Publications

[15] Collins RL, Brand H, Redin CE, Hanscom C, Antolik C, Stone MR, Glessner JT, Mason T, Pregno G, Dorrani N, Mandrile G, Giachino D, Perrin D, Walsh C, Cipicchio M, Costello M, Stortchevoi A, An J, Currall BB, Seabra CM, Ragavendran A, Margolin L, Martinez-Agosto JA, Lucente D, Levy B, Sanders SJ, Wapner RJ, Quintero-Rivera F, Kloosterman W, Talkowski ME. Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome. Genome Biology, 18(36), 1-21. PMID: 28260531. DOI: 10.1186/s13059-017-1158-6. PDF

[14] Shaw ND*, Brand H*, Kupchinsky ZA, Bengani H, Plummer L, Jones TI, Erdin S, Williamson KA, Rainger J, Stortchevoi A, Samocha K, Currall BB, Dunican DS, Collins RL, Willer JR, Lek A, Lek M, Nassan M, Pereira S, Kammin T, Lucente D, Silva A, Seabra CM, Chiang C, An Y, Ansari M, Rainger JK, Joss S, Smith JC, Lippincott MF, Singh SS, Patel N, Jing JW, Law JR, Ferraro N, Verloes A, Rauch A, Steindl K, Zweier M, Scheer I, Sato D, Okamoto N, Jacobsen C, Tryggestad J, Chernausek S, Schimmenti LA, Brasseur B, Cesaretti C, García-Ortiz JE, Buitrago TP, Silva OP, Hoffman JD, Mühlbauer W, Ruprecht KW, Loeys BL, Shino M, Kaindl AM, Cho C, Morton CC, Meehan RR, van Heyningen V, Liao EC, Balasubramanian R, Hall JE, Seminara SB, Macarthur D, Moore SA, Yoshiura K, Gusella JF, Marsh JA, Graham Jr JM, Lin AE, Katsanis N, Jones PL, Crowley Jr WF, Davis EE°, FitzPatrick DR°, Talkowski ME°. SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome. Nature Genetics, 49(2): 238-248. PMID: 28067909. DOI: 10.1038/ng.3743. PDF

[13] Redin C, Brand H, Collins RL, Kammin T, Mitchell E, Hodge JC, Hanscom C, Pillalamarri V, Seabra CM, Abbott M, Abdul-Rahman OA, Aberg E, Adley R, Alcaraz-Estrada SL, Alkuraya FS, An Y, Anderson M, Antolik C, Anyane-Yeboa K, Atkin JF, Bartell T, Bernstein JA, Beyer E, Bongers EMHF, Brilstra EH, Brown CW, Brüggenwirth HT, Callewaert B, Corning K, Cox H, Cuppen E, Currall BB, Cushing T, David D, Deardorff MA, Dheedene A, D’hooghe M, de Vries BBA, Earl DL, Ferguson HL, Fisher H, FitzPatrick DR, Gerrol P, Giachino D, Glessner JT, Gliem T, Grady M, Graham BH, Griffis C, Gripp KW, Gropman AL, Hanson-Kahn A, Harris DJ, Hayden MA, Hochstenbach R, Hoffman JD, Hopkin RJ, Hubshman MW, Innes AM, Irons M, Irving M, Janssens S, Jewett T, Johnson JP, Jongmans MC, Kahler SG, Koolen DA, Korzelius J, Kroisel PM, Lacassie Y, Lawless W, Lemyre E, Leppig K, Levin AV, Li H, Li H, Liao EC, Lim C, Lose EJ, Lucente D, Macera MJ, Manavalan P, Mandrile G, Marcelis CL, Margolin L, Mason T, Masser-Frye D, McClellan MW, Mendoza CZ, Menten B, Middelkamp S, Mikami LR, Moe E, Mohammed S, Mononen T, Mortenson ME, Moya G, Nieuwint A, Ordulu Z, Parkash S, Pauker SP, Pereira S, Perrin D, Phelan K, Piña-Aguilar RE, Poddighe PJ, Pregno G, Raskin S, Reis L, Rhead W, Rita D, Renkens I, Roelens F, Ruliera J, Rump P, Schilit SLP, Shaheen R, Sparkes R, Spiegel E, Stevens B, Stone MR, Tagoe J, Thakuria JV, van Bon BW, van de Kamp J, van der Burgt I, van Essen T, van Ravenswaaij-Arts CM, van Roosmalen MJ, Vergult S, Volker-Touw CML, Warburton DP, Waterman MJ, Wiley S, Wilson A, Vega M, Zori RT, Levy B, Brunner HG, de Leeuw N, Kloosterman WP, Thorland EC, Morton CC, Gusella JF, Talkowski ME. The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. Nature Genetics (2017), 49(1): 36-45. PMID: 27841880. DOI: 10.1002/ajmg.a.38021.PDF

[12] Maussion G*, Cruceanu C*, Rosenfeld JA, Bell SC, Jollant F, Szatkiewicz J, Collins RL, Hanscom C, Kolobova I, de Champfleur NM, Blumenthal I, Chiang C, Ota V, Hultman C, O'Dushlaine C, McCarroll S, Alda M, Jacquemont S, Ordulu Z, Marshall CR, Carter MT, Shaffer LG, Sklar P, Girirajan S, Morton CC, Gusella JF, Turecki G, Stavropoulos DJ, Sullivan PF, Scherer SW, Talkowski ME, Ernst C. Implication of LRRC4C and DPP6 in neurodevelopmental disorders. American Journal of Medical Genetics (2016), online ahead of print. PMID: 27759917. DOI: 10.1002/ajmg.a.38021. PDF

[11] Ordulu Z, Kammin T, Brand H, Pillalamarri V, Redin CE, Collins RL, Blumenthal I, Hanscom C, Pereira S, Bradley I, Crandall BF, Gerrol P, Hayden MA, Hussain N, Kanengisser-Pines B, Kantarci S, Levy B, Macera MJ, Quintero-Rivera F, Spiegel E, Stevens B, Ulm JE, Warburton D, Wilkins-Haug LE, Yachelevich N, Gusella JF, Talkowski ME, Morton CC. Structural chromosome rearrangements require nucleotide level resolution: lessons from next-generation sequencing in prenatal diagnosis. American Journal of Human Genetics, 99(5): 1015-1033. PMID: 27745839. DOI: 10.1016/j.ajhg.2016.08.022. PDF

[10] Schilit S, Currall B, Yao R, Hanscom C, Collins RL, Pillalamarri V, Lee DYD, Kammin T, Zepeda-Mendoza CJ, Mononen T, Nolan LS, Gusella JF, Shen J, Talkowski M, Morton CC. Estrogen-Related Receptor Gamma (ESRRG) Implicated in a Phenotype Including Hearing Loss and Mild Developmental Delay. European Journal of Human Genetics (2016), online ahead of print (July 6 2016). PMID: 27381092. DOI: 10.1038/ejhg.2016.64PDF

[9] Macakova M, Bohuslavova B, Vochozkova P, Pavlok A, Sedlackova M, Vidinska D, Vochyanova K, Liskova I, Valekova I, Baxa M, Ellederova Z, Klima J, Juhas S, Juhasova J, Klouckova J, Haluzik M, Klempir J, Hansikova H, Spacilova J, Collins RL, Blumenthal I, Talkowski M, Gusella JF, Howland DS, DiFiglia M, Motlik J. Mutated Huntingtin causes testicular pathology in transgenic minipig boars. Neurodegenerative Diseases (2016), 16(3-4): 245-259. PMID: 26959244. DOI: 10.1159/000443665PDF

[8] Tai DJC, Ragavendran A, Manavalan P, Stortchevoi A, Seabra C, Erdin S, Collins RL, Blumenthal I, Chen X, Shen Y, Sahin M, Zheng C, Lee C, Gusella JF, Talkowski ME. Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR. Nature Neuroscience (2016), 19(3): 517-522. PMID: 26829649. DOI: 10.1038/nn.4235PDF

[7] Brand H*, Collins RL*, Hanscom C, Rosenfeld JA, Pillalamarri V, Stone MR, Kelley F, Mason T, Margolin L, Eggert S, Mitchell E, Hodge J, Gusella JF, Sanders SJ, Talkowski ME. Paired duplications mark cryptic inversions and are a common signature of complex structural variation. American Journal of Human Genetics (2015), 97:1, 170-176. PMID: 26094575. DOI: 10.1016/j.ajhg.2015.05.012PDF

[6] Turner T, Sharma K, Oh EC, Liu YP, Collins RL, Sosa MX, Auer D, Brand H, Sanders SJ, Moreno-De-Luca D, Pihur V, Piona T, Pike K, Soppet D, Smith MW, Cheung SW, Martin CL, State M, Talkowski ME, Cook E, Huganir R, Katsanis N, Chakravarti A. Loss of delta catenin function in severe autism. Nature (2015), 519:7543, 51-56. PMID: 25807484. DOI: 10.1038/nature14186PDF

[5] Mandal PK*, Ferreira LMR*, Collins RL, Meissner TB, Boutwell CL, Friesen M, Garrison BS, Stortchevoi A, Bryder D, Musunuru K, Brand H, Allen TM, Talkowski ME, Rossi DJ, Cowan CA. Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. Cell Stem Cell (2014), 15:5, 643-652. PMID: 25517468. DOI: 10.1016/j.stem.2014.10.004PDFDF

[4] Brand H*, Pillalamarri V*, Collins RL, Eggert S, O’Dushlaine C, Braaten EB, Stone M, Chambert K, Doty ND, Hanscom C, Ditmars H, Blais J, Mills R, Lee C, Gusella JF, McCarroll S, Smoller JW, Talkowski ME, Doyle AE. Cryptic and complex chromosomal aberrations in early onset neuropsychiatric disorders. American Journal of Human Genetics (2014). 95:4, 454-461. PMID: 25279985. DOI: 10.1016/j.ajhg.2014.09.005PDF

[3] Veres A, Gosis BS, Ding Q, Collins RL, Ragavendran A, Brand H, Erdin S, Talkowski ME, Musunuru K. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell (2014), 15:1, 27-30. PMID: 24996167. DOI: 10.1016/j.stem.2014.04.020PDF

[2Collins RL, Hu T, Wejse C, Sirugo G, Williams SM, Moore JH. Multifactor dimensionality reduction reveals a three-locus epistatic interaction associated with susceptibility to pulmonary tuberculosis. BioData Mining (2013), 6:4. PMID: 23418869. DOI: 10.1186/1756-0381-6-4PDF

[1] Hu T, Chen Y, Kiralis JW, Collins RL, Wejse C, Sirugo G, Williams SM, Moore JH. An information-gain approach to detecting three-way epistatic interactions in genetic association studies.  Journal of the American Medical Informatics Association (2013), 20:4, 630-636. PMID: 23396514. DOI: 10.1136/amiajnl-2012-001525PDF

Preprints

  • Aneichyk T*, Hendriks WT*, Yadav R*, Shin D*, Gao D*, Vaine CA, Collins RL, Stortchevoi A, Currall B, Brand H, Hanscom C, Antolik C, Dy M, Ragavendran A, Acuña P, Go C, Wainger BJ, Henderson D, Dhakal J, Ito N, Weisenfeld N, Jaffe D, Sharma N, Breakefield X, Ozelius L, Bragg DC°, Talkowski ME°. Dissecting the causal mechanism of X-Linked Dystonia-Parkinsonism by integrating genome and transcriptome assembly. bioRxiv (2017). DOI: 10.1101/149872. PDF
  • Pedersen B, Collins RL, Talkowski ME, Quinlan A. Indexcov: fast whole-genome coverage quality-control from BAM or CRAM indexes. bioRxiv (2017). DOI: 10.1101/148296. PDF
  • Werling DM*, Brand H*, An J*, Stone MR*, Glessner JT*, Zhe L, Collins RL, Dong S, Layer RM, Markenscoff-Papadimitriou E, Farrell A, Schwartz GB, Currall BB, Dea J, Docherty AR, Duhn C, Erdman C, Gilson M, Handsaker RE, Kashin S, Klei L, Mandell JD, Nowakowski TJ, Liu Y, Pochareddy S, Smith L, Wang HZ, Waterman MJ, He X, Kriegstein AR, Rubenstein JL, Sestan N, McCarroll SA, Neale BM, Coon H, Willsey AJ, Buxbaum JD, Daly MJ, State MW, Quinlan A, Marth G, Roeder K, Devlin B°, Talkowski ME°, Sanders SJ°. Limited contribution of rare or noncoding variation to autism spectrum disorder from sequencing of 2,076 genomes in quartet families. bioRxiv (2017). DOI: 10.1101/127043. PDF
  • Collins RL, Stone MR, Brand H, Glessner JT, Talkowski ME. CNView: a visualization and annotation tool for copy number variation from whole-genome sequencing. bioRxiv (2016). DOI: 10.1101/049536. PDF