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Items: 33

1.

Detection of long repeat expansions from PCR-free whole-genome sequence data.

Dolzhenko E, van Vugt JJFA, Shaw RJ, Bekritsky MA, van Blitterswijk M, Narzisi G, Ajay SS, Rajan V, Lajoie BR, Johnson NH, Kingsbury Z, Humphray SJ, Schellevis RD, Brands WJ, Baker M, Rademakers R, Kooyman M, Tazelaar GHP, van Es MA, McLaughlin R, Sproviero W, Shatunov A, Jones A, Al Khleifat A, Pittman A, Morgan S, Hardiman O, Al-Chalabi A, Shaw C, Smith B, Neo EJ, Morrison K, Shaw PJ, Reeves C, Winterkorn L, Wexler NS; US–Venezuela Collaborative Research Group, Housman DE, Ng CW, Li AL, Taft RJ, van den Berg LH, Bentley DR, Veldink JH, Eberle MA.

Genome Res. 2017 Nov;27(11):1895-1903. doi: 10.1101/gr.225672.117. Epub 2017 Sep 8.

2.

5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells.

Poterlowicz K, Yarker JL, Malashchuk I, Lajoie BR, Mardaryev AN, Gdula MR, Sharov AA, Kohwi-Shigematsu T, Botchkarev VA, Fessing MY.

PLoS Genet. 2017 Sep 1;13(9):e1006966. doi: 10.1371/journal.pgen.1006966. eCollection 2017 Sep.

3.

X-linked hypomyelination with spondylometaphyseal dysplasia (H-SMD) associated with mutations in AIFM1.

Miyake N, Wolf NI, Cayami FK, Crawford J, Bley A, Bulas D, Conant A, Bent SJ, Gripp KW, Hahn A, Humphray S, Kimura-Ohba S, Kingsbury Z, Lajoie BR, Lal D, Micha D, Pizzino A, Sinke RJ, Sival D, Stolte-Dijkstra I, Superti-Furga A, Ulrick N, Taft RJ, Ogata T, Ozono K, Matsumoto N, Neubauer BA, Simons C, Vanderver A.

Neurogenetics. 2017 Dec;18(4):185-194. doi: 10.1007/s10048-017-0520-x. Epub 2017 Aug 26.

4.

RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells.

Barutcu AR, Hong D, Lajoie BR, McCord RP, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Imbalzano AN, Stein GS.

Biochim Biophys Acta. 2016 Nov;1859(11):1389-1397. doi: 10.1016/j.bbagrm.2016.08.003. Epub 2016 Aug 9.

5.

Structural organization of the inactive X chromosome in the mouse.

Giorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E, Dekker J.

Nature. 2016 Jul 28;535(7613):575-9. Epub 2016 Jul 18.

6.

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells.

Barutcu AR, Lajoie BR, Fritz AJ, McCord RP, Nickerson JA, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Stein GS, Imbalzano AN.

Genome Res. 2016 Sep;26(9):1188-201. doi: 10.1101/gr.201624.115. Epub 2016 Jul 19.

7.

Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma.

McGeachie MJ, Yates KP, Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT, Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Strunk RC, Weiss ST; CAMP Research Group.

Am J Respir Crit Care Med. 2016 Dec 15;194(12):1465-1474.

8.

Patterns of Growth and Decline in Lung Function in Persistent Childhood Asthma.

McGeachie MJ, Yates KP, Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT, Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Weiss ST, Strunk RC.

N Engl J Med. 2016 May 12;374(19):1842-1852. doi: 10.1056/NEJMoa1513737.

9.

Activation of proto-oncogenes by disruption of chromosome neighborhoods.

Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, Dekker J, Young RA.

Science. 2016 Mar 25;351(6280):1454-1458. doi: 10.1126/science.aad9024. Epub 2016 Mar 3.

10.

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.

Smith EM, Lajoie BR, Jain G, Dekker J.

Am J Hum Genet. 2016 Jan 7;98(1):185-201. doi: 10.1016/j.ajhg.2015.12.002.

11.

The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.

Belton JM, Lajoie BR, Audibert S, Cantaloube S, Lassadi I, Goiffon I, Baù D, Marti-Renom MA, Bystricky K, Dekker J.

Cell Rep. 2015 Dec 1;13(9):1855-67. doi: 10.1016/j.celrep.2015.10.063. Epub 2015 Nov 19.

12.

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.

Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, Heard E, Dekker J, Barillot E.

Genome Biol. 2015 Dec 1;16:259. doi: 10.1186/s13059-015-0831-x.

13.

High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila.

Ramírez F, Lingg T, Toscano S, Lam KC, Georgiev P, Chung HR, Lajoie BR, de Wit E, Zhan Y, de Laat W, Dekker J, Manke T, Akhtar A.

Mol Cell. 2015 Oct 1;60(1):146-62. doi: 10.1016/j.molcel.2015.08.024.

14.

Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells.

Barutcu AR, Lajoie BR, McCord RP, Tye CE, Hong D, Messier TL, Browne G, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Imbalzano AN, Stein GS.

Genome Biol. 2015 Sep 28;16:214. doi: 10.1186/s13059-015-0768-0.

15.

Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis.

Wang X, Le TB, Lajoie BR, Dekker J, Laub MT, Rudner DZ.

Genes Dev. 2015 Aug 1;29(15):1661-75. doi: 10.1101/gad.265876.115.

16.

Condensin-driven remodelling of X chromosome topology during dosage compensation.

Crane E, Bian Q, McCord RP, Lajoie BR, Wheeler BS, Ralston EJ, Uzawa S, Dekker J, Meyer BJ.

Nature. 2015 Jul 9;523(7559):240-4. doi: 10.1038/nature14450. Epub 2015 Jun 1.

17.

The Hitchhiker's guide to Hi-C analysis: practical guidelines.

Lajoie BR, Dekker J, Kaplan N.

Methods. 2015 Jan 15;72:65-75. doi: 10.1016/j.ymeth.2014.10.031. Epub 2014 Nov 6.

18.

Organization of the mitotic chromosome.

Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J.

Science. 2013 Nov 22;342(6161):948-53. doi: 10.1126/science.1236083. Epub 2013 Nov 7.

19.

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.

Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, Lenhard B, Giorgetti L, Heard E, Fisher AG, Flicek P, Dekker J, Merkenschlager M.

Genome Res. 2013 Dec;23(12):2066-77. doi: 10.1101/gr.161620.113. Epub 2013 Sep 3.

20.

Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network.

Reece-Hoyes JS, Pons C, Diallo A, Mori A, Shrestha S, Kadreppa S, Nelson J, Diprima S, Dricot A, Lajoie BR, Ribeiro PS, Weirauch MT, Hill DE, Hughes TR, Myers CL, Walhout AJ.

Mol Cell. 2013 Jul 11;51(1):116-27. doi: 10.1016/j.molcel.2013.05.018. Epub 2013 Jun 20.

21.

Architectural protein subclasses shape 3D organization of genomes during lineage commitment.

Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, Bland MJ, Wagstaff W, Dalton S, McDevitt TC, Sen R, Dekker J, Taylor J, Corces VG.

Cell. 2013 Jun 6;153(6):1281-95. doi: 10.1016/j.cell.2013.04.053. Epub 2013 May 23.

22.

The long-range interaction landscape of gene promoters.

Sanyal A, Lajoie BR, Jain G, Dekker J.

Nature. 2012 Sep 6;489(7414):109-13. doi: 10.1038/nature11279.

23.

Iterative correction of Hi-C data reveals hallmarks of chromosome organization.

Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA.

Nat Methods. 2012 Oct;9(10):999-1003. doi: 10.1038/nmeth.2148. Epub 2012 Sep 2.

24.

HiTC: exploration of high-throughput 'C' experiments.

Servant N, Lajoie BR, Nora EP, Giorgetti L, Chen CJ, Heard E, Dekker J, Barillot E.

Bioinformatics. 2012 Nov 1;28(21):2843-4. doi: 10.1093/bioinformatics/bts521. Epub 2012 Aug 24.

25.

An encyclopedia of mouse DNA elements (Mouse ENCODE).

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB.

Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418.

26.

MORC family ATPases required for heterochromatin condensation and gene silencing.

Moissiard G, Cokus SJ, Cary J, Feng S, Billi AC, Stroud H, Husmann D, Zhan Y, Lajoie BR, McCord RP, Hale CJ, Feng W, Michaels SD, Frand AR, Pellegrini M, Dekker J, Kim JK, Jacobsen SE.

Science. 2012 Jun 15;336(6087):1448-51. doi: 10.1126/science.1221472. Epub 2012 May 3.

27.

Spatial partitioning of the regulatory landscape of the X-inactivation centre.

Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Blüthgen N, Dekker J, Heard E.

Nature. 2012 Apr 11;485(7398):381-5. doi: 10.1038/nature11049.

28.

Spatial organization of the mouse genome and its role in recurrent chromosomal translocations.

Zhang Y, McCord RP, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, Becker MS, Alt FW, Dekker J.

Cell. 2012 Mar 2;148(5):908-21. doi: 10.1016/j.cell.2012.02.002. Epub 2012 Feb 16.

29.

Evidence for transcript networks composed of chimeric RNAs in human cells.

Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR.

PLoS One. 2012;7(1):e28213. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4.

30.

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression.

Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY.

Nature. 2011 Apr 7;472(7341):120-4. doi: 10.1038/nature09819. Epub 2011 Mar 20.

31.

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.

Baù D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA.

Nat Struct Mol Biol. 2011 Jan;18(1):107-14. doi: 10.1038/nsmb.1936. Epub 2010 Dec 5.

32.

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J.

Science. 2009 Oct 9;326(5950):289-93. doi: 10.1126/science.1181369.

33.

My5C: web tools for chromosome conformation capture studies.

Lajoie BR, van Berkum NL, Sanyal A, Dekker J.

Nat Methods. 2009 Oct;6(10):690-1. doi: 10.1038/nmeth1009-690. No abstract available.

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