Resources and challenges for integrative analysis of nuclear architecture data

Authors: Jung, Youngsook L, Kirli, Koray, Alver, Burak H, Park, Peter J

Source: In Current Opinion in Genetics & Development April 2021 67:103-110

Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

Authors: Lee, Soohyun, Bakker, Clara R, Vitzthum, Carl, Alver, Burak H, Park, Peter J

Source: Bioinformatics. 38(6):1729-1731

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100145286723.0x000001&indx=1&recIds=ETOCvdc_100145286723.0x000001

Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation

Authors: Shetty, Ameet, Kallgren, Scott P., Demel, Carina, Maier, Kerstin C., Spatt, Dan, Alver, Burak H., Cramer, Patrick, Park, Peter J., Winston, Fred

Source: In Molecular Cell 6 April 2017 66(1):77-88

Tibanna: software for scalable execution of portable pipelines on the cloud

Authors: Lee, Soohyun, Johnson, Jeremy, Vitzthum, Carl, Kırlı, Koray, Alver, Burak H, Park, Peter J

Source: Bioinformatics. 35(21):4424-4426

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100097107137.0x000001&indx=1&recIds=ETOCvdc_100097107137.0x000001

HiNT: a computational method for detecting copy number variations and translocations from Hi-C data

Authors: Wang, Su, Lee, Soohyun, Chu, Chong, Jain, Dhawal, Kerpedjiev, Peter, Nelson, Geoffrey M., Walsh, Jennifer M., Alver, Burak H., Park, Peter J.

Source: Genome biology. 21(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100171989730.0x000001&indx=1&recIds=ETOCvdc_100171989730.0x000001

Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters

Authors: Tolstorukov, Michael Y., Sansam, Courtney G., Lu, Ping, Koellhoffer, Edward C., Helming, Katherine C., Alver, Burak H., Tillman, Erik J., Evans, Julia A., Wilson, Boris G., Park, Peter J., Roberts, Charles W. M.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2013 Jun . 110(25), 10165-10170.

Access URL: https://www.jstor.org/stable/42706161

HiGlass: web-based visual exploration and analysis of genome interaction maps

Authors: Kerpedjiev, Peter, Abdennur, Nezar, Lekschas, Fritz, McCallum, Chuck, Dinkla, Kasper, Strobelt, Hendrik, Luber, Jacob M., Ouellette, Scott B., Azhir, Alaleh, Kumar, Nikhil, Hwang, Jeewon, Lee, Soohyun, Alver, Burak H., Pfister, Hanspeter, Mirny, Leonid A., Park, Peter J., Gehlenborg, Nils

Source: Genome biology. 19(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100129318290.0x000001&indx=1&recIds=ETOCvdc_100129318290.0x000001

Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

Authors: Rigano, Alessandro, Ehmsen, Shannon, Öztürk, Serkan Utku, Ryan, Joel, Balashov, Alexander, Hammer, Mathias, Kirli, Koray, Boehm, Ulrike, Brown, Claire M., Bellve, Karl, Chambers, James J., Cosolo, Andrea, Coleman, Robert A., Faklaris, Orestis, Fogarty, Kevin E., Guilbert, Thomas, Hamacher, Anna B., Itano, Michelle S., Keeley, Daniel P., Kunis, Susanne, Lacoste, Judith, Laude, Alex, Ma, Willa Y., Marcello, Marco, Montero-Llopis, Paula, Nelson, Glyn, Nitschke, Roland, Pimentel, Jaime A., Weidtkamp-Peters, Stefanie, Park, Peter J., Alver, Burak H., Grunwald, David, Strambio-De-Castillia, Caterina

Source: Nature Methods; December 2021, Vol. 18 Issue: 12 p1489-1495, 7p

The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae.

Authors: Reim, Natalia I, Chuang, James, Jain, Dhawal, Alver, Burak H, Park, Peter J, Winston, Fred

Source: Nucleic Acids Research; 10/9/2020, Vol. 48 Issue 18, p10241-10258, 18p

GiniQC: a measure for quantifying noise in single-cell Hi-C data.

Authors: Horton, Connor A¹ (AUTHOR), Alver, Burak H¹ (AUTHOR), Park, Peter J¹ (AUTHOR) peter_park@hms.harvard.edu

Source: Bioinformatics. 5/1/2020, Vol. 36 Issue 9, p2902-2904. 3p.

Subject Terms: *QUALITY control, *ELECTRONIC data processing, *NOISE, *DATA quality, *SOURCE code, *COMPLEMENT receptors

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Comparative analysis of metazoan chromatin organization.

Authors: Ho, Joshua W. K., Jung, Youngsook L., Liu, Tao, Alver, Burak H., Lee, Soohyun, Ikegami, Kohta, Sohn, Kyung-Ah, Minoda, Aki, Tolstorukov, Michael Y., Appert, Alex, Parker, Stephen C. J., Gu, Tingting, Kundaje, Anshul, Riddle, Nicole C., Bishop, Eric, Egelhofer, Thea A., Hu, Sheng'en Shawn, Alekseyenko, Artyom A., Rechtsteiner, Andreas, Asker, Dalal

Source: Nature. 8/28/2014, Vol. 512 Issue 7515, p449-452. 4p. 1 Diagram, 1 Chart, 5 Graphs.

Subjects: CHROMATIN, PROTEINS, RNA, DNA, DROSOPHILA melanogaster

Comparative analysis of the transcriptome across distant species.

Authors: Gerstein, Mark B., Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B., Davis, Carrie A., Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O., Duff, Michael O., Djebali, Sarah, Alexander, Roger P., Alver, Burak H., Auerbach, Raymond, Bell, Kimberly, Bickel, Peter J., Boeck, Max E.

Source: Nature. 8/28/2014, Vol. 512 Issue 7515, p445-448. 4p. 2 Diagrams, 9 Graphs.

Subjects: RNA sequencing, GENOMICS, DEVELOPMENTAL genetics, ENCODE Project, COMPARATIVE studies, GENE expression

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Author Correction: Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

Authors: Rigano, Alessandro, Ehmsen, Shannon, Öztürk, Serkan Utku, Ryan, Joel, Balashov, Alexander, Hammer, Mathias, Kirli, Koray, Boehm, Ulrike, Brown, Claire M., Bellve, Karl, Chambers, James J., Cosolo, Andrea, Coleman, Robert A., Faklaris, Orestis, Fogarty, Kevin E., Guilbert, Thomas, Hamacher, Anna B., Itano, Michelle S., Keeley, Daniel P., Kunis, Susanne, Lacoste, Judith, Laude, Alex, Ma, Willa Y., Marcello, Marco, Montero-Llopis, Paula, Nelson, Glyn, Nitschke, Roland, Pimentel, Jaime A., Weidtkamp-Peters, Stefanie, Park, Peter J., Alver, Burak H., Grunwald, David, Strambio-De-Castillia, Caterina

Source: Nature Methods; 20210101, Issue: Preprints p1-1, 1p