Pre-print
Wang L, Alizada A, Rathnakumar K, Khyzha N, Taylor T, Campitelli LF, Patel ZM, Antounians L, Hughes T, Roy S, Mitchell JA, Fish JE, Wilson MD. Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-κB binding. bioRxiv. 2022 Oct 26.
bioRxiv
Mufteev M, Rodrigues DC, Yuki KE, Narula A, Wei W, Piekna A, Liu J, Pasceri P, Rissland OS, Wilson MD, Ellis J. Transcriptional buffering and 3'UTR lengthening are shaped during human neurodevelopment by shifts in mRNA stability and microRNA load. bioRxiv. 2023 Mar 1:2023.03.01.530249. doi:10.1101/2023.03.01.530249.
bioRxiv
2022-present
Rodrigues DC, Mufteev M, Yuki KE, Narula A, Wei W, Piekna A, Liu J, Pasceri P, Rissland OS, Wilson MD, Ellis J.
Buffering of transcription rate by mRNA half-life is a conserved feature of Rett syndrome models.
Nat Commun. 2023 Apr 5;14(1):1896. doi: 10.1038/s41467-023-37339-6.
PubMed | PDF
Deshwar AR*, Yuki KE*, Hou H*, Liang Y, Khan T, Celik A, Ramani A, Mendoza-Londono R, Marshall CR, Brudno M, Shlien A, Meyn MS,
Hayeems RZ, McKinlay BJ, Klentrou P, Wilson MD, Kyriakopoulou L, Costain G, Dowling JJ.
Trio RNA sequencing in a cohort of medically complex children.
Am J Hum Genet. 2023 Mar 21;S0002-9297(23)00090-3. doi: 10.1016/j.ajhg.2023.03.006. Online ahead of print.
*co-first authors
PubMed | PDF
Brieño-Enríquez MA, Faykoo-Martinez M, Goben M, Grenier JK, McGrath A, Prado AM, Sinopoli J,
Wagner K, Walsh PT, Lopa SH, Laird DJ, Cohen PE, Wilson MD, Holmes M, Place NJ.
Postnatal oogenesis leads to an exceptionally large ovarian reserve and protracted fertility in naked mole-rats.
Nat Commun. 2023 Feb 21;14(1):670. doi: 10.1038/s41467-023-36284-8.
PubMed | PDF
Smith RJ*, Liang M*, Loe AKH, Yung T, Kim JE, Hudson M, Wilson MD, Kim TH.
Epigenetic control of cellular crosstalk defines gastrointestinal organ fate and function. Nat Commun. 2023 Jan 30;14(1):497. doi: 10.1038/s41467-023-36228-2.
*co-first authors
PubMed | PDF
Sokolowski DJ#, Ahn J, Erdman L, Hou H, Ellis K, Wang L, Goldenberg A, Wilson MDE.
Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression.
NAR Genom Bioinform. 2023 Jan 23;5(1):lqad003. doi: 10.1093/nargab/lqad003. eCollection 2023 Mar.
#co-SRA
PubMed | PDF
Langille E, Al-Zahrani KN, Ma Z, Liang M, Uusküla-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, Ghamrasni SE, Afiuni-Zadeh S,
Tsai R, Alvi S, Elia A, Lü Y, Oh RH, Kozma KJ, Trcka D, Narimatsu M, Liu JC, Nguyen T, Barutcu S, Loganathan SK, Bremner R, Bader GD,
Egan SE, Cescon DW, Sørlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D.
Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer.
Cancer Discov. 2022 Dec 2;12(12):2930-2953. doi: 10.1158/2159-8290.CD-21-0865.
PubMed | Full text
Oh RY, Deshwar AR, Marwaha A, Sabha N, Tropak M, Hou H, Yuki KE, Wilson MD, Rump P, Lunsing R, Elserafy N, Chung CWT,
Hewson S, Klein-Rodewald T, Calzada-Wack J, Sanz-Moreno A, Kraiger M, Marschall S, Fuchs H, Gailus-Durner V, Hrabe de Angelis M, Dowling J, Schulze A.
Biallelic loss-of-function variants in RABGAP1 cause a novel neurodevelopmental syndrome.
Genet Med. 2022 Nov;24(11):2399-2407. doi: 10.1016/j.gim.2022.07.024. Epub 2022 Sep 9.
PubMed | Full text
Uusküla-Reimand L, Wilson MD.
Untangling the roles of TOP2A and TOP2B in transcription and cancer.
Sci Adv. 2022 Nov 4;8(44):eadd4920. doi: 10.1126/sciadv.add4920. Epub 2022 Nov 2.
PubMed | PDF
Hou H*, Chan C*, Yuki KE, Sokolowski D, Roy A, Qu R, Uusküla-Reimand L,
Faykoo-Martinez M, Hudson M, Corre C, Goldenberg A, Zhang Z, Palmert MR# Wilson MD#.
Postnatal developmental trajectory of sex-biased gene expression in the mouse pituitary gland.
Biol Sex Differ. 2022 Oct 11;13(1):57. doi: 10.1186/s13293-022-00467-7.
*co-first authors; #co-corresponding authors;
PubMed | PDF
Yanchus C*, Drucker KL*, Kollmeyer TM, Tsai R, Winick-Ng W, Liang M, Malik A, Pawling J, De Lorenzo SB, Ali A, Decker PA, Kosel ML, Panda A, Al-Zahrani KN, Jiang L,
Browning JWL, Lowden C, Geuenich M, Hernandez JJ, Gosio JT, Ahmed M, Loganathan SK, Berman J, Trcka D, Michealraj KA, Fortin J, Carson B, Hollingsworth EW,
Jacinto S, Mazrooei P, Zhou L, Elia A, Lupien M, He HH, Murphy DJ, Wang L, Abyzov A, Dennis JW, Maass PG, Campbell K, Wilson MD, Lachance DH, Wrensch M,
Wiencke J, Mak T, Pennacchio LA, Dickel DE, Visel A, Wrana J, Taylor MD, Zadeh G, Dirks P, Eckel-Passow JE, Attisano L, Pombo A, Ida CM, Kvon EZ, Jenkins RB, Schramek D.
A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation.
Science. 2022 Oct 7;378(6615):68-78. doi: 10.1126/science.abj2890. Epub 2022 Oct 6.
*co-first authors
PubMed | Full text
Marwaha AK, Laxer R, Liang M, Muise AM, Eiwegger T; IMMUNE DYSREGULATION GROUP
(Wilson MD, Yuki KE are co-authors listed within the "IMMUNE DYSREGULATION GROUP").
A Chromosomal Duplication Encompassing Interleukin-33 Causes a Novel Hyper IgE Phenotype Characterized by Eosinophilic Esophagitis and Generalized Autoimmunity.
Gastroenterology. 2022 Aug;163(2):510-513.e3. doi: 10.1053/j.gastro.2022.04.026. Epub 2022 Apr 28.
PubMed | Full text
Volpatti JR, Ghahramani-Seno MM, Mansat M, Sabha N, Sarikaya E, Goodman SJ, Chater-Diehl E, Celik A, Pannia E, Froment C, Combes-Soia L, Maani N,
Yuki KE, Chicanne G, Uusküla-Reimand L, Monis S, Alvi SA, Genetti CA,
Payrastre B, Beggs AH, Bonnemann CG, Muntoni F, Wilson MD, Weksberg R, Viaud J, Dowling JJ.
X-linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition.
Acta Neuropathol. 2022 Sep;144(3):537-563. doi: 10.1007/s00401-022-02468-7. Epub 2022 Jul 17.
PubMed | PDF
McQuaid ME, Ahmed K, Tran S, Rousseau J, Shaheen R, Kernohan KD, Yuki KE, Grover P, Dreseris ES, Ahmed S, Dupuis L, Stimec J, Shago M, Al-Hassnan ZN, Tremblay R, Maass PG,
Wilson MD, Grunebaum E, Boycott KM, Boisvert FM, Maddirevula S, Faqeih EA, Almanjomi F, Khan ZU, Alkuraya FS, Campeau PM#, Kannu P#, Campos EI#, Wurtele H#.
Hypomorphic GINS3 variants alter DNA replication and cause Meier-Gorlin syndrome.
JCI Insight. 2022 May 23;7(10):e155648. doi: 10.1172/jci.insight.155648.
#co-corresponding authors
PubMed | PDF
Gustafson D, Ngai M, Wu R, Hou H, Schoffel AC, Erice C, Mandla S, Billia F, Wilson MD, Radisic M, Fan E, Trahtemberg U,
Baker A, McIntosh C, Fan CS, Dos Santos CC, Kain KC, Hanneman K, Thavendiranathan P, Fish JE, Howe KL.
Cardiovascular signatures of COVID-19 predict mortality and identify barrier stabilizing therapies.
EBioMedicine. 2022 Apr;78:103982. doi: 10.1016/j.ebiom.2022.103982. Epub 2022 Apr 8.
PubMed | PDF
Song M*, Yuan X*, Racioppi C, Leslie M, Aleksandrova A, Christiaen L, Wilson MD#, Scott IC#.
GATA4/5/6 family transcription factors are conserved determinants of cardiac versus pharyngeal mesoderm fate.
Sci Adv. 2022 Mar 11;8(10):eabg0834. doi: 10.1126/sciadv.abg0834. Epub 2022 Mar 11.
*co-first authors; #co-corresponding authors;
PubMed | PDF
2017-2021
Subramanian A, Hall M, Hou H, Mufteev M, Yu B, Yuki KE, Nishimura H, Sathaseevan A, Lant B, Zhai B, Ellis J, Wilson MD, Daugaard M, Derry WB. Alternative polyadenylation is a determinant of oncogenic Ras function. Sci Adv. 2021 Dec 17;7(51):eabh0562. doi: 10.1126/sciadv.abh0562. Epub 2021 Dec 17. PubMed | PDF
Stutt N, Song M, Wilson MD, Scott IC. Cardiac specification during gastrulation - The Yellow Brick Road leading to Tinman. Semin Cell Dev Biol. 2021 Dec 2;S1084-9521(21)00288-3. doi: 10.1016/j.semcdb.2021.11.011. Online ahead of print. PubMed | PDF
Byres LP, Mufteev M, Yuki KE, Wei W, Piekna A, Wilson MD, Rodrigues DC, Ellis J. Identification of TIA1 mRNA targets during human neuronal development. Mol Biol Rep. 2021 Sep;48(9):6349-6361. doi: 10.1007/s11033-021-06634-0. Epub 2021 Aug 19. PubMed | PDF
Antounians L, Catania VD, Montalva L, Liu BD, Hou H, Chan C, Matei AC, Tzanetakis A, Li B, Figueira RL, Miura da Costa K, Wong AP, Mitchell R, David AL, Patel K, De Coppi P, Neto LS, Wilson MD, Rossant J, Zani A. Fetal lung underdevelopment is rescued by administration of amniotic fluid stem cell extracellular vesicles in rodents. Science Translational Medicine. 2021 Apr 21. doi: 10.1126/scitranslmed.aax5941 PubMed | PDF
Yuan X#, Scott IC#, Wilson MD#. Heart Enhancers: Development and Disease Control at a Distance. Frontiers in Genetics. 2021 Mar 10;12:642975. doi: 10.3389/fgene.2021.642975.
#co-corresponding authors
PubMed | PDF
Sokolowski DJ#, Faykoo-Martinez M, Erdman L, Hou H, Chan C, Zhu H, Holmes MM, Goldenberg A, Wilson MD#. Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes. NAR Genomics and Bioinformatics. 2021 Feb 22;3(1). doi: 10.1093/nargab/lqab011
#co-corresponding authors
PudMed | PDF | CRAN
Alizada A*, Khyzha N*, Wang L, Antounians L, Chen X, Khor M, Liang M, Rathnakumar K, Weirauch MT, Medina-Rivera A, Fish JE#, Wilson MD#. Conserved regulatory logic at accessible and inaccessible chromatin during the acute inflammatory response in mammals. Nat Comm. 2021 Jan 25;12:567. doi: 10.1038/s41467-020-20765-1
*co-first authors; #co-corresponding authors;
PubMed | PDF
Ahmed A, Liang M, Chi L, Zhou YQ, Sled JG, Wilson MD, Delgado-Olguín P. Maternal obesity persistently alters cardiac progenitor gene expression and programs adult-onset heart disease susceptibility. Mol Metab. 2021 Jan;101116. doi: 10.1016/j.molmet.2020.101116. Epub 2020 Nov 17. PubMed | PDF
van Eif VWW, Protze SI, Bosada FM, Yuan X, Sinha T, van Duijvenboden K, Ernault AC, Mohan RA, Wakker V, de Gier-de Vries C, Hooijkaas IB, Wilson MD, Verkerk AO, Bakkers J, Boukens BJ, Black BL, Scott IC, Christoffels VM. Genome-Wide Analysis Identifies an Essential Human TBX3 Pacemaker Enhancer. Circ Res. 2020 Dec 4;127(12):1522-1535. doi: 10.1161/CIRCRESAHA.120.317054. Epub 2020 Oct 12. PubMed | PDF
Liang M, Soomro A, Tasneem S, Abatti LE, Alizada A, Yuan X, Uusküla-Reimand L, Antounians L, Alvi SA, Paterson AD, Rivard GE, Scott IC, Mitchell JA, Hayward CPM#, Wilson MD#. Enhancer-gene rewiring in the pathogenesis of Quebec platelet disorder. Blood 2020 Dec 3;136(23):2679-2690. doi: 10.1182/blood.2020005394.
#co-corresponding authors
PubMed | PDF
Brunet JG, Sharma T, Tasneem S, Liang M, Wilson MD, Rivard GE, Hayward CPM. Thrombin generation abnormalities in Quebec platelet disorder. Int J Lab Hematol. 2020 Dec;42(6):801-809. doi: 10.1111/ijlh.13302. Epub 2020 Aug 6. PubMed | PDF
Kao CS, van Bruggen R, Kim JR, Chen XXL, Chan C, Lee J, Cho WI, Zhao M, Arndt C, Maksimovic K, Khan M, Tan Q, Wilson MD, Park J. T Selective neuronal degeneration in MATR3 S85C knock-in mouse model of early-stage ALS. Nat Commun. 2020 Oct 20;11(1):5304. doi: 10.1038/s41467-020-18949-w. PubMed | PDF
Shchuka VM, Abatti LE, Hou H, Khader N, Dorogin A, Wilson MD, Shynlova O, Mitchell JA. The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice. PLoS Biol. 2020 Jul 15;18(7):e3000710. doi: 10.1371/journal.pbio.3000710. eCollection 2020 Jul. PubMed | PDF
Zhu H*, Uusküla-Reimand L*, Isaev K, Wadi L, Alizada A, Shuai S, Huang V, Aduluso-Nwaobasi D, Paczkowska M, Abd-Rabbo D, Ocsenas O, Liang M, Thompson JD, Li Y, Ruan L, Krassowski M, Dzneladze I, Simpson JT, Lupien M, Stein LD, Boutros PC, Wilson MD, Reimand J. Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. Mol Cell. 2020 Mar 19;77(6):1307-1321.e10. doi: 10.1016/j.molcel.2019.12.027. Epub 2020 Jan 17.
*co-first authors
PubMed | Full text
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
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
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.
#co-corresponding authors;
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.
*co-first authors; #co-corresponding authors;
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.
#co-corresponding authors;
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.
*co-first authors; #co-corresponding authors;
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
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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.
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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
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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.
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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
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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
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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
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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.
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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
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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
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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
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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.
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Wilson MD, Odom DT: Evolution of transcriptional control in mammals. Curr Opin Genet Dev 2009, 19:579-585.
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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.
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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
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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.
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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
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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.
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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.
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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.
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Scherer SW et al.: Human chromosome 7: DNA sequence and biology. Science 2003, 300:767-772.
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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.
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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.
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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.
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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.
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Wilson MD, Ruttan C, Koop B, Glickman B: ERCC1: A comparative genomic perspective. Environ Mol Mutagen 2001, 38:209-215.
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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.
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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.
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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.
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