Wilson Lab

Publications


Pre-print


    Razmara A, Ellis SE, Sokolowski DJ, Davis S, Wilson MD, Leek JT, Jaffe AE, Collado-Torres L. recount-brain: a curated repository of human brain RNA-seq datasets metadata. bioRxiv. 2019 Apr 24.
    bioRxiv



2017-present


    Yung T, Poon F, Liang M, Coquenlorge S, McGaugh EC, Hui CC, Wilson MD, Nostro MC, Kim TH. Sufu- and Spop-mediated downregulation of Hedgehog signaling promotes beta cell differentiation through organ-specific niche signals. Nat Commun. 2019 Oct 11;10(1):4647. doi: 10.1038/s41467-019-12624-5.
    PubMed | PDF

    Khyzha N, Khor M, DiStefano PV, Wang L, Matic L, Hedin U, Wilson MD, Maegdefessel L, Fish JE. Regulation of CCL2 expression in human vascular endothelial cells by a neighboring divergently transcribed long noncoding RNA. Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16410-16419. doi: 10.1073/pnas.1904108116. Epub 2019 Jul 26.
    PubMed | PDF

    Uusküla-Reimand L, Wilson MD. Break Check: Transcription-Driven Topoisomerase II Collisions near Chromatin Loop Anchors Are Hotspots for DNA Damage and Translocations. 2019 Jul 25;75(2):203-205. doi: 10.1016/j.molcel.2019.07.003.
    PubMed | PDF

    Lambert JP, Picaud S, Fujisawa T, Hou H, Savitsky P, Uusküla-Reimand L, Gupta GD, Abdouni H, Lin ZY, Tucholska M, Knight JDR, Gonzalez-Badillo B, St-Denis N, Newman JA, Stucki M, Pelletier L, Bandeira N, Wilson MD, Filippakopoulos P, Gingras AC. Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains. Mol Cell. 2019 Feb 7;73(3):621-638.e17. doi: 10.1016/j.molcel.2018.11.006. Epub 2018 Dec 13.
    PubMed | PDF

    Yin WC, Satkunendran T, Mo R, Morrissy S, Zhang X, Huang ES, Uusküla-Reimand L, Hou H, Son JE, Liu W, Liu YC, Zhang J, Parker J, Wang X, Farooq H, Selvadurai H, Chen X, Sau-Wai Ngan E, Cheng SY, Dirks PB, Angers S, Wilson MD, Taylor MD, Hui CC. Dual Regulatory Functions of SUFU and Targetome of GLI2 in SHH Subgroup Medulloblastoma. Dev Cell. 2019 Jan 28;48(2):167-183.e5. doi: 10.1016/j.devcel.2018.11.015. Epub 2018 Dec 13.
    PubMed | PDF

    Yuan X, Song M, Devine P, Bruneau BG, Scott IC, Wilson MD. Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development. Nat Commun. 2018 Nov 26;9(1):4977. doi: 10.1038/s41467-018-07451-z.
    PubMed | PDF

    Gibb N, Lazic S, Yuan X, Deshwar AR, Leslie M, Wilson MD, Scott IC. Hey2 regulates the size of the cardiac progenitor pool during vertebrate heart development. Development. 2018 Nov 21;145(22). pii: dev167510. doi: 10.1242/dev.167510.
    PubMed | PDF

    MacParland SA, Liu JC, Ma XZ, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I, Gupta R, Cheng ML, Liu LY, Camat D, Chung SW, Seliga RK, Shao Z, Lee E, Ogawa S, Ogawa M, Wilson MD, Fish JE, Selzner M, Ghanekar A, Grant D, Greig P, Sapisochin G, Selzner N, Winegarden N, Adeyi O, Keller G, Bader GD, McGilvray ID. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat Commun. 2018 Oct 22;9(1):4383. doi: 10.1038/s41467-018-06318-7.
    PubMed | PDF

    Roy AR, Ahmed A, DiStefano PV, Chi L, Khyzha N, Galjart N, Wilson MD, Fish JE, Delgado-Olguín P. The transcriptional regulator CCCTC-binding factor limits oxidative stress in endothelial cells. J Biol Chem. 2018 Jun 1;293(22):8449-8461. doi: 10.1074/jbc.M117.814699. Epub 2018 Apr 2.
    PubMed | PDF

    Hou H, Uusküla-Reimand L, Makarem M, Corre C, Saleh S, Metcalf A, Goldenberg A, Palmert MR, Wilson MD. Gene expression profiling of puberty-associated genes reveals abundant tissue and sex-specific changes across postnatal development. Hum Mol Genet. 2017 Sep 15;26(18):3585-3599. doi: 10.1093/hmg/ddx246.
    PubMed | PDF

    Kemaladewi DU, Maino E, Hyatt E, Hou H, Ding M, Place KM, Zhu X, Bassi P, Baghestani Z, Deshwar AG, Merico D, Xiong HY, Frey BJ, Wilson MD, Ivakine EA, Cohn RD. Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism. Nat Med. 2017 Aug;23(8):984-989. doi: 10.1038/nm.4367. Epub 2017 Jul 17.
    PubMed | PDF

    Dennis J, Medina-Rivera A, Truong V, Antounians L, Zwingerman N, Carrasco G, Strug L, Wells P, Trégouët DA, Morange PE, Wilson MD, Gagnon F. Leveraging cell type specific regulatory regions to detect SNPs associated with tissue factor pathway inhibitor plasma levels. Genet Epidemiol. 2017 Jul;41(5):455-466. doi: 10.1002/gepi.22049. Epub 2017 Apr 18.
    PubMed | PDF

    Zwingerman N, Medina-Rivera A, Kassam I, Wilson MD, Morange PE, Trégouët DA, Gagnon F. Sex-specific effect of CPB2 Ala147Thr but not Thr325Ile variants on the risk of venous thrombosis: A comprehensive meta-analysis. PLoS One. 2017 May 26;12(5):e0177768. doi: 10.1371/journal.pone.0177768. eCollection 2017.
    PubMed | PDF

    Hayward CP, Liang M, Tasneem S, Soomro A, Waye JS, Paterson AD, Rivard GE, Wilson MD. The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes. PLoS One. 2017 Mar 16;12(3):e0173991. doi: 10.1371/journal.pone.0173991. eCollection 2017.
    PubMed | PDF

    Khyzha N, Alizada A, Wilson MD, Fish JE. Epigenetics of Atherosclerosis: Emerging Mechanisms and Methods. Trends Mol Med. 2017 Mar 10. pii:S1471-4914(17)30023-0. doi: 10.1016/j.molmed.2017.02.004. Review. PMID: 28291707.
    PubMed | PDF

    Barbé L, Lanni S, López-Castel A, Franck S, Spits C, Keymolen K, Seneca S, Tomé S, Miron I, Letourneau J, Liang M, Choufani S, Weksberg R, Wilson MD, Sedlacek Z, Gagnon C, Musova Z, Chitayat D, Shannon P, Mathieu J, Sermon K, Pearson CE. CpG Methylation, a Parent-of-Origin Effect for Maternal-Biased Transmission of Congenital Myotonic Dystrophy. Am J Hum Genet. 2017 Mar 2;100(3):488-505. doi: 10.1016/j.ajhg.2017.01.033.
    PubMed | PDF



2012-2016


    Dennis J, Truong V, Aïssi D, Medina-Rivera A, Blankenberg S, Germain M, Lemire M, Antounians L, Civelek M, Schnabel R, Wells P, Wilson MD, Morange PE, Trégouët DA, Gagnon F. Single nucleotide polymorphisms in an intergenic chromosome 2q region associated with tissue factor pathway inhibitor plasma levels and venous thromboembolism. J Thromb Haemost. 2016 Oct;14(10):1960-1970. doi: 10.1111/jth.13431. Epub 2016 Sep 17. PMID: 27490645.
    PubMed | PDF

    Panjwani N, Wilson MD, Addis L, Crosbie J, Wirrell E, Auvin S, Caraballo RH, Kinali M, McCormick D, Oren C, Taylor J, Trounce J, Clarke T, Akman CI, Kugler SL, Mandelbaum DE, McGoldrick P, Wolf SM, Arnold P, Schachar R, Pal DK, Strug LJ. A microRNA-328 binding site in PAX6 is associated with centrotemporal spikes of rolandic epilepsy. Ann Clin Transl Neurol. 2016 Jun 2;3(7):512-22. doi: 10.1002/acn3.320. eCollection 2016 Jun 2. PMID: 27386500; PubMed Central PMCID: PMC4931716.
    PubMed | PDF

    Douglas GM, Wilson MD, Moses AM. Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration. Mol Biol Evol. 2016 Jun;33(6):1478-85. doi: 10.1093/molbev/msw030. Epub 2016 Feb 16. PMID: 26882985.
    PubMed | PDF

    Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R. A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Res. 2016 Feb 29;44(4):1977-8. doi:10.1093/nar/gkv1181. Epub 2015 Nov 5. PubMed PMID: 26546512; PubMed Central PMCID: PMC4770215.
    PubMed | PDF

    Uusküla-Reimand L*, Hou H*, Samavarchi-Tehrani P, Rudan MV, Liang M, Medina-Rivera A , Mohammed H, Schmidt D, Schwalie P, Young EJ, Reimand J, Hadjur S, Gingras A, Wilson MD*.Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders. Genome Biology. 2016 Aug 31;17:172. doi: 10.1186/s13059-016-1043-8.
    *co-first authors
    PubMed | PDF

    Gonorazky H, Liang M, Cummings B, Lek M, Micallef J, Hawkins C, Basran R, Cohn R, Wilson MD, MacArthur D, Marshall CR, Ray PN, Dowling JJ. RNAseq analysis for the diagnosis of muscular dystrophy. Ann Clin Transl Neurol. 2015 Dec 8;3(1):55-60. doi: 10.1002/acn3.267. eCollection 2015 Dec 8. PMID: 26783550.
    PubMed | PDF

    Wojtal D, Kemaladewi DU, Malam Z, Abdullah S, Wong TW, Hyatt E, Baghestani Z, Pereira S, Stavropoulos J, Mouly V, Mamchaoui K, Muntoni F, Voit T, Gonorazky HD, Dowling JJ, Wilson MD, Mendoza-Londono R, Ivakine EA, Cohn RD. Spell Checking Nature: Versatility of CRISPR/Cas9 for Developing Treatments for Inherited Disorders. Am J Hum Genet. 2016 Jan 7;98(1):90-101. doi: 10.1016/j.ajhg.2015.11.012. Epub 2015 Dec 10. PMID: 26686765.
    PubMed | PDF

    Shin J, Bourdon C, Bernard M, Wilson MD, Reischl E, Waldenberger M, Ruggeri B, Schumann G, Desrivieres S, Leemans A; IMAGEN Consortium.; SYS Consortium., Abrahamowicz M, Leonard G, Richer L, Bouchard L, Gaudet D, Paus T, Pausova Z. Layered genetic control of DNA methylation and gene expression: a locus of multiple sclerosis in healthy individuals. Hum Mol Genet. 2015 Oct 15;24(20):5733-45. doi: 10.1093/hmg/ddv294. Epub 2015 Jul 28. PubMed PMID: 26220975.
    PubMed | PDF

    Ballester B*#, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD*#. Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. Elife. 2014 Oct 3;3. doi: 10.7554/eLife.02626.
    *co-first authors; #co-corresponding authors;
    PubMed | PDF

    Wang L, Chen J, Wang C, Uusküla-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W. MACE: model based analysis of ChIP-exo. Nucleic Acids Res. 2014 Sep 23. pii: gku846.
    PubMed | PDF

    Rzeczkowska PA, Hou H, Wilson MD, Palmert MR. Epigenetics: A New Player in the Regulation of Mammalian Puberty. Neuroendocrinology. 2014 Apr 4:139-155.
    PubMed | PDF

    Stefflova K*, Thybert D*, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell. 2013 Aug 1;154(3):530-40. PMID: 23911320
    PubMed | PDF

    Funnell AP, Wilson MD, Ballester B, Mak KS, Burdach J, Magan N, Pearson RC, Lemaigre FP, Stowell KM, Odom DT, Flicek P, Crossley M. A CpG Mutational Hotspot in a ONECUT Binding Site Accounts for the Prevalent Variant of Hemophilia B Leyden. Am J Hum Genet. 2013 Mar 7;92(3):460-7.
    PubMed | PDF

    Ward MC*, Wilson MD*#, Barbosa-Morais NL, Schmidt D, Stark R; Pan Q; Schwalie PC, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K; Flicek P, Blencowe BJ and Odom DT#. Latent regulatory potential of human-specific repetitive elements. Mol. Cell. 2013 Jan 24;49(2):262-72.
    *co-first authors; #co-corresponding authors
    PubMed | PDF

    Barbosa-Morais N, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Çolak R, Kim TH, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ. The evolutionary landscape of alternative splicing in vertebrate species. Science 2012 Dec 21;338(6114):1587-93.
    PubMed | PDF

    Kutter C*, Watt S*, Stefflova K, Wilson MD, Goncalves A, Ponting CP, Odom DT, Marques AC. Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression. PLoS Genet. 2012 Jul;8(7):e1002841. Epub 2012 Jul 26. *co-first author
    PubMed | PDF

    Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, Nũnez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Babu MM, Bazett-Jones DP, Tavaré S, Edwards PA, Lowe SW, Kimura H, Gilbert DM, Narita M. Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation. Mol. Cell. 2012. online Jul 10.
    PubMed | PDF

    Faure AJ*, Schmidt D*, Watt S, Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P. Cohesin regulates tissue-specific expression by stabilising highly occupied cis-regulatory modules. Genome Res. 2012 online Jul 10.
    *co-first authors
    PubMed | PDF

    Pope BD*, Chandra T*, Buckley Q, Hoare M, Ryba T, Wiseman FK, Kuta A, Wilson MD, Odom DT, Gilbert DM. Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse. Hum. Mol. Genet. 2012 online Jul 20.
    *co-first authors
    PubMed | PDF

    Schmidt D*, Schwalie PC*, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT. Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages. Cell. 2012 Jan 20;148(1-2):335-48. Epub 2012 Jan 12.
    *co-first authors
    PubMed | PDF

    Laudadio I, Manfroid I, Achouri Y, Schmidt D, Wilson MD, Cordi S, Thorrez L, Knoops L, Jacquemin P, Schuit F, Pierreux CE, Odom DT, Peers B, Lemaigre FPA Feedback Loop Between The Liver-Enriched Transcription Factor Network and Mir-122 Controls Hepatocyte Differentiation. Gastroenterology. 2011 Sep 12.
    PubMed | PDF

    2007-2011


    Kutter C*, Brown GD*, Gonçalves A, Wilson MD, Watt S, Brazma A, White RJ, Odom DT. Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. Nat Genet. 2011 Aug 28;43(10):948-55.
    *co-first authors
    PubMed | PDF

    Tardif S*, Wilson MD*, Wagner R, Hunt P, Gertsenstein M, Nagy A, Lobe C, Koop BF, Hardy DM: Zonadhesin is essential for species specificity of sperm adhesion to the egg zona pellucida.< J Biol Chem 2010, 285:24863-24870.
    *co-first authors
    PubMed | PDF

    Schmidt D*, Wilson MD*, Ballester B*, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT: Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 2010, 328:1036-1040.
    *co-first authors
    PubMed | PDF

    Wu S, Wilson MD, Busby ER, Isaac ER, Sherwood NM: Disruption of the Single Copy Gonadotropin-Releasing Hormone Receptor in Mice by Gene Trap: Severe Reduction of Reproductive Organs and Functions in Developing and Adult Mice. Endocrinology 2010, 151:1142-1152.
    PubMed | PDF

    Wilson MD, Odom DT: Evolution of transcriptional control in mammals. Curr Opin Genet Dev 2009, 19:579-585.
    PubMed | PDF

    Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT: ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 2009, 48:240-248.
    PubMed | PDF

    Wilson MD*, Barbosa-Morais NL*, Schmidt D, Conboy CM, Vanes L, Tybulewicz VLJ, Fisher EMC, Tavaré S, Odom DT: Species-specific transcription in mice carrying human chromosome 21. Science 2008, 322:434-438.
    *co-first authors
    PubMed | PDF

    Wilson MD, Wang D, Wagner R, Breyssens H, Gertsenstein M, Lobe C, Lu X, Nagy A, Burke RD, Koop BF, Howard PL: ARS2 is a conserved eukaryotic gene essential for early mammalian development. Mol Cell Biol 2008, 28:1503-1514.
    PubMed | PDF

    Schmidt D*, Stark R*, Wilson MD, Brown GD, Odom DT: Genome-scale validation of deep-sequencing libraries. PLoS ONE 2008, 3:e371310.1371.
    *co-first authors
    PubMed | PDF

    Conboy CM, Spyrou C, Thorne NP, Wade EJ, Barbosa-Morais NL, Wilson MD, Bhattacharjee A, Young RA, Tavare S, Lees JA, Odom DT: Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor. PLoS ONE 2007.
    PubMed | PDF



Before 2007


    Wilson MD, Cheung J, Martindale DW, Scherer SW, Koop BF: Comparative analysis of the paired immunoglobulin-like receptor (PILR) locus in six mammalian genomes: duplication, conversion, and the birth of new genes. Physiol Genomics 2006, 27:201-218.
    PubMed | PDF

    Hunt P, Wilson MD, Schalburg von K, Davidson W, Koop BF: Expression and genomic organization of zonadhesin-like genes in three species of fish give insight into the evolutionary history of a mosaic protein. BMC Genomics 2005, 6:16510.1186/1471-2164-6-165.
    PubMed | PDF

    Scherer SW et al.: Human chromosome 7: DNA sequence and biology. Science 2003, 300:767-772.
    PubMed | PDF

    Cheung J, Wilson MD, Zhang J, Khaja R, MacDonald JR, Heng HHQ, Koop BF, Scherer SW: Recent segmental and gene duplications in the mouse genome. Genome Biol 2003, 4:R4710.1186/gb-2003-4-8-r47.
    PubMed | PDF

    Montpetit A, Wilson MD, Chevrette M, Koop BF, Sinnett D: Analysis of the conservation of synteny between Fugu and human chromosome 12. BMC Genomics. 2003, Jul 23;4(1):30.
    PubMed | PDF

    Wen XY, Hegele RA, Wang J, Wang DY, Cheung J, Wilson M, Yahyapour M, Bai Y, Zhuang L, Skaug J, Young TK, Connelly PW, Koop BF, Tsui LC, Stewart AK. Identification of a novel lipase gene mutated in lpd mice with hypertriglyceridemia and associated with dyslipidemia in humans. Hum Mol Genet. 2003 May 15;12(10):1131-43.
    PubMed | PDF

    Shuttleworth TL, Wilson MD, Wicklow BA, Wilkins JA, Triggs-Raine BL: Characterization of the murine hyaluronidase gene region reveals complex organization and cotranscription of Hyal1 with downstream genes, Fus2 and Hyal3. J Biol Chem 2002, 277:23008-23018.
    PubMed | PDF

    Wilson MD, Ruttan C, Koop B, Glickman B: ERCC1: A comparative genomic perspective. Environ Mol Mutagen 2001, 38:209-215.
    PubMed | PDF

    Wilson MD, Riemer C, Martindale D, Schnupf P, Boright A, Cheung T, Hardy D, Schwartz S, Scherer S, Tsui L, Miller W, Koop B: Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5. Nucleic Acids Res 2001, 29:1352-1365.
    PubMed | PDF

    Martindale DW, Wilson MD, Wang D, Burke RD, Chen X, Duronio V, Koop BF: Comparative genomic sequence analysis of the Williams syndrome region (LIMK1-RFC2) of human chromosome 7q11.23. Mamm Genome 2000, 11:890-898.
    PubMed | PDF

    Brown G, Martindale D, Wilson MD, Koop BF. Mouse and human DNA sequence comparisons: further evidence for a mosaic model of genomic evolution. In Sankoff D, Nadeau JH, eds. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families. Volume 1 of Series in Computational Biology. Dordrecht, NL: Kluwer Academic Press; 2000.
    PDF