformatics Epub, Nov. 26 2010

PMID: 21092284

Putting epigenome comparison into practice

Milosavljevic A

Nat Biotechnol., 2010 Oct;28(10):1053-6

PMID: 20944597

The NIH Roadmap Epigenomics Mapping Consortium

Bernstein BE, Stamatoyannopoulus JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA

Nat Biotechnol., 2010 Oct;28(10):1045-8

PMID: 20944595

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

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

Nat Biotechnol., 2010 Oct;28(10):1097-105

PMID: 20852635

Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics

Shao L, Kang SH, Li J, Hixson P, Taylor J, Yatsenko SA, Shaw CA, Milosavljevic A, Chang CC, Cheung SW, Patel A

J Mol Diagn., 2010 Sep;12(5):670-9

PMID: 20724749

Proinflammatory Role for let-7 MicroRNAS in Experimental Asthma

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

Biol Chem., 2010 Sep 24;285(39):30139-49

PMID: 20630862

MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing

Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A.

Molecular and Human Reproduction, March 10, 2010.

PMID: 20215419

Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution

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.

PLoS Genetics, June 5, 2009.

PMID: 19557196

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

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.

Genome Research, December 3, 2008.

PMID: 19056696

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

The Cancer Genome Atlas Research Network.

Nature, 455, 1061-1068 (23 October 2008)

PMID: 18772890

Pash 2.0: Scaleable Sequence Anchoring for Next-Generation Sequencing Technologies

Coarfa, C, Milosavljevic, A

Pacific Symposium on Biocomputing , 2008 13:102-113.

Human-specific changes of genome structure detected by genomic triangulation

Harris RA, Rogers J, Milosavljevic A

Science, Apr 13 2007;316(5822):235-7.

PMID: 17431168

Evolutionary and biomedical insights from the rhesus macaque genome

Rhesus Macaque Genome Sequencing and Analysis Consortium

Science, Apr 13 2007;316(5822):222-34.

PMID: 17431167

Pooled Genomic Indexing of Rhesus Macaque

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

Genome Res. 2005 Feb;15(2):292-301.

PMID: 15687293

Pooled Genomic Indexing (PGI): Analysis and Design of Experiments

Csuros M, Milosavljevic A

J Comput Biol. 2004;11(5):1001-21.

PMID: 15700414

Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing

Kalafus KJ, Jackson AR, and Milosavljevic A

Genome Res. 2004 Apr;14(4):672-8.

PMID: 15060009

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Rat Genome Sequencing Consortium

Nature. 2004 Apr 1;428(6982):493-521.

PMID: 15057822

Shotgun sequencing, clone pooling, and comparative stategies for mapping and sequencing

Milosavljevic A, Csuros M, Weinstock G, Gibbs RA

TARGETS, 2003, 2(6): 245-252.

Pooled genomic indexing (PGI): mathematical analysis and experiment design

Csuros M, Milosavljevic A

Algorithms in Bioinformatics, Second International Workshop, WABI 2002, Guigo R. and Gusfield D. (eds.). Springer Verlag: Heidelberg, Germany. p. 10-28.

Identification of genes regulated by UV/salicylic acid

Paunesku T, Chang-Liu CM, Shearin-Jones P, Watson C, Milton J, Oryhon J, Salbego D, Milosavljevic A, Woloschak GE

Int J Radiat Biol. 2000 Feb;76(2):189-98.

PMID: 10716640

Discovering Patterns in DNA Sequences by the Algorithmic Significance Method

Milosavljevic A.

Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications, 1999, Oxford: Oxford University Press, p. 3-23.