Search Results - "Lajoie, Bryan R."

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing by Servant, Nicolas, Varoquaux, Nelle, Lajoie, Bryan R, Viara, Eric, Chen, Chong-Jian, Vert, Jean-Philippe, Heard, Edith, Dekker, Job, Barillot, Emmanuel

“…HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation…”
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The long-range interaction landscape of gene promoters by Sanyal, Amartya, Lajoie, Bryan R., Jain, Gaurav, Dekker, Job

“…Chromosome conformation capture carbon copy (5C) is used to look at the relationships between functional elements and distal target genes in 1% of the human…”
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Heterochromatin drives compartmentalization of inverted and conventional nuclei by Falk, Martin, Feodorova, Yana, Naumova, Natalia, Imakaev, Maxim, Lajoie, Bryan R., Leonhardt, Heinrich, Joffe, Boris, Dekker, Job, Fudenberg, Geoffrey, Solovei, Irina, Mirny, Leonid A.

“…The nucleus of mammalian cells displays a distinct spatial segregation of active euchromatic and inactive heterochromatic regions of the genome 1 , 2 . In…”
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Organization of the Mitotic Chromosome by Naumova, Natalia, Imakaev, Maxim, Fudenberg, Geoffrey, Zhan, Ye, Lajoie, Bryan R., Mirny, Leonid A., Dekker, Job

“…Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a century their internal organization remains largely unsolved. We…”
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Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations by Zhang, Yu, McCord, Rachel Patton, Ho, Yu-Jui, Lajoie, Bryan R., Hildebrand, Dominic G., Simon, Aline C., Becker, Michael S., Alt, Frederick W., Dekker, Job

“…The extent to which the three-dimensional organization of the genome contributes to chromosomal translocations is an important question in cancer genomics. We…”
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Structural organization of the inactive X chromosome in the mouse by Giorgetti, Luca, Lajoie, Bryan R., Carter, Ava C., Attia, Mikael, Zhan, Ye, Xu, Jin, Chen, Chong Jian, Kaplan, Noam, Chang, Howard Y., Heard, Edith, Dekker, Job

“…An in-depth analysis of the structure, chromatin accessibility and expression status of the mouse inactive X (Xi) chromosome provides insights into the…”
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Iterative correction of Hi-C data reveals hallmarks of chromosome organization by Imakaev, Maxim, Fudenberg, Geoffrey, McCord, Rachel Patton, Naumova, Natalia, Goloborodko, Anton, Lajoie, Bryan R, Dekker, Job, Mirny, Leonid A

“…ICE (iterative correction and eigenvector decomposition) provides insight into inter- and intrachromosome interaction patterns. Extracting biologically…”
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Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus by Smith, Emily M., Lajoie, Bryan R., Jain, Gaurav, Dekker, Job

“…Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while,…”
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Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment by Phillips-Cremins, Jennifer E., Sauria, Michael E.G., Sanyal, Amartya, Gerasimova, Tatiana I., Lajoie, Bryan R., Bell, Joshua S.K., Ong, Chin-Tong, Hookway, Tracy A., Guo, Changying, Sun, Yuhua, Bland, Michael J., Wagstaff, William, Dalton, Stephen, McDevitt, Todd C., Sen, Ranjan, Dekker, Job, Taylor, James, Corces, Victor G.

“…Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate…”
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Activation of proto-oncogenes by disruption of chromosome neighborhoods by Hnisz, Denes, Weintraub, Abraham S., Day, Daniel S., Valton, Anne-Laure, Bak, Rasmus O., Li, Charles H., Goldmann, Johanna, Lajoie, Bryan R., Fan, Zi Peng, Sigova, Alla A., Reddy, Jessica, Borges-Rivera, Diego, Lee, Tong Ihn, Jaenisch, Rudolf, Porteus, Matthew H., Dekker, Job, Young, Richard A.

“…Oncogenes are activated through well-known chromosomal alterations such as gene fusion, translocation, and focal amplification. In light of recent evidence…”
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Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis by Wang, Xindan, Le, Tung B K, Lajoie, Bryan R, Dekker, Job, Laub, Michael T, Rudner, David Z

“…SMC condensin complexes play a central role in compacting and resolving replicated chromosomes in virtually all organisms, yet how they accomplish this remains…”
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ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions by Dolzhenko, Egor, Deshpande, Viraj, Schlesinger, Felix, Krusche, Peter, Petrovski, Roman, Chen, Sai, Emig-Agius, Dorothea, Gross, Andrew, Narzisi, Giuseppe, Bowman, Brett, Scheffler, Konrad, van Vugt, Joke J F A, French, Courtney, Sanchis-Juan, Alba, Ibáñez, Kristina, Tucci, Arianna, Lajoie, Bryan R, Veldink, Jan H, Raymond, F Lucy, Taft, Ryan J, Bentley, David R, Eberle, Michael A

“…Abstract Summary We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to…”
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Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments by Seitan, Vlad C, Faure, Andre J, Zhan, Ye, McCord, Rachel Patton, Lajoie, Bryan R, Ing-Simmons, Elizabeth, Lenhard, Boris, Giorgetti, Luca, Heard, Edith, Fisher, Amanda G, Flicek, Paul, Dekker, Job, Merkenschlager, Matthias

“…Chromosome conformation capture approaches have shown that interphase chromatin is partitioned into spatially segregated Mb-sized compartments and sub-Mb-sized…”
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Measuring the reproducibility and quality of Hi-C data by Yardımcı, Galip Gürkan, Ozadam, Hakan, Sauria, Michael E G, Ursu, Oana, Yan, Koon-Kiu, Yang, Tao, Chakraborty, Abhijit, Kaul, Arya, Lajoie, Bryan R, Song, Fan, Zhan, Ye, Ay, Ferhat, Gerstein, Mark, Kundaje, Anshul, Li, Qunhua, Taylor, James, Yue, Feng, Dekker, Job, Noble, William S

“…Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and…”
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Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells by Barutcu, A Rasim, Lajoie, Bryan R, McCord, Rachel P, Tye, Coralee E, Hong, Deli, Messier, Terri L, Browne, Gillian, van Wijnen, Andre J, Lian, Jane B, Stein, Janet L, Dekker, Job, Imbalzano, Anthony N, Stein, Gary S

“…Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been…”
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ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data by Dolzhenko, Egor, Bennett, Mark F, Richmond, Phillip A, Trost, Brett, Chen, Sai, van Vugt, Joke J F A, Nguyen, Charlotte, Narzisi, Giuseppe, Gainullin, Vladimir G, Gross, Andrew M, Lajoie, Bryan R, Taft, Ryan J, Wasserman, Wyeth W, Scherer, Stephen W, Veldink, Jan H, Bentley, David R, Yuen, Ryan K C, Bahlo, Melanie, Eberle, Michael A

“…Repeat expansions are responsible for over 40 monogenic disorders, and undoubtedly more pathogenic repeat expansions remain to be discovered. Existing methods…”
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Highly structured homolog pairing reflects functional organization of the Drosophila genome by AlHaj Abed, Jumana, Erceg, Jelena, Goloborodko, Anton, Nguyen, Son C., McCole, Ruth B., Saylor, Wren, Fudenberg, Geoffrey, Lajoie, Bryan R., Dekker, Job, Mirny, Leonid A., Wu, C.-ting

“…Trans -homolog interactions have been studied extensively in Drosophila , where homologs are paired in somatic cells and transvection is prevalent…”
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HiTC: exploration of high-throughput 'C' experiments by SERVANT, Nicolas, LAJOIE, Bryan R, NORA, Elphège P, GIORGETTI, Luca, CHEN, Chong-Jian, HEARD, Edith, DEKKER, Job, BARILLOT, Emmanuel

“…The R/Bioconductor package HiTC facilitates the exploration of high-throughput 3C-based data. It allows users to import and export 'C' data, to transform,…”
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MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing by Moissiard, Guillaume, Cokus, Shawn J., Cary, Joshua, Feng, Suhua, Billi, Allison C., Stroud, Hume, Husmann, Dylan, Zhan, Ye, Lajoie, Bryan R., McCord, Rachel Patton, Hale, Christopher J., Feng, Wei, Michaels, Scott D., Frand, Alison R., Pellegrini, Matteo, Dekker, Job, Kim, John K., Jacobsen, Steven E.

“…Transposable elements (TEs) and DNA repeats are commonly targeted by DNA and histone methylation to achieve epigenetic gene silencing. We isolated mutations in…”
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The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos by Erceg, Jelena, AlHaj Abed, Jumana, Goloborodko, Anton, Lajoie, Bryan R., Fudenberg, Geoffrey, Abdennur, Nezar, Imakaev, Maxim, McCole, Ruth B., Nguyen, Son C., Saylor, Wren, Joyce, Eric F., Senaratne, T. Niroshini, Hannan, Mohammed A., Nir, Guy, Dekker, Job, Mirny, Leonid A., Wu, C.-ting

“…Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans…”
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