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Elinor Kathryn Karlsson PhD

TitleAssistant Professor
InstitutionUniversity of Massachusetts Medical School
DepartmentProgram in Molecular Medicine
AddressUniversity of Massachusetts Medical School
368 Plantation Street, Sherman Center, AS4.1065
Worcester MA 01605
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentProgram in Molecular Medicine

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentBioinformatics and Computational Biology

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentNeuroscience


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    Collapse Biography 
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    Rice University, Houston, TX, United StatesBABiochemistry & Cell Biology
    Boston University, Boston, MA, United StatesPHDBioinformatics

    Collapse Overview 
    Collapse overview


    Elinor Karlsson uses evolution as a tool for understanding how the human genome works. By combining signals of natural selection with genome-wide association studies, Dr. Karlsson aim to identify genes, pathways, and the functional variants underlying polygenic diseases, and translate these discoveries into advances in human health care. She is currently using this approach to find the  genetic risk factors for susceptibility to infectious diseases, like cholera and viral hemorrhagic fevers, as well as psychiatric disorders (using dogs as a model organism). Elinor received her B.A. in biochemistry/cell biology from Rice University, and earned her Ph.D. in bioinformatics from Boston University for research she did on dog genetics at the Broad Institute. She did her postdoctoral research with Dr. Pardis Sabeti at Harvard University. 



    Collapse Rotation Projects


    We are looking for students interested in designing and applying new computational methods to genomic datasets, with the goal of translating basic genomics into improved medical care. Our current projects include:




    • developing improved methods to combine GWAS and natural selection to pinpoint functional genomic variation


    • identifying and functionally investigating genes associated with cholera resistance in Bangladesh 


    • investigating shared and divergent patterns of natural selection in Bangladesh, India and East Asia


    • combining genetic and RNA expression data to understand immune response to cholera and other intestinal diseases 



    We are also starting a new project on behavioral genetics in mixed breed dogs.



    Please contact us if you are interested! 



    iccdr,b



    Visiting our collaborators in Dhaka



     



    Collapse Post Docs


    We are actively recruiting postdocs interested in developing creative new computational methods to investigate large genomic datasets. 



    We have two major research efforts ongoing:




    1. Investigating the genetics of infectious disease susceptibility by integrating signals of natural selection with association and functional data. This includes our work on cholera in Bangladesh, and we are now expanding to additional diseases and geographic regions.


    2. Investigating the genetics of psychiatric disease susceptibility by integrating signals of artificial selection and genetic association in mixed breed dogs. 



    Please email us, and included your CV, if you are interested in joining our group. 



    pet dogs 



    two potential research collaborators




    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Karlsson E, Andersson E, Dogan J, Gianni S, Jemth P, Camilloni C. A structurally heterogeneous transition state underlies coupled binding and folding of disordered proteins. J Biol Chem. 2018 Dec 04. PMID: 30514761.
      View in: PubMed
    2. Jemth P, Karlsson E, Vögeli B, Guzovsky B, Andersson E, Hultqvist G, Dogan J, Güntert P, Riek R, Chi CN. Structure and dynamics conspire in the evolution of affinity between intrinsically disordered proteins. Sci Adv. 2018 Oct; 4(10):eaau4130. PMID: 30397651.
      View in: PubMed
    3. Goodman L, Karlsson EK. America's lost dogs. Science. 2018 07 06; 361(6397):27-28. PMID: 29976811.
      View in: PubMed
    4. Moses L, Niemi S, Karlsson E. Pet genomics medicine runs wild. Nature. 2018 Jul; 559(7715):470-472. PMID: 30046086.
      View in: PubMed
    5. Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka S, Karpinski E, Ivancevic AM, To TH, Kortschak RD, Raison JM, Qu Z, Chin TJ, Alt KW, Claesson S, Dalén L, MacPhee RDE, Meller H, Roca AL, Ryder OA, Heiman D, Young S, Breen M, Williams C, Aken BL, Ruffier M, Karlsson E, Johnson J, Di Palma F, Alfoldi J, Adelson DL, Mailund T, Munch K, Lindblad-Toh K, Hofreiter M, Poinar H, Reich D. A comprehensive genomic history of extinct and living elephants. Proc Natl Acad Sci U S A. 2018 Mar 13; 115(11):E2566-E2574. PMID: 29483247.
      View in: PubMed
    6. Bourque DL, Bhuiyan TR, Genereux DP, Rashu R, Ellis CN, Chowdhury F, Khan AI, Alam NH, Paul A, Hossain L, Mayo-Smith LM, Charles RC, Weil AA, LaRocque RC, Calderwood SB, Ryan ET, Karlsson EK, Qadri F, Harris JB. Analysis of the Human Mucosal Response to Cholera Reveals Sustained Activation of Innate Immune Signaling Pathways. Infect Immun. 2018 Feb; 86(2). PMID: 29133347.
      View in: PubMed
    7. Noh HJ, Tang R, Flannick J, O'Dushlaine C, Swofford R, Howrigan D, Genereux DP, Johnson J, van Grootheest G, Grünblatt E, Andersson E, Djurfeldt DR, Patel PD, Koltookian M, M Hultman C, Pato MT, Pato CN, Rasmussen SA, Jenike MA, Hanna GL, Stewart SE, Knowles JA, Ruhrmann S, Grabe HJ, Wagner M, Rück C, Mathews CA, Walitza S, Cath DC, Feng G, Karlsson EK, Lindblad-Toh K. Integrating evolutionary and regulatory information with a multispecies approach implicates genes and pathways in obsessive-compulsive disorder. Nat Commun. 2017 10 17; 8(1):774. PMID: 29042551.
      View in: PubMed
    8. Al-Mamun MM, Sarker SK, Qadri SK, Shirin T, Mohammad QD, LaRocque R, Karlsson EK, Saha N, Asaduzzaman M, Qadri F, Mannoor MK. Examination of Huntington's disease with atypical clinical features in a Bangladeshi family tree. Clin Case Rep. 2016 Dec; 4(12):1191-1194. PMID: 27980761.
      View in: PubMed
    9. Vieira NM, Elvers I, Alexander MS, Moreira YB, Eran A, Gomes JP, Marshall JL, Karlsson EK, Verjovski-Almeida S, Lindblad-Toh K, Kunkel LM, Zatz M. Jagged 1 Rescues the Duchenne Muscular Dystrophy Phenotype. Cell. 2015 Nov 19; 163(5):1204-13. PMID: 26582133.
      View in: PubMed
    10. Kamberov YG, Karlsson EK, Kamberova GL, Lieberman DE, Sabeti PC, Morgan BA, Tabin CJ. A genetic basis of variation in eccrine sweat gland and hair follicle density. Proc Natl Acad Sci U S A. 2015 Aug 11; 112(32):9932-7. PMID: 26195765.
      View in: PubMed
    11. Tonomura N, Elvers I, Thomas R, Megquier K, Turner-Maier J, Howald C, Sarver AL, Swofford R, Frantz AM, Ito D, Mauceli E, Arendt M, Noh HJ, Koltookian M, Biagi T, Fryc S, Williams C, Avery AC, Kim JH, Barber L, Burgess K, Lander ES, Karlsson EK, Azuma C, Modiano JF, Breen M, Lindblad-Toh K. Genome-wide association study identifies shared risk loci common to two malignancies in golden retrievers. PLoS Genet. 2015 Feb; 11(2):e1004922. PMID: 25642983.
      View in: PubMed
    12. Ellis CN, LaRocque RC, Uddin T, Krastins B, Mayo-Smith LM, Sarracino D, Karlsson EK, Rahman A, Shirin T, Bhuiyan TR, Chowdhury F, Khan AI, Ryan ET, Calderwood SB, Qadri F, Harris JB. Comparative proteomic analysis reveals activation of mucosal innate immune signaling pathways during cholera. Infect Immun. 2015 Mar; 83(3):1089-103. PMID: 25561705.
      View in: PubMed
    13. Baranowska Körberg I, Sundström E, Meadows JR, Rosengren Pielberg G, Gustafson U, Hedhammar Å, Karlsson EK, Seddon J, Söderberg A, Vilà C, Zhang X, Åkesson M, Lindblad-Toh K, Andersson G, Andersson L. A simple repeat polymorphism in the MITF-M promoter is a key regulator of white spotting in dogs. PLoS One. 2014; 9(8):e104363. PMID: 25116146.
      View in: PubMed
    14. Karlsson EK, Kwiatkowski DP, Sabeti PC. Natural selection and infectious disease in human populations. Nat Rev Genet. 2014 Jun; 15(6):379-93. PMID: 24776769.
      View in: PubMed
    15. Tang R, Noh HJ, Wang D, Sigurdsson S, Swofford R, Perloski M, Duxbury M, Patterson EE, Albright J, Castelhano M, Auton A, Boyko AR, Feng G, Lindblad-Toh K, Karlsson EK. Candidate genes and functional noncoding variants identified in a canine model of obsessive-compulsive disorder. Genome Biol. 2014 Mar 14; 15(3):R25. PMID: 24995881.
      View in: PubMed
    16. Karlsson EK, Sigurdsson S, Ivansson E, Thomas R, Elvers I, Wright J, Howald C, Tonomura N, Perloski M, Swofford R, Biagi T, Fryc S, Anderson N, Courtay-Cahen C, Youell L, Ricketts SL, Mandlebaum S, Rivera P, von Euler H, Kisseberth WC, London CA, Lander ES, Couto G, Comstock K, Starkey MP, Modiano JF, Breen M, Lindblad-Toh K. Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B. Genome Biol. 2013 Dec 12; 14(12):R132. PMID: 24330828.
      View in: PubMed
    17. Karlsson EK, Harris JB, Tabrizi S, Rahman A, Shlyakhter I, Patterson N, O'Dushlaine C, Schaffner SF, Gupta S, Chowdhury F, Sheikh A, Shin OS, Ellis C, Becker CE, Stuart LM, Calderwood SB, Ryan ET, Qadri F, Sabeti PC, Larocque RC. Natural selection in a bangladeshi population from the cholera-endemic ganges river delta. Sci Transl Med. 2013 Jul 3; 5(192):192ra86. PMID: 23825302.
      View in: PubMed
    18. Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, Cabili M, Adegbola RA, Bamezai RN, Hill AV, Vannberg FO, Rinn JL. Identifying recent adaptations in large-scale genomic data. Cell. 2013 Feb 14; 152(4):703-13. PMID: 23415221.
      View in: PubMed
    19. Larson G, Karlsson EK, Perri A, Webster MT, Ho SY, Peters J, Stahl PW, Piper PJ, Lingaas F, Fredholm M, Comstock KE, Modiano JF, Schelling C, Agoulnik AI, Leegwater PA, Dobney K, Vigne JD, Vilà C, Andersson L, Lindblad-Toh K. Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proc Natl Acad Sci U S A. 2012 Jun 5; 109(23):8878-83. PMID: 22615366.
      View in: PubMed
    20. Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Rosengren Pielberg G, Sigurdsson S, Fall T, Seppälä EH, Hansen MS, Lawley CT, Karlsson EK. Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genet. 2011 Oct; 7(10):e1002316. PMID: 22022279.
      View in: PubMed
    21. Seppälä EH, Jokinen TS, Fukata M, Fukata Y, Webster MT, Karlsson EK, Kilpinen SK, Steffen F, Dietschi E, Leeb T, Eklund R, Zhao X, Rilstone JJ, Lindblad-Toh K, Minassian BA, Lohi H. LGI2 truncation causes a remitting focal epilepsy in dogs. PLoS Genet. 2011 Jul; 7(7):e1002194. PMID: 21829378.
      View in: PubMed
    22. Karlsson E, Waltersson MA, Bostner J, Pérez-Tenorio G, Olsson B, Hallbeck AL, Stål O. High-resolution genomic analysis of the 11q13 amplicon in breast cancers identifies synergy with 8p12 amplification, involving the mTOR targets S6K2 and 4EBP1. Genes Chromosomes Cancer. 2011 Oct; 50(10):775-87. PMID: 21748818.
      View in: PubMed
    23. Van Tyne D, Park DJ, Schaffner SF, Neafsey DE, Angelino E, Cortese JF, Barnes KG, Rosen DM, Lukens AK, Daniels RF, Milner DA, Johnson CA, Shlyakhter I, Grossman SR, Becker JS, Yamins D, Karlsson EK, Ndiaye D, Sarr O, Mboup S, Happi C, Furlotte NA, Eskin E, Kang HM, Hartl DL, Birren BW, Wiegand RC, Lander ES, Wirth DF, Volkman SK, Sabeti PC. Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum. PLoS Genet. 2011 Apr; 7(4):e1001383. PMID: 21533027.
      View in: PubMed
    24. Olsson M, Meadows JR, Truvé K, Rosengren Pielberg G, Puppo F, Mauceli E, Quilez J, Tonomura N, Zanna G, Docampo MJ, Bassols A, Avery AC, Karlsson EK, Thomas A, Kastner DL, Bongcam-Rudloff E, Webster MT, Sanchez A, Hedhammar A, Remmers EF, Andersson L, Ferrer L, Tintle L, Lindblad-Toh K. A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs. PLoS Genet. 2011 Mar; 7(3):e1001332. PMID: 21437276.
      View in: PubMed
    25. Wilbe M, Jokinen P, Truvé K, Seppala EH, Karlsson EK, Biagi T, Hughes A, Bannasch D, Andersson G, Hansson-Hamlin H, Lohi H, Lindblad-Toh K. Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex. Nat Genet. 2010 Mar; 42(3):250-4. PMID: 20101241.
      View in: PubMed
    26. Grossman SR, Shlyakhter I, Shylakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, Lander ES, Schaffner SF, Sabeti PC. A composite of multiple signals distinguishes causal variants in regions of positive selection. Science. 2010 Feb 12; 327(5967):883-6. PMID: 20056855.
      View in: PubMed
    27. Thomas R, Valli VE, Ellis P, Bell J, Karlsson EK, Cullen J, Lindblad-Toh K, Langford CF, Breen M. Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas. Chromosome Res. 2009; 17(8):987-1000. PMID: 19941159.
      View in: PubMed
    28. Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AM, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JI, Bulone V, Cai G, Cakir C, Carrington JC, Chawner M, Conti L, Costanzo S, Ewan R, Fahlgren N, Fischbach MA, Fugelstad J, Gilroy EM, Gnerre S, Green PJ, Grenville-Briggs LJ, Griffith J, Grünwald NJ, Horn K, Horner NR, Hu CH, Huitema E, Jeong DH, Jones AM, Jones JD, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma L, Maclean D, Chibucos MC, McDonald H, McWalters J, Meijer HJ, Morgan W, Morris PF, Munro CA, O'Neill K, Ospina-Giraldo M, Pinzón A, Pritchard L, Ramsahoye B, Ren Q, Restrepo S, Roy S, Sadanandom A, Savidor A, Schornack S, Schwartz DC, Schumann UD, Schwessinger B, Seyer L, Sharpe T, Silvar C, Song J, Studholme DJ, Sykes S, Thines M, van de Vondervoort PJ, Phuntumart V, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PR, Whisson SC, Judelson HS, Nusbaum C. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 2009 Sep 17; 461(7262):393-8. PMID: 19741609.
      View in: PubMed
    29. Drögemüller C, Karlsson EK, Hytönen MK, Perloski M, Dolf G, Sainio K, Lohi H, Lindblad-Toh K, Leeb T. A mutation in hairless dogs implicates FOXI3 in ectodermal development. Science. 2008 Sep 12; 321(5895):1462. PMID: 18787161.
      View in: PubMed
    30. Karlsson EK, Lindblad-Toh K. Leader of the pack: gene mapping in dogs and other model organisms. Nat Rev Genet. 2008 Sep; 9(9):713-25. PMID: 18714291.
      View in: PubMed
    31. Karlsson EK, Baranowska I, Wade CM, Salmon Hillbertz NH, Zody MC, Anderson N, Biagi TM, Patterson N, Pielberg GR, Kulbokas EJ, Comstock KE, Keller ET, Mesirov JP, von Euler H, Kämpe O, Hedhammar A, Lander ES, Andersson G, Andersson L, Lindblad-Toh K. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet. 2007 Nov; 39(11):1321-8. PMID: 17906626.
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    32. Salmon Hillbertz NH, Isaksson M, Karlsson EK, Hellmén E, Pielberg GR, Savolainen P, Wade CM, von Euler H, Gustafson U, Hedhammar A, Nilsson M, Lindblad-Toh K, Andersson L, Andersson G. Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in Ridgeback dogs. Nat Genet. 2007 Nov; 39(11):1318-20. PMID: 17906623.
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    33. Thomas R, Duke SE, Bloom SK, Breen TE, Young AC, Feiste E, Seiser EL, Tsai PC, Langford CF, Ellis P, Karlsson EK, Lindblad-Toh K, Breen M. A cytogenetically characterized, genome-anchored 10-Mb BAC set and CGH array for the domestic dog. J Hered. 2007; 98(5):474-84. PMID: 17702974.
      View in: PubMed
    34. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SM, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005 Dec 8; 438(7069):803-19. PMID: 16341006.
      View in: PubMed
    35. Thomas R, Scott A, Langford CF, Fosmire SP, Jubala CM, Lorentzen TD, Hitte C, Karlsson EK, Kirkness E, Ostrander EA, Galibert F, Lindblad-Toh K, Modiano JF, Breen M. Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors. Genome Res. 2005 Dec; 15(12):1831-7. PMID: 16339382.
      View in: PubMed
    36. Vinson JP, Jaffe DB, O'Neill K, Karlsson EK, Stange-Thomann N, Anderson S, Mesirov JP, Satoh N, Satou Y, Nusbaum C, Birren B, Galagan JE, Lander ES. Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res. 2005 Aug; 15(8):1127-35. PMID: 16077012.
      View in: PubMed
    37. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ, Gingeras TR, Schreiber SL, Lander ES. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005 Jan 28; 120(2):169-81. PMID: 15680324.
      View in: PubMed
    38. O'Lone R, Frith MC, Karlsson EK, Hansen U. Genomic targets of nuclear estrogen receptors. Mol Endocrinol. 2004 Aug; 18(8):1859-75. PMID: 15031323.
      View in: PubMed
    39. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 5; 420(6915):520-62. PMID: 12466850.
      View in: PubMed
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