Publications

NSD2 overexpression drives clustered chromatin and transcriptional changes in insulated domains

Priscillia Lhoumaud, Sana Badri, Javier Rodriguez Hernaez, Gunjan Sethia, Andreas Kloetgen, MacIntosh Cornwell, Sourya Bhattacharyya Ferhat Ay, Richard Bonneau, Aristotelis Tsirigos & Jane A. Skok

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Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression

William W. Greenwald, He Li, Paola Benaglio, David Jakubosky, Hiroko Matsui, Anthony Schmitt, Siddarth Selvaraj, Matteo D’Antonio, Agnieszka D’Antonio-Chronowska, Erin N. Smith & Kelly A. Frazer

Click Below For Arima Genomics’ interviews with authors Kelly Frazer and Bill Greenwald

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Spatial co-fragmentation pattern of cell-free DNA recapitulates in vivo chromatin organization and identifies tissues-of-origin

Yaping Liu, Tzu-Yu Liu, David E Weinberg, Brandon W White, Chris J De La Torre, Catherine L Tan, Anthony D Schmitt, Siddarth Selvaraj, Vy Tran, Louise C Laurent, Luc Cabel, Francois-Clement Bidard, Girish Putcha, Imran S Haque

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Disease and phenotype relevant genetic variants identified from histone acetylomes in human hearts

Tan Wilson Lek Wen, George Anene, Eleanor Wong, Hui San Tan, Banfang Pan, Mick Lee, Matias Autio, Michael Morley, Kenneth Margulies, Thomas Cappola, Marie Loh, John Chambers, Shyam Prabhakar, Roger Foo

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RNA interactions with CTCF are essential for its proper function

Ricardo Saldana-Meyer, Javier Rodriguez-Hernaez, Mayilaadumveettil Nishana, Karina Jacome-Lopez, Elphege P. Nora, Benoit G. Bruneau, Mayra Furlan-Magaril, Jane Skok, Danny Reinberg

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Integrating Hi-C links with assembly graphs for chromosome-scale assembly

Jay Ghurye, Arang Rhie, Brian P. Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M. Phillippy, Sergey Koren

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Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk

Prashanth Rajarajan, Tyler Borrman, Will Liao, Nadine Schrode, Erin Flaherty, Charlize Casiño, Samuel Powell, Chittampalli Yashaswini, Elizabeth A. LaMarca, Bibi Kassim, Behnam Javidfar, Sergio Espeso-Gil, Aiqun Li, Hyejung Won, Daniel H. Geschwind, Seok-Man Ho, Matthew MacDonald, Gabriel E. Hoffman, Panos Roussos, Bin Zhang, Chang-Gyu Hahn, Zhiping Weng, Kristen J. Brennand, Schahram Akbarian (2018)

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Agnostic detection of genomic alterations by holistic DNA structural interrogation.

Shultzaberger RK, Abrams RE, Sullivan CJ, Schmitt AD, Thompson TWJ, Dresios J (2018)

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Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

Verena M. Link, Sascha H. Duttke, Hyun B. Chun, Inge R. Holtman, Emma Westin, Marten A. Hoeksema, Yohei Abe, Dylan Skola, Casey E. Romanoski, Jenhan Tao, Gregory J. Fonseca, Ty D. Troutman, Nathanael J. Spann, Tobias Strid, Mashito Sakai, Miao Yu, Rong Hu, Rongxin Fang, Dirk Metzler, Bing Ren, Christopher K. Glass (2018)

Pub Link
Highly-accurate chromosome-length human genome assembly via hybrid analyses of Oxford Nanopore and Arima-HiC

Arima-HiC when combined with contigs from Oxford Nanopore generates highly accurate and chromosome-length genome assemblies. To access open-source software developed by this team, see below: