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1.

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.

Rozowsky, Joel; Gao, Jiahao; Borsari, Beatrice; Yang, Yucheng T; Galeev, Timur; Gürsoy, Gamze; Epstein, Charles B; Xiong, Kun; Xu, Jinrui; Li, Tianxiao; Liu, Jason; Yu, Keyang; Berthel, Ana; Chen, Zhanlin; Navarro, Fabio; Sun, Maxwell S; Wright, James; Chang, Justin; Cameron, Christopher J F; Shoresh, Noam; Gaskell, Elizabeth; Drenkow, Jorg; Adrian, Jessika; Aganezov, Sergey; Aguet, François; Balderrama-Gutierrez, Gabriela; Banskota, Samridhi; Corona, Guillermo Barreto; Chee, Sora; Chhetri, Surya B; Cortez Martins, Gabriel Conte; Danyko, Cassidy; Davis, Carrie A; Farid, Daniel; Farrell, Nina P; Gabdank, Idan; Gofin, Yoel; Gorkin, David U; Gu, Mengting; Hecht, Vivian; Hitz, Benjamin C; Issner, Robbyn; Jiang, Yunzhe; Kirsche, Melanie; Kong, Xiangmeng; Lam, Bonita R; Li, Shantao; Li, Bian; Li, Xiqi; Lin, Khine Zin.

Cell; 186(7): 1493-1511.e40, 2023 03 30.

Artículo en Inglés | MEDLINE | ID: mdl-37001506

2.

Multicenter integrated analysis of noncoding CRISPRi screens.

Yao, David; Tycko, Josh; Oh, Jin Woo; Bounds, Lexi R; Gosai, Sager J; Lataniotis, Lazaros; Mackay-Smith, Ava; Doughty, Benjamin R; Gabdank, Idan; Schmidt, Henri; Guerrero-Altamirano, Tania; Siklenka, Keith; Guo, Katherine; White, Alexander D; Youngworth, Ingrid; Andreeva, Kalina; Ren, Xingjie; Barrera, Alejandro; Luo, Yunhai; Yardimci, Galip Gürkan; Tewhey, Ryan; Kundaje, Anshul; Greenleaf, William J; Sabeti, Pardis C; Leslie, Christina; Pritykin, Yuri; Moore, Jill E; Beer, Michael A; Gersbach, Charles A; Reddy, Timothy E; Shen, Yin; Engreitz, Jesse M; Bassik, Michael C; Reilly, Steven K.

Nat Methods; 21(4): 723-734, 2024 Apr.

Artículo en Inglés | MEDLINE | ID: mdl-38504114

3.

Recompleting the Caenorhabditis elegans genome.

Yoshimura, Jun; Ichikawa, Kazuki; Shoura, Massa J; Artiles, Karen L; Gabdank, Idan; Wahba, Lamia; Smith, Cheryl L; Edgley, Mark L; Rougvie, Ann E; Fire, Andrew Z; Morishita, Shinichi; Schwarz, Erich M.

Genome Res; 29(6): 1009-1022, 2019 06.

Artículo en Inglés | MEDLINE | ID: mdl-31123080

4.

New developments on the Encyclopedia of DNA Elements (ENCODE) data portal.

Luo, Yunhai; Hitz, Benjamin C; Gabdank, Idan; Hilton, Jason A; Kagda, Meenakshi S; Lam, Bonita; Myers, Zachary; Sud, Paul; Jou, Jennifer; Lin, Khine; Baymuradov, Ulugbek K; Graham, Keenan; Litton, Casey; Miyasato, Stuart R; Strattan, J Seth; Jolanki, Otto; Lee, Jin-Wook; Tanaka, Forrest Y; Adenekan, Philip; O'Neill, Emma; Cherry, J Michael.

Nucleic Acids Res; 48(D1): D882-D889, 2020 01 08.

Artículo en Inglés | MEDLINE | ID: mdl-31713622

5.

The Encyclopedia of DNA elements (ENCODE): data portal update.

Davis, Carrie A; Hitz, Benjamin C; Sloan, Cricket A; Chan, Esther T; Davidson, Jean M; Gabdank, Idan; Hilton, Jason A; Jain, Kriti; Baymuradov, Ulugbek K; Narayanan, Aditi K; Onate, Kathrina C; Graham, Keenan; Miyasato, Stuart R; Dreszer, Timothy R; Strattan, J Seth; Jolanki, Otto; Tanaka, Forrest Y; Cherry, J Michael.

Nucleic Acids Res; 46(D1): D794-D801, 2018 01 04.

Artículo en Inglés | MEDLINE | ID: mdl-29126249

6.

ENCODE data at the ENCODE portal.

Sloan, Cricket A; Chan, Esther T; Davidson, Jean M; Malladi, Venkat S; Strattan, J Seth; Hitz, Benjamin C; Gabdank, Idan; Narayanan, Aditi K; Ho, Marcus; Lee, Brian T; Rowe, Laurence D; Dreszer, Timothy R; Roe, Greg; Podduturi, Nikhil R; Tanaka, Forrest; Hong, Eurie L; Cherry, J Michael.

Nucleic Acids Res; 44(D1): D726-32, 2016 Jan 04.

Artículo en Inglés | MEDLINE | ID: mdl-26527727

7.

A streamlined tethered chromosome conformation capture protocol.

Gabdank, Idan; Ramakrishnan, Sreejith; Villeneuve, Anne M; Fire, Andrew Z.

BMC Genomics; 17: 274, 2016 Apr 01.

Artículo en Inglés | MEDLINE | ID: mdl-27036078

8.

The RNAmute web server for the mutational analysis of RNA secondary structures.

Churkin, Alexander; Gabdank, Idan; Barash, Danny.

Nucleic Acids Res; 39(Web Server issue): W92-9, 2011 Jul.

Artículo en Inglés | MEDLINE | ID: mdl-21478166

9.

The ENCODE Uniform Analysis Pipelines.

Hitz, Benjamin C; Jin-Wook, Lee; Jolanki, Otto; Kagda, Meenakshi S; Graham, Keenan; Sud, Paul; Gabdank, Idan; Strattan, J Seth; Sloan, Cricket A; Dreszer, Timothy; Rowe, Laurence D; Podduturi, Nikhil R; Malladi, Venkat S; Chan, Esther T; Davidson, Jean M; Ho, Marcus; Miyasato, Stuart; Simison, Matt; Tanaka, Forrest; Luo, Yunhai; Whaling, Ian; Hong, Eurie L; Lee, Brian T; Sandstrom, Richard; Rynes, Eric; Nelson, Jemma; Nishida, Andrew; Ingersoll, Alyssa; Buckley, Michael; Frerker, Mark; Kim, Daniel S; Boley, Nathan; Trout, Diane; Dobin, Alex; Rahmanian, Sorena; Wyman, Dana; Balderrama-Gutierrez, Gabriela; Reese, Fairlie; Durand, Neva C; Dudchenko, Olga; Weisz, David; Rao, Suhas S P; Blackburn, Alyssa; Gkountaroulis, Dimos; Sadr, Mahdi; Olshansky, Moshe; Eliaz, Yossi; Nguyen, Dat; Bochkov, Ivan; Shamim, Muhammad Saad.

bioRxiv; 2023 Apr 06.

Artículo en Inglés | MEDLINE | ID: mdl-37066421

10.

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.

Reese, Fairlie; Williams, Brian; Balderrama-Gutierrez, Gabriela; Wyman, Dana; Çelik, Muhammed Hasan; Rebboah, Elisabeth; Rezaie, Narges; Trout, Diane; Razavi-Mohseni, Milad; Jiang, Yunzhe; Borsari, Beatrice; Morabito, Samuel; Liang, Heidi Yahan; McGill, Cassandra J; Rahmanian, Sorena; Sakr, Jasmine; Jiang, Shan; Zeng, Weihua; Carvalho, Klebea; Weimer, Annika K; Dionne, Louise A; McShane, Ariel; Bedi, Karan; Elhajjajy, Shaimae I; Upchurch, Sean; Jou, Jennifer; Youngworth, Ingrid; Gabdank, Idan; Sud, Paul; Jolanki, Otto; Strattan, J Seth; Kagda, Meenakshi S; Snyder, Michael P; Hitz, Ben C; Moore, Jill E; Weng, Zhiping; Bennett, David; Reinholdt, Laura; Ljungman, Mats; Beer, Michael A; Gerstein, Mark B; Pachter, Lior; Guigó, Roderic; Wold, Barbara J; Mortazavi, Ali.

bioRxiv; 2023 May 16.

Artículo en Inglés | MEDLINE | ID: mdl-37292896

11.

The ENCODE Uniform Analysis Pipelines.

Hitz, Benjamin C; Lee, Jin-Wook; Jolanki, Otto; Kagda, Meenakshi S; Graham, Keenan; Sud, Paul; Gabdank, Idan; Strattan, J Seth; Sloan, Cricket A; Dreszer, Timothy; Rowe, Laurence D; Podduturi, Nikhil R; Malladi, Venkat S; Chan, Esther T; Davidson, Jean M; Ho, Marcus; Miyasato, Stuart; Simison, Matt; Tanaka, Forrest; Luo, Yunhai; Whaling, Ian; Hong, Eurie L; Lee, Brian T; Sandstrom, Richard; Rynes, Eric; Nelson, Jemma; Nishida, Andrew; Ingersoll, Alyssa; Buckley, Michael; Frerker, Mark; Kim, Daniel S; Boley, Nathan; Trout, Diane; Dobin, Alex; Rahmanian, Sorena; Wyman, Dana; Balderrama-Gutierrez, Gabriela; Reese, Fairlie; Durand, Neva C; Dudchenko, Olga; Weisz, David; Rao, Suhas S P; Blackburn, Alyssa; Gkountaroulis, Dimos; Sadr, Mahdi; Olshansky, Moshe; Eliaz, Yossi; Nguyen, Dat; Bochkov, Ivan; Shamim, Muhammad Saad.

Res Sq; 2023 Jul 19.

Artículo en Inglés | MEDLINE | ID: mdl-37503119

12.

Preferential translation of Hsp83 in Leishmania requires a thermosensitive polypyrimidine-rich element in the 3' UTR and involves scanning of the 5' UTR.

David, Maya; Gabdank, Idan; Ben-David, Miriam; Zilka, Alon; Orr, Irit; Barash, Danny; Shapira, Michal.

RNA; 16(2): 364-74, 2010 Feb.

Artículo en Inglés | MEDLINE | ID: mdl-20040590

13.

FineStr: a web server for single-base-resolution nucleosome positioning.

Gabdank, Idan; Barash, Danny; Trifonov, Edward N.

Bioinformatics; 26(6): 845-6, 2010 Mar 15.

Artículo en Inglés | MEDLINE | ID: mdl-20106816

14.

Energy minimization methods applied to riboswitches: a perspective and challenges.

Barash, Danny; Gabdank, Idan.

RNA Biol; 7(1): 90-7, 2010.

Artículo en Inglés | MEDLINE | ID: mdl-20061789

15.

The ENCODE Portal as an Epigenomics Resource.

Jou, Jennifer; Gabdank, Idan; Luo, Yunhai; Lin, Khine; Sud, Paul; Myers, Zachary; Hilton, Jason A; Kagda, Meenakshi S; Lam, Bonita; O'Neill, Emma; Adenekan, Philip; Graham, Keenan; Baymuradov, Ulugbek K; R Miyasato, Stuart; Strattan, J Seth; Jolanki, Otto; Lee, Jin-Wook; Litton, Casey; Y Tanaka, Forrest; Hitz, Benjamin C; Cherry, J Michael.

Curr Protoc Bioinformatics; 68(1): e89, 2019 12.

Artículo en Inglés | MEDLINE | ID: mdl-31751002

16.

Prevention of data duplication for high throughput sequencing repositories.

Gabdank, Idan; Chan, Esther T; Davidson, Jean M; Hilton, Jason A; Davis, Carrie A; Baymuradov, Ulugbek K; Narayanan, Aditi; Onate, Kathrina C; Graham, Keenan; Miyasato, Stuart R; Dreszer, Timothy R; Strattan, J Seth; Jolanki, Otto; Tanaka, Forrest Y; Hitz, Benjamin C; Sloan, Cricket A; Cherry, J Michael.

Database (Oxford); 20182018 01 01.

Artículo en Inglés | MEDLINE | ID: mdl-29688363

17.

In silico design of small RNA switches.

Avihoo, Assaf; Gabdank, Idan; Shapira, Michal; Barash, Danny.

IEEE Trans Nanobioscience; 6(1): 4-11, 2007 Mar.

Artículo en Inglés | MEDLINE | ID: mdl-17393844

18.

Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens.

Shoura, Massa J; Gabdank, Idan; Hansen, Loren; Merker, Jason; Gotlib, Jason; Levene, Stephen D; Fire, Andrew Z.

G3 (Bethesda); 7(10): 3295-3303, 2017 10 05.

Artículo en Inglés | MEDLINE | ID: mdl-28801508

19.

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.

Hitz, Benjamin C; Rowe, Laurence D; Podduturi, Nikhil R; Glick, David I; Baymuradov, Ulugbek K; Malladi, Venkat S; Chan, Esther T; Davidson, Jean M; Gabdank, Idan; Narayana, Aditi K; Onate, Kathrina C; Hilton, Jason; Ho, Marcus C; Lee, Brian T; Miyasato, Stuart R; Dreszer, Timothy R; Sloan, Cricket A; Strattan, J Seth; Tanaka, Forrest Y; Hong, Eurie L; Cherry, J Michael.

PLoS One; 12(4): e0175310, 2017.

Artículo en Inglés | MEDLINE | ID: mdl-28403240

20.

Tracing ancient mRNA hairpins.

Gabdank, Idan; Barash, Danny; Trifonov, Edward N.

J Biomol Struct Dyn; 24(2): 163-9, 2006 Oct.

Artículo en Inglés | MEDLINE | ID: mdl-16928139

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The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.

Multicenter integrated analysis of noncoding CRISPRi screens.

Recompleting the Caenorhabditis elegans genome.

New developments on the Encyclopedia of DNA Elements (ENCODE) data portal.

The Encyclopedia of DNA elements (ENCODE): data portal update.

ENCODE data at the ENCODE portal.

A streamlined tethered chromosome conformation capture protocol.

The RNAmute web server for the mutational analysis of RNA secondary structures.

The ENCODE Uniform Analysis Pipelines.

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.

The ENCODE Uniform Analysis Pipelines.

Preferential translation of Hsp83 in Leishmania requires a thermosensitive polypyrimidine-rich element in the 3' UTR and involves scanning of the 5' UTR.

FineStr: a web server for single-base-resolution nucleosome positioning.

Energy minimization methods applied to riboswitches: a perspective and challenges.

The ENCODE Portal as an Epigenomics Resource.

Prevention of data duplication for high throughput sequencing repositories.

In silico design of small RNA switches.

Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens.

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.

Tracing ancient mRNA hairpins.