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The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers
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SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation
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HiNT: a computational method for detecting copy number variations and translocations from Hi-C data
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Published in Genome Biology (23.03.2020)
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MNase titration reveals differences between nucleosome occupancy and chromatin accessibility
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Published in Nature communications (06.05.2016)
Published in Nature communications (06.05.2016)
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Comparative analysis of metazoan chromatin organization
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Published in Nature (London) (28.08.2014)
Published in Nature (London) (28.08.2014)
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The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae
Reim, Natalia I, Chuang, James, Jain, Dhawal, Alver, Burak H, Park, Peter J, Winston, Fred
Published in Nucleic acids research (09.10.2020)
Published in Nucleic acids research (09.10.2020)
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The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data
Reiff, Sarah B., Schroeder, Andrew J., Kırlı, Koray, Cosolo, Andrea, Bakker, Clara, Mercado, Luisa, Lee, Soohyun, Veit, Alexander D., Balashov, Alexander K., Vitzthum, Carl, Ronchetti, William, Pitman, Kent M., Johnson, Jeremy, Ehmsen, Shannon R., Kerpedjiev, Peter, Abdennur, Nezar, Imakaev, Maxim, Öztürk, Serkan Utku, Çamoğlu, Uğur, Mirny, Leonid A., Gehlenborg, Nils, Alver, Burak H., Park, Peter J.
Published in Nature communications (02.05.2022)
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Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters
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.
Published in Proceedings of the National Academy of Sciences - PNAS (18.06.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (18.06.2013)
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Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming
West, Jason A., Cook, April, Alver, Burak H., Stadtfeld, Matthias, Deaton, Aimee M., Hochedlinger, Konrad, Park, Peter J., Tolstorukov, Michael Y., Kingston, Robert E.
Published in Nature communications (27.08.2014)
Published in Nature communications (27.08.2014)
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Spt6 Regulates Intragenic and Antisense Transcription, Nucleosome Positioning, and Histone Modifications Genome-Wide in Fission Yeast
DeGennaro, Christine M., Alver, Burak H., Marguerat, Samuel, Stepanova, Ekaterina, Davis, Christopher P., Bähler, Jürg, Park, Peter J., Winston, Fred
Published in Molecular and Cellular Biology (01.12.2013)
Published in Molecular and Cellular Biology (01.12.2013)
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Author Correction: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data
Reiff, Sarah B., Schroeder, Andrew J., Kırlı, Koray, Cosolo, Andrea, Bakker, Clara, Mercado, Luisa, Lee, Soohyun, Veit, Alexander D., Balashov, Alexander K., Vitzthum, Carl, Ronchetti, William, Pitman, Kent M., Johnson, Jeremy, Ehmsen, Shannon R., Kerpedjiev, Peter, Abdennur, Nezar, Imakaev, Maxim, Öztürk, Serkan Utku, Çamoğlu, Uğur, Mirny, Leonid A., Gehlenborg, Nils, Alver, Burak H., Park, Peter J.
Published in Nature communications (02.11.2022)
Published in Nature communications (02.11.2022)
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Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation
Shetty, Ameet, Kallgren, Scott P., Demel, Carina, Maier, Kerstin C., Spatt, Dan, Alver, Burak H., Cramer, Patrick, Park, Peter J., Winston, Fred
Published in Molecular cell (06.04.2017)
Published in Molecular cell (06.04.2017)
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Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs
Lee, Soohyun, Bakker, Clara R, Vitzthum, Carl, Alver, Burak H, Park, Peter J
Published in Bioinformatics (04.03.2022)
Published in Bioinformatics (04.03.2022)
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Resources and challenges for integrative analysis of nuclear architecture data
Jung, Youngsook L, Kirli, Koray, Alver, Burak H, Park, Peter J
Published in Current opinion in genetics & development (01.04.2021)
Published in Current opinion in genetics & development (01.04.2021)
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Tibanna: software for scalable execution of portable pipelines on the cloud
Lee, Soohyun, Johnson, Jeremy, Vitzthum, Carl, Kırlı, Koray, Alver, Burak H, Park, Peter J
Published in Bioinformatics (01.11.2019)
Published in Bioinformatics (01.11.2019)
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Comparative analysis of the transcriptome across distant species
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., Boley, Nathan P., Booth, Benjamin W., Cherbas, Lucy, Cherbas, Peter, Di, Chao, Dobin, Alex, Drenkow, Jorg, Ewing, Brent, Fang, Gang, Fastuca, Megan, Feingold, Elise A., Frankish, Adam, Gao, Guanjun, Good, Peter J., Guigó, Roderic, Hammonds, Ann, Harrow, Jen, Hoskins, Roger A., Howald, Cédric, Hu, Long, Huang, Haiyan, Hubbard, Tim J. P., Huynh, Chau, Jha, Sonali, Kasper, Dionna, Kato, Masaomi, Kaufman, Thomas C., Kitchen, Robert R., Ladewig, Erik, Lagarde, Julien, Lai, Eric, Leng, Jing, Lu, Zhi, MacCoss, Michael, May, Gemma, McWhirter, Rebecca, Merrihew, Gennifer, Miller, David M., Mortazavi, Ali, Murad, Rabi, Oliver, Brian, Olson, Sara, Park, Peter J., Pazin, Michael J., Perrimon, Norbert, Pervouchine, Dmitri, Reinke, Valerie, Reymond, Alexandre, Robinson, Garrett, Samsonova, Anastasia, Saunders, Gary I., Schlesinger, Felix, Sethi, Anurag, Slack, Frank J., Spencer, William C., Stoiber, Marcus H., Strasbourger, Pnina, Tanzer, Andrea, Thompson, Owen A., Wan, Kenneth H., Wang, Guilin, Wang, Huaien, Watkins, Kathie L., Wen, Jiayu, Wen, Kejia, Xue, Chenghai, Yang, Li, Yip, Kevin, Zaleski, Chris, Zhang, Yan, Zheng, Henry, Brenner, Steven E., Graveley, Brenton R., Celniker, Susan E., Gingeras, Thomas R., Waterston, Robert
Published in Nature (London) (28.08.2014)
Published in Nature (London) (28.08.2014)
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Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications
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
Published in Nature methods (01.12.2021)
Published in Nature methods (01.12.2021)
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ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice
Mathur, Radhika, Alver, Burak H, San Roman, Adrianna K, Wilson, Boris G, Wang, Xiaofeng, Agoston, Agoston T, Park, Peter J, Shivdasani, Ramesh A, Roberts, Charles W M
Published in Nature genetics (01.02.2017)
Published in Nature genetics (01.02.2017)
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