Items where Community is "Gene Regulation and Inheritance Program"

Group by: Item Type | No Grouping
Jump to: Paper
Number of items at this level: 209.

Paper

Maia-Silva, Diogo, Cunniff, Patrick J, Schier, Allison C, Skopelitis, Damianos, Trousdell, Marygrace C, Moresco, Philip, Gao, Yuan, Kechejian, Vahag, He, Xue-Yan, Sahin, Yunus, Wan, Ledong, Alpsoy, Aktan, Liverpool, Jynelle, Krainer, Adrian R, Egeblad, Mikala, Spector, David L, Fearon, Douglas T, Dos Santos, Camila O, Taatjes, Dylan J, Vakoc, Christopher R (June 2024) Interaction between MED12 and ΔNp63 activates basal identity in pancreatic ductal adenocarcinoma. Nature Genetics. ISSN 1061-4036

Segovia, Danilo, Adams, Dexter W, Hoffman, Nickolas, Safaric Tepes, Polona, Wee, Tse-Luen, Cifani, Paolo, Joshua-Tor, Leemor, Krainer, Adrian R (May 2024) SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23. Proceedings of the National Academy of Sciences of the United States of America, 121 (21). e2322974121. ISSN 0027-8424 (Public Dataset)

Wan, Ledong, Kral, Alexander J, Voss, Dillon, Schäfer, Balázs, Sudheendran, Kavitha, Danielsen, Mathias, Caruthers, Marvin H, Krainer, Adrian R (May 2024) Screening Splice-Switching Antisense Oligonucleotides in Pancreas-Cancer Organoids. Nucleic Acid Therapeutics. ISSN 2159-3337

Ishigami, Yuma, Wong, Mandy S, Martí-Gómez, Carlos, Ayaz, Andalus, Kooshkbaghi, Mahdi, Hanson, Sonya M, McCandlish, David M, Krainer, Adrian R, Kinney, Justin B (February 2024) Specificity, synergy, and mechanisms of splice-modifying drugs. Nature Communications, 15 (1). p. 1880. ISSN 2041-1723 (Public Dataset)

He, Xue-Yan, Gao, Yuan, Ng, David, Michalopoulou, Evdokia, George, Shanu, Adrover, Jose M, Sun, Lijuan, Albrengues, Jean, Daßler-Plenker, Juliane, Han, Xiao, Wan, Ledong, Wu, Xiaoli Sky, Shui, Longling S, Huang, Yu-Han, Liu, Bodu, Su, Chang, Spector, David L, Vakoc, Christopher R, Van Aelst, Linda, Egeblad, Mikala (February 2024) Chronic stress increases metastasis via neutrophil-mediated changes to the microenvironment. Cancer Cell. ISSN 1535-6108

Xiang, Xiyan, Bhowmick, Krishanu, Shetty, Kirti, Ohshiro, Kazufumi, Yang, Xiaochun, Wong, Linda L, Yu, Herbert, Latham, Patricia S, Satapathy, Sanjaya K, Brennan, Christina, Dima, Richard J, Chambwe, Nyasha, Sharifova, Gulru, Cacaj, Fellanza, John, Sahara, Crawford, James M, Huang, Hai, Dasarathy, Srinivasan, Krainer, Adrian R, He, Aiwu R, Amdur, Richard L, Mishra, Lopa (2024) Mechanistically based blood proteomic markers in the TGF-β pathway stratify risk of hepatocellular cancer in patients with cirrhosis. Genes and Cancer, 15. pp. 1-14. ISSN 1947-6019

Hazra, Rasmani, Utama, Raditya, Naik, Payal, Dobin, Alexander, Spector, David L (October 2023) Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA sequencing datasets. Stem Cell Reports. ISSN 2213-6711

Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M, Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L, Hatzigeorgiou, Artemis G, Johnson, Rory, Murphy, Terence D, Pertea, Mihaela, Pruitt, Kim D, Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A, Yandell, Mark, Carninci, Piero, Salzberg, Steven L (October 2023) The status of the human gene catalogue. Nature, 622 (7981). pp. 41-47. ISSN 0028-0836

Qian, Zhe, Song, Dongyan, Ipsaro, Jonathan J, Bautista, Carmelita, Joshua-Tor, Leemor, Yeh, Johannes T-H, Tonks, Nicholas K (September 2023) Manipulating PTPRD function with ectodomain antibodies. Genes and Development. ISSN 0890-9369

Sroka, Martyna W, Skopelitis, Damianos, Vermunt, Marit W, Preall, Jonathan B, El Demerdash, Osama, de Almeida, Larissa MN, Chang, Kenneth, Utama, Raditya, Gryder, Berkley, Caligiuri, Giuseppina, Ren, Diqiu, Nalbant, Benan, Milazzo, Joseph P, Tuveson, David A, Dobin, Alexander, Hiebert, Scott W, Stengel, Kristy R, Mantovani, Roberto, Khan, Javed, Kohli, Rahul M, Shi, Junwei, Blobel, Gerd A, Vakoc, Christopher R (September 2023) Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma. Proceedings of the National Academy of Sciences of USA, 120 (36). e2303859120. ISSN 0027-8424 (Public Dataset)

Girish, Vishruth, Lakhani, Asad A, Thompson, Sarah L, Scaduto, Christine M, Brown, Leanne M, Hagenson, Ryan A, Sausville, Erin L, Mendelson, Brianna E, Kandikuppa, Pranav K, Lukow, Devon A, Yuan, Monet Lou, Stevens, Eric C, Lee, Sophia N, Schukken, Klaske M, Akalu, Saron M, Vasudevan, Anand, Zou, Charles, Salovska, Barbora, Li, Wenxue, Smith, Joan C, Taylor, Alison M, Martienssen, Robert A, Liu, Yansheng, Sun, Ruping, Sheltzer, Jason M (August 2023) Oncogene-like addiction to aneuploidy in human cancers. Science, 381 (6660). eadg4521. ISSN 0036-8075 (Public Dataset)

Lee, Seung Cho, Adams, Dexter W, Ipsaro, Jonathan J, Cahn, Jonathan, Lynn, Jason, Kim, Hyun-Soo, Berube, Benjamin, Major, Viktoria, Calarco, Joseph P, LeBlanc, Chantal, Bhattacharjee, Sonali, Ramu, Umamaheswari, Grimanelli, Daniel, Jacob, Yannick, Voigt, Philipp, Joshua-Tor, Leemor, Martienssen, Robert A (August 2023) Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation. Cell, 186 (19). 4100-4116.e15. ISSN 0092-8674 (Public Dataset)

Fisher, Matthew L, Balinth, Seamus, Hwangbo, Yon, Wu, Caizhi, Ballon, Carlos, Goldberg, Gary L, Mills, Alea A (August 2023) Cancer-associated fibroblasts promote cancer stemness by inducing expression of the chromatin-modifying protein CBX4 in squamous cell carcinoma. Carcinogenesis, 44 (6). pp. 485-496. ISSN 0143-3334

Wan, Ledong, Lin, Kuan-Ting, Rahman, Mohammad Alinoor, Ishigami, Yuma, Wang, Zhikai, Jensen, Mads A, Wilkinson, John E, Park, Youngkyu, Tuveson, David A, Krainer, Adrian R (July 2023) Splicing Factor SRSF1 Promotes Pancreatitis and KRASG12D-Mediated Pancreatic Cancer. Cancer Discovery, 13 (7). pp. 1678-1695. ISSN 2159-8274 (Public Dataset)

Haas, Brian J, Dobin, Alexander, Ghandi, Mahmoud, Van Arsdale, Anne, Tickle, Timothy, Robinson, James T, Gillani, Riaz, Kasif, Simon, Regev, Aviv (May 2023) Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector. Cell Reports: Methods, 3 (5). p. 100467. ISSN 2667-2375

Majdandzic, Antonio, Rajesh, Chandana, Koo, Peter K (May 2023) Correcting gradient-based interpretations of deep neural networks for genomics. Genome Biology, 24 (1). p. 109. ISSN 1474-760X

Lee, Nicholas Keone, Tang, Ziqi, Toneyan, Shushan, Koo, Peter K (May 2023) EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome Biology, 24 (1). p. 105. ISSN 1474-760X

Velt, Amandine, Frommer, Bianca, Blanc, Sophie, Holtgräwe, Daniela, Duchêne, Éric, Dumas, Vincent, Grimplet, Jérôme, Hugueney, Philippe, Kim, Catherine, Lahaye, Marie, Matus, José Tomás, Navarro-Payá, David, Orduña, Luis, Tello-Ruiz, Marcela K, Vitulo, Nicola, Ware, Doreen, Rustenholz, Camille (May 2023) An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype. G3: Genes, Genomes, Genetics, 13 (5). jkad067. ISSN 2160-1836

Jbara, Amina, Lin, Kuan-Ting, Stossel, Chani, Siegfried, Zahava, Shqerat, Haya, Amar-Schwartz, Adi, Elyada, Ela, Mogilevsky, Maxim, Raitses-Gurevich, Maria, Johnson, Jared L, Yaron, Tomer M, Ovadia, Ofek, Jang, Gun Ho, Danan-Gotthold, Miri, Cantley, Lewis C, Levanon, Erez Y, Gallinger, Steven, Krainer, Adrian R, Golan, Talia, Karni, Rotem (May 2023) RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer. Nature, 617 (7959). pp. 147-153. ISSN 0028-0836 (Public Dataset)

Ferrer, Miriam, Anthony, Tracy G, Ayres, Janelle S, Biffi, Giulia, Brown, Justin C, Caan, Bette J, Cespedes Feliciano, Elizabeth M, Coll, Anthony P, Dunne, Richard F, Goncalves, Marcus D, Grethlein, Jonas, Heymsfield, Steven B, Hui, Sheng, Jamal-Hanjani, Mariam, Lam, Jie Min, Lewis, David Y, McCandlish, David, Mustian, Karen M, O'Rahilly, Stephen, Perrimon, Norbert, White, Eileen P, Janowitz, Tobias (April 2023) Cachexia: A systemic consequence of progressive, unresolved disease. Cell, 186 (9). pp. 1824-1845. ISSN 0092-8674

Zhang, Qian, Yang, Lucia, Liu, Ying Hsiu, Wilkinson, John E, Krainer, Adrian R (April 2023) Antisense oligonucleotide therapy for H3.3K27M diffuse midline glioma. Science Translational Medicine, 15 (691). eadd8280. ISSN 1946-6234

Hastings, Michelle L, Krainer, Adrian R (April 2023) RNA therapeutics. RNA, 29 (4). pp. 393-395. ISSN 1355-8382

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 JF, 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, Luo, Ruibang, Mackiewicz, Mark, Meng, Ran, Moore, Jill E, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry E, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob M, Sedlazeck, Fritz J, See, Lei Hoon, Sherman, Rachel M, Shi, Xu, Shi, Minyi, Sloan, Cricket Alicia, Strattan, J Seth, Tan, Zhen, Tanaka, Forrest Y, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Ardlie, Kristin, Cherry, J Michael, Mendenhall, Eric M, Noble, William S, Weng, Zhiping, Levine, Morgan E, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard M, Snyder, Michael P, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael C, Bernstein, Bradley E, Guigó, Roderic, Gingeras, Thomas R, Gerstein, Mark (March 2023) The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell, 186 (7). 1493-1511.e40. ISSN 0092-8674

Meze, Katarina, Axhemi, Armend, Thomas, Dennis R, Doymaz, Ahmet, Joshua-Tor, Leemor (February 2023) A shape-shifting nuclease unravels structured RNA. Nature Structural and Molecular Biology. ISSN 1545-9993 (Public Dataset)

Aggarwal, Disha, Russo, Suzanne, Naik, Payal, Bhatia, Sonam, Spector, David L (February 2023) Establishment and Culture of Patient-Derived Breast Organoids. Journal of Visualized Experiments (192). ISSN 1940-087X

Kim, Young Jin, Krainer, Adrian R (January 2023) Antisense Oligonucleotide Therapeutics for Cystic Fibrosis: Recent Developments and Perspectives. Molecules and Cells, 46 (1). pp. 10-20. ISSN 1016-8478

Gao, Yuan, He, Xue-Yan, Wu, Xiaoli S, Huang, Yu-Han, Toneyan, Shushan, Ha, Taehoon, Ipsaro, Jonathan J, Koo, Peter K, Joshua-Tor, Leemor, Bailey, Kelly M, Egeblad, Mikala, Vakoc, Christopher R (January 2023) ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nature Cell Biology. ISSN 1465-7392 (Public Dataset)

Shrestha, Padmina, Jaganathan, Anbalagan, Huilgol, Dhananjay, Ballon, Carlos, Hwangbo, Yon, Mills, Alea A (January 2023) Chd5 regulates the transcription factor Six3 to promote neuronal differentiation. Stem Cells. sxad002. ISSN 1066-5099 (Public Dataset)

Hu, Yixin, Stillman, Bruce (January 2023) Origins of DNA replication in eukaryotes. Molecular Cell. S1097-2765(22)01203. ISSN 1097-2765

Mattick, John S, Amaral, Paulo P, Carninci, Piero, Carpenter, Susan, Chang, Howard Y, Chen, Ling-Ling, Chen, Runsheng, Dean, Caroline, Dinger, Marcel E, Fitzgerald, Katherine A, Gingeras, Thomas R, Guttman, Mitchell, Hirose, Tetsuro, Huarte, Maite, Johnson, Rory, Kanduri, Chandrasekhar, Kapranov, Philipp, Lawrence, Jeanne B, Lee, Jeannie T, Mendell, Joshua T, Mercer, Timothy R, Moore, Kathryn J, Nakagawa, Shinichi, Rinn, John L, Spector, David L, Ulitsky, Igor, Wan, Yue, Wilusz, Jeremy E, Wu, Mian (January 2023) Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews Molecular Cell Biology. ISSN 1471-0072

Koo, Peter K, Ploenzke, Matt, Anand, Praveen, Paul, Steffan, Majdandzic, Antonio (2023) ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks. Methods in Molecular Biology, 2586. pp. 197-215. ISSN 1064-3745

Sun, Xueqin, Klingbeil, Olaf, Lu, Bin, Wu, Caizhi, Ballon, Carlos, Ouyang, Meng, Wu, Xiaoli S, Jin, Ying, Hwangbo, Yon, Huang, Yu-Han, Somerville, Tim DD, Chang, Kenneth, Park, Jung, Chung, Taemoon, Lyons, Scott K, Shi, Junwei, Vogel, Hannes, Schulder, Michael, Vakoc, Christopher R, Mills, Alea A (December 2022) BRD8 maintains glioblastoma by epigenetic reprogramming of the p53 network. Nature. ISSN 0028-0836

Yu, Allen T, Aggarwal, Disha, Pappin, Darryl, Spector, David L (December 2022) Single Oligonucleotide Capture of RNA And Temperature Elution Series ( SOCRATES ) for Identification of RNA-binding Proteins. Bio-protocol, 12 (24). e4572. ISSN 2331-8325

Sheu, Yi-Jun, Kawaguchi, Risa Karakida, Gillis, Jesse, Stillman, Bruce (December 2022) Prevalent and dynamic binding of the cell cycle checkpoint kinase Rad53 to gene promoters. eLife, 11. e84320. ISSN 2050-084X (Public Dataset)

Moravec, Jiří C, Lanfear, Robert, Spector, David L, Diermeier, Sarah D, Gavryushkin, Alex (December 2022) Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data. Journal of Computational Biology. ISSN 1066-5277

Petti, Samantha, Bhattacharya, Nicholas, Rao, Roshan, Dauparas, Justas, Thomas, Neil, Zhou, Juannan, Rush, Alexander M, Koo, Peter, Ovchinnikov, Sergey (November 2022) End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman. Bioinformatics. ISSN 1367-4803

Hazra, Rasmani, Brine, Lily, Garcia, Libia, Benz, Brian, Chirathivat, Napon, Shen, Michael M, Wilkinson, John Erby, Lyons, Scott K, Spector, David L (November 2022) Platr4 is an early embryonic lncRNA that exerts its function downstream on cardiogenic mesodermal lineage commitment. Developmental Cell, 57 (21). 2450-2468.e7. ISSN 1534-5807

Anderson, Erik W, Jin, Ying, Shih, Andrew, Arazi, Arnon, Goodwin, Sara, Roeser, Julien, Furie, Richard A, Aranow, Cynthia, Volpe, Bruce, Diamond, Betty, Mackay, Meggan (November 2022) Associations between circulating interferon and kynurenine/tryptophan pathway metabolites: support for a novel potential mechanism for cognitive dysfunction in SLE. Lupus Science & Medicine, 9 (1). e000808. ISSN 2053-8790

Majdandzic, Antonio, Rajesh, Chandana, Tang, Amber, Toneyan, Shushan, Labelson, Ethan, Tripathy, Rohit, Koo, Peter K (November 2022) Selecting deep neural networks that yield consistent attribution-based interpretations for genomics. Proc Mach Learn Res, 200. pp. 131-149. ISSN 2640-3498

Balasooriya, Gayan I, Spector, David L (October 2022) Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage. Nature Communications, 13 (1). p. 5984. ISSN 2041-1723

Liang, Yuanxue, Yu, Xiao‐Hong, Anaokar, Sanket, Shi, Hai, Dahl, William B, Cai, Yingqi, Luo, Guangbin, Chai, Jin, Cai, Yuanheng, Mollá‐Morales, Almudena, Altpeter, Fredy, Ernst, Evan, Schwender, Jorg, Martienssen, Robert A, Shanklin, John (October 2022) Engineering Triacylglycerol Accumulation in Duckweed (Lemna japonica). Plant Biotechnology Journal. ISSN 1467-7644

Hazra, Rasmani, Spector, David L (October 2022) Simultaneous visualization of RNA transcripts and proteins in whole-mount mouse preimplantation embryos using single-molecule fluorescence in situ hybridization and immunofluorescence microscopy. Frontiers in Cell and Developmental Biology, 10. ISSN 2296-634X

Auguste, Yohan SS, Ferro, Austin, Kahng, Jessica A, Xavier, Andre M, Dixon, Jessica R, Vrudhula, Uma, Nichitiu, Anne-Sarah, Rosado, Daniele, Wee, Tse-Luen, Pedmale, Ullas V, Cheadle, Lucas (September 2022) Oligodendrocyte precursor cells engulf synapses during circuit remodeling in mice. Nature Neuroscience. ISSN 1097-6256

Fisher, Matthew L, Balinth, Seamus, Mills, Alea A (September 2022) ΔNp63α in cancer: importance and therapeutic opportunities. Trends in Cell Biology. S0962-8924(22)00194. ISSN 0962-8924

Aubert, Juliette, Bellegarde, Fanny, Oltehua-Lopez, Omar, Leblanc, Olivier, Arteaga-Vazquez, Mario A, Martienssen, Robert A, Grimanelli, Daniel (August 2022) AGO104 is a RdDM effector of paramutation at the maize b1 locus. PLoS One, 17 (8). e0273695-e0273695. ISSN 1932-6203

Balinth, Seamus, Fisher, Matthew L, Hwangbo, Yon, Wu, Caizhi, Ballon, Carlos, Sun, Xueqin, Mills, Alea A (July 2022) EZH2 regulates a SETDB1/ΔNp63α axis via RUNX3 to drive a cancer stem cell phenotype in squamous cell carcinoma. Oncogene. ISSN 0950-9232 (Public Dataset)

Marasco, Luciano E, Dujardin, Gwendal, Sousa-Luís, Rui, Liu, Ying Hsiu, Stigliano, Jose N, Nomakuchi, Tomoki, Proudfoot, Nick J, Krainer, Adrian R, Kornblihtt, Alberto R (June 2022) Counteracting chromatin effects of a splicing-correcting antisense oligonucleotide improves its therapeutic efficacy in spinal muscular atrophy. Cell, 185 (12). 2057-2070.e15. ISSN 0092-8674

Kim, Young Jin, Nomakuchi, Tomoki, Papaleonidopoulou, Foteini, Yang, Lucia, Zhang, Qian, Krainer, Adrian R (May 2022) Gene-specific nonsense-mediated mRNA decay targeting for cystic fibrosis therapy. Nature Communications, 13 (1). p. 2978. ISSN 2041-1723

Wu, Xiaoli S, He, Xue-Yan, Ipsaro, Jonathan J, Huang, Yu-Han, Preall, Jonathan B, Ng, David, Shue, Yan Ting, Sage, Julien, Egeblad, Mikala, Joshua-Tor, Leemor, Vakoc, Christopher R (May 2022) OCA-T1 and OCA-T2 are coactivators of POU2F3 in the tuft cell lineage. Nature. ISSN 0028-0836

Gutbrod, MJ, Roche, B, Steinberg, JI, Lakhani, AA, Chang, K, Schorn, AJ, Martienssen, RA (February 2022) Dicer promotes genome stability via the bromodomain transcriptional co-activator BRD4. Nature Communications, 13 (1). p. 1001. ISSN 2041-1723

Bhatia, Sonam, Kramer, Melissa, Russo, Suzanne, Naik, Payal, Arun, Gayatri, Brophy, Kyle, Andrews, Peter, Fan, Cheng, Perou, Charles M, Preall, Jonathan, Ha, Taehoon, Plenker, Dennis, Tuveson, David A, Rishi, Arvind, Wilkinson, John E, McCombie, W Richard, Kostroff, Karen, Spector, David L (February 2022) Patient-derived triple-negative breast cancer organoids provide robust model systems that recapitulate tumor-intrinsic characteristics. Cancer Research. ISSN 0008-5472

Stefanski, Heather E, Xing, Yan, Nicholls, Jemma, Jonart, Leslie, Goren, Emily, Taylor, Patricia A, Mills, Alea A, Riddle, Megan, McGrath, John, Tolar, Jakub, Hollander, Georg A, Blazar, Bruce R (January 2022) P63 targeted deletion under the FOXN1 promoter disrupts pre-and post-natal thymus development, function and maintenance as well as induces severe hair loss. PLoS One, 17 (1). ISSN 1932-6203

Kim, Young Jin, Sivetz, Nicole, Layne, Jessica, Voss, Dillon M, Yang, Lucia, Zhang, Qian, Krainer, Adrian R (January 2022) Exon-skipping antisense oligonucleotides for cystic fibrosis therapy. Proceedings of the National Academy of Sciences of USA, 119 (3). e2114858118-e2114858118. ISSN 0027-8424

Bibel, Brianna, Elkayam, Elad, Silletti, Steve, Komives, Elizabeth, Joshua-Tor, Leemor (January 2022) Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release. Elife, 11 (e76908). ISSN 2050-084x

Ma, Wai Kit, Voss, Dillon M, Scharner, Juergen, Costa, Ana SH, Lin, Kuang-Ting, Jeon, Hyun Yong, Wilkinson, John E, Jackson, Michaela, Rigo, Frank, Bennett, C Frank, Krainer, Adrian R (December 2021) ASO-based PKM splice-switching therapy inhibits hepatocellular carcinoma growth. Cancer Research. canres.0948.2020-canres.0948.2020. ISSN 0008-5472

Hanasoge Somasundara, Amritha Varshini, Moss, Matthew A, Feigman, Mary J, Chen, Chen, Cyrill, Samantha L, Ciccone, Michael F, Trousdell, Marygrace C, Vollbrecht, Macy, Li, Siran, Kendall, Jude, Beyaz, Semir, Wilkinson, John E, Dos Santos, Camila O (December 2021) Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis. Cell Reports, 37 (10). p. 110099. ISSN 2211-1247

Ortiz-Ramírez, Carlos, Guillotin, Bruno, Xu, Xiaosa, Rahni, Ramin, Zhang, Sanqiang, Yan, Zhe, Coqueiro Dias Araujo, Poliana, Demesa-Arevalo, Edgar, Lee, Laura, Van Eck, Joyce, Gingeras, Thomas R, Jackson, David, Gallagher, Kimberly L, Birnbaum, Kenneth D (December 2021) Ground tissue circuitry regulates organ complexity in maize and Setaria. Science, 374 (6572). pp. 1247-1252. ISSN 0036-8075

Naish, Matthew, Alonge, Michael, Wlodzimierz, Piotr, Tock, Andrew J, Abramson, Bradley W, Schmücker, Anna, Mandáková, Terezie, Jamge, Bhagyshree, Lambing, Christophe, Kuo, Pallas, Yelina, Natasha, Hartwick, Nolan, Colt, Kelly, Smith, Lisa M, Ton, Jurriaan, Kakutani, Tetsuji, Martienssen, Robert A, Schneeberger, Korbinian, Lysak, Martin A, Berger, Frédéric, Bousios, Alexandros, Michael, Todd P, Schatz, Michael C, Henderson, Ian R (November 2021) The genetic and epigenetic landscape of the Arabidopsis centromeres. Science, 374 (6569). eabi7489. ISSN 0036-8075

Smedley, Christopher J, Homer, Joshua A, Gialelis, Timothy L, Barrow, Andrew S, Koelln, Rebecca A, Moses, John Edward (November 2021) Accelerated SuFEx Click Chemistry For Modular Synthesis. Angewandte Chemie International Edition. ISSN 1433-7851

Carlston, Colleen, Weinmann, Robin, Stec, Natalia, Abbatemarco, Simona, Schwager, Francoise, Wang, Jing, Ouyang, Huiwu, Ewald, Collin Y, Gotta, Monica, Hammell, Christopher M (November 2021) PQN-59 antagonizes microRNA-mediated repression during post-embryonic temporal patterning and modulates translation and stress granule formation in C. elegans. PLoS Genetics, 17 (11). e1009599. ISSN 1553-7390

Fisher, Matthew L, Balinth, Seamus, Hwangbo, Yon, Wu, Caizhi, Ballon, Carlos, Wilkinson, John E, Goldberg, Gary L, Mills, Alea A (October 2021) BRD4 REGULATES TRANSCRIPTION FACTOR ∆Np63αTO DRIVE A CANCER STEM CELL PHENOTYPE IN SQUAMOUS CELL CARCINOMAS. Cancer Research. canres.0707.2021-canres.0707.2021. ISSN 0008-5472

Zhang, Xian, Guan, Wuqiang, Yang, Tao, Furlan, Alessandro, Xiao, Xiong, Yu, Kai, An, Xu, Galbavy, William, Ramakrishnan, Charu, Deisseroth, Karl, Ritola, Kimberly, Hantman, Adam, He, Miao, Josh Huang, Z, Li, Bo (October 2021) Genetically identified amygdala-striatal circuits for valence-specific behaviors. Nature Neuroscience, 24. pp. 1586-1600. ISSN 1097-6256

Abbatemarco, Simona, Bondaz, Alexandra, Schwager, Francoise, Wang, Jing, Hammell, Christopher M, Gotta, Monica (October 2021) PQN-59 and GTBP-1 contribute to stress granule formation but are not essential for their assembly in C. elegans embryos. Journal of Cell Science. ISSN 0021-9533

Hills-Muckey, Kelly, Martinez, Michael AQ, Stec, Natalia, Hebbar, Shilpa, Saldanha, Joanne, Medwig-Kinney, Taylor N, Moore, Frances EQ, Ivanova, Maria, Morao, Ana, Ward, JD, Moss, Eric G, Ercan, Sevinc, Zinovyeva, Anna Y, Matus, David Q, Hammell, Christopher M (October 2021) An engineered, orthogonal auxin analog/AtTIR1(F79G) pairing improves both specificity and efficacy of the auxin degradation system in Caenorhabditis elegans. Genetics: a periodical record of investigations bearing on heredity and variation. ISSN 1943-2631

Chen, Wei-Chia, Zhou, Juannan, Sheltzer, Jason M, Kinney, Justin B, McCandlish, David M (October 2021) Field-theoretic density estimation for biological sequence space with applications to 5' splice site diversity and aneuploidy in cancer. Proceedings of the National Academy of Sciences of USA, 118 (40). ISSN 1091-6490

Abou-el-Enein, M, Angelis, A, Appelbaum, FR, Andrews, NC, Bates, SE, Bierman, AS, Brenner, MK, Cavazzana, M, Caligiuri, MA, Clevers, H, Cooke, E, Daley, GQ, Dzau, VJ, Ellis, LM, Fineberg, HV, Goldstein, LSB, Gottschalk, S, Hamburg, MA, Ingber, DE, Kohn, DB, Krainer, AR, Maus, MV, Marks, P, Mummery, CL, Pettigrew, RI, Rutter, JL, Teichmann, SA, Terzic, A, Urnov, FD, Williams, DA, Wolchok, JD, Lawler, M, Turtle, CJ, Bauer, G, Ioannidis, JPA (September 2021) Evidence generation and reproducibility in cell and gene therapy research: A call to action. Molecular Therapy - Methods and Clinical Development, 22. pp. 11-14. ISSN 2329-0501 (In Press)

Sun, Lijuan, Kees, Tim, Almeida, Ana Santos, Liu, Bodu, He, Xue-Yan, Ng, David, Han, Xiao, Spector, David L, McNeish, Iain A, Gimotty, Phyllis, Adams, Sylvia, Egeblad, Mikala (September 2021) Activating a collaborative innate-adaptive immune response to control metastasis. Cancer Cell. ISSN 1535-6108

Moore, Keith J. M., Cahill, Jeremy, Aidelberg, Guy, Aronoff, Rachel, Bektaş, Ali, Bezdan, Daniela, Butler, Daniel J., Chittur, Sridar V., Codyre, Martin, Federici, Fernan, Tanner, Nathan A., Tighe, Scott W., True, Randy, Ware, Sarah B., Wyllie, Anne L., Afshin, Evan E., Bendesky, Andres, Chang, Connie B., Dela Rosa, Richard, Elhaik, Eran, Erickson, David, Goldsborough, Andrew S., Grills, George, Hadasch, Kathrin, Hayden, Andrew, Her, Seong-Young, Karl, Julie A., Kim, Chang Hee, Kriegel, Alison J., Kunstman, Thomas, Landau, Zeph, Land, Kevin, Langhorst, Bradley W., Lindner, Ariel B., Mayer, Benjamin E., McLaughlin, Lee A., McLaughlin, Matthew T., Molloy, Jenny, Mozsary, Christopher, Nadler, Jerry L., D'Silva, Melinee, Ng, David, O'Connor, David H., Ongerth, Jerry E., Osuolale, Olayinka, Pinharanda, Ana, Plenker, Dennis, Ranjan, Ravi, Rosbash, Michael, Rotem, Assaf, Segarra, Jacob, Schürer, Stephan, Sherrill-Mix, Scott, Solo-Gabriele, Helena, To, Shaina, Vogt, Merly C., Yu, Albert D., Mason, Christopher E. (September 2021) Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. Journal of Biomolecular Techniques : JBT, 32 (3). pp. 228-275. ISSN 1524-0215

Li, Suhua, Li, Gencheng, Gao, Bing, Pujari, Sidharam P, Chen, Xiaoyan, Kim, Hyunseok, Zhou, Feng, Klivansky, Liana M, Liu, Yi, Driss, Hafedh, Liang, Dong-Dong, Lu, Jianmei, Wu, Peng, Zuilhof, Han, Moses, John, Sharpless, K Barry (August 2021) SuFExable polymers with helical structures derived from thionyl tetrafluoride. Nature Chemistry. ISSN 1755-4330

Kweon, Hyae Yon, Lee, Mi-Ni, Dorfel, Max, Seo, Seungwoon, Gottlieb, Leah, PaPazyan, Thomas, McTiernan, Nina, Ree, Rasmus, Bolton, David, Garcia, Andrew, Flory, Michael, Crain, Jonathan, Sebold, Alison, Lyons, Scott, Ismail, Ahmed, Marchi, Elaine, Sonn, Seong-Keun, Jeong, Se-Jin, Jeon, Sejin, Ju, Shinyeong, Conway, Simon J, Kim, Taesoo, Kim, Hyun-Seok, Lee, Cheolju, Roh, Tae-Young, Arnesen, Thomas, Marmorstein, Ronen, Oh, Gootaeg, Lyon, Gholson J (August 2021) Naa12 compensates for Naa10 in mice in the amino-terminal acetylation pathway. eLife, 10. ISSN 2050-084X

Ajiro, Masahiko, Awaya, Tomonari, Kim, Young Jin, Iida, Kei, Denawa, Masatsugu, Tanaka, Nobuo, Kurosawa, Ryo, Matsushima, Shingo, Shibata, Saiko, Sakamoto, Tetsunori, Studer, Rolenz, Krainer, Adrian R, Hagiwara, Masatoshi (July 2021) Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia. Nature Communications, 12 (1). p. 4507. ISSN 2041-1723

Yu, Jia-Ray, LeRoy, Gary, Bready, Devin, Frenster, Joshua D., Saldaña-Meyer, Ricardo, Jin, Ying, Descostes, Nicolas, Stafford, James M., Placantonakis, Dimitris G., Reinberg, Danny (July 2021) The H3K36me2 writer-reader dependency in H3K27M-DIPG. Science Advances, 7 (29). ISSN 2375-2548

Feng, Xiang, Noguchi, Yasunori, Barbon, Marta, Stillman, Bruce, Speck, Christian, Li, Huilin (June 2021) The structure of ORC–Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6. Nature Communications, 12 (1). ISSN 2041-1723

Giel, Marie-Claire, Barrow, Andrew S, Smedley, Christopher J, Lewis, William, Moses, John E (June 2021) Aminium cation-radical catalysed selective hydration of (E)-aryl enynes. Chemical Communications. ISSN 1359-7345

Truong, Thu H, Benner, Elizabeth A, Hagen, Kyla M, Temiz, Nuri A, Kerkvliet, Carlos Perez, Wang, Ying, Cortes-Sanchez, Emilio, Yang, Chieh-Hsiang, Trousdell, Marygrace C, Pengo, Thomas, Guillen, Katrin P, Welm, Bryan E, Dos Santos, Camila O, Telang, Sucheta, Lange, Carol A, Ostrander, Julie H (June 2021) PELP1/SRC-3-dependent regulation of metabolic PFKFB kinases drives therapy resistant ER+ breast cancer. Oncogene. ISSN 0950-9232

Parent, Jean-Sébastien, Cahn, Jonathan, Herridge, Rowan P, Grimanelli, Daniel, Martienssen, Robert A (June 2021) Small RNAs guide histone methylation in Arabidopsis embryos. Genes and Development. ISSN 0890-9369

Yu, Allen T, Berasain, Carmen, Bhatia, Sonam, Rivera, Keith, Liu, Bodu, Rigo, Frank, Pappin, Darryl J, Spector, David L (May 2021) PHAROH lncRNA regulates Myc translation in hepatocellular carcinoma via sequestering TIAR. eLife, 10. ISSN 2050-084X

Henry, Samantha, Trousdell, Marygrace C, Cyrill, Samantha L, Zhao, Yixin, Feigman, Mary J, Bouhuis, Julia M, Aylard, Dominik A, Siepel, Adam, Dos Santos, Camila O (May 2021) Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland. Journal of Mammary Gland Biology and Neoplasia. ISSN 1083-3021

Koo, Peter K, Majdandzic, Antonio, Ploenzke, Matthew, Anand, Praveen, Paul, Steffan B (May 2021) Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks. PLoS Computational Biology, 17 (5). e1008925. ISSN 1553-7358

Steele, Nina G, Biffi, Giulia, Kemp, Samantha B, Zhang, Yaqing, Drouillard, Donovan, Syu, LiJyun, Hao, Yuan, Oni, Tobiloba E, Brosnan, Erin, Elyada, Ela, Doshi, Abhishek, Hansma, Christa, Espinoza, Carlos, Abbas, Ahmed, The, Stephanie, Irizarry-Negron, Valerie, Halbrook, Christopher J, Franks, Nicole E, Hoffman, Megan T, Brown, Kristee, Carpenter, Eileen S, Nwosu, Zeribe C, Johnson, Craig, Lima, Fatima, Anderson, Michelle A, Park, Youngkyu, Crawford, Howard C, Lyssiotis, Costas A, Frankel, Timothy L, Rao, Arvind, Bednar, Filip, Dlugosz, Andrzej A, Preall, Jonathan B, Tuveson, David A, Allen, Benjamin L, Pasca di Magliano, Marina (April 2021) Inhibition of Hedgehog Signaling Alters Fibroblast Composition in Pancreatic Cancer. Clinical Cancer Research, 27 (7). pp. 2023-2037. ISSN 1078-0432

Ipsaro, Jonathan J, O'Brien, Paul A, Bhattacharya, Shibani, Palmer, Arthur G, Joshua-Tor, Leemor (March 2021) Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons. Cell Reports, 34 (13). p. 108914. ISSN 2211-1247

Hossain, Manzar, Bhalla, Kuhulika, Stillman, Bruce (March 2021) Multiple, short protein binding motifs in ORC1 and CDC6 control the initiation of DNA replication. Molecular Cell. ISSN 1097-2765

Frederiksen, Sabrina B, Holm, Lise L, Larsen, Martin R, Doktor, Thomas K, Andersen, Henriette S, Hastings, Michelle L, Hua, Yimin, Krainer, Adrian R, Andresen, Brage S (March 2021) Identification of SRSF10 as a regulator of SMN2 ISS-N1. Human Mutation, 42 (3). pp. 246-260. ISSN 1059-7794

Koo, Peter K, Ploenzke, Matt (March 2021) Improving representations of genomic sequence motifs in convolutional networks with exponential activations. Nature Machine Intelligence, 3 (3). pp. 258-266. ISSN 2522-5839

Chou, Hsiang-Chen, Bhalla, Kuhulika, Demerdesh, Osama El, Klingbeil, Olaf, Hanington, Kaarina, Aganezov, Sergey, Andrews, Peter, Alsudani, Habeeb, Chang, Kenneth, Vakoc, Christopher R, Schatz, Michael C, McCombie, W Richard, Stillman, Bruce (February 2021) The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure. eLife, 10. ISSN 2050-084X

Vasudevan, Anand, Schukken, Klaske M, Sausville, Erin L, Girish, Vishruth, Adebambo, Oluwadamilare A, Sheltzer, Jason M (February 2021) Aneuploidy as a promoter and suppressor of malignant growth. Nature Reviews Cancer, 21 (2). pp. 89-103. ISSN 1474-175X

Khouider, Souraya, Borges, Filipe, LeBlanc, Chantal, Ungru, Alexander, Schnittger, Arp, Martienssen, Robert, Colot, Vincent, Bouyer, Daniel (January 2021) Male fertility in Arabidopsis requires active DNA demethylation of genes that control pollen tube function. Nature Communications, 12 (1). p. 410. ISSN 2041-1723

Chang, KC, Spector, DL (January 2021) MaTAR25: a long non-coding RNA involved in breast cancer progression. Molecular and Cellular Oncology, 8 (2). p. 1882286. ISSN 2372-3556

He, C., Bozler, J., Janssen, K. A., Wilusz, J. E., Garcia, B. A., Schorn, A. J., Bonasio, R. (January 2021) TET2 chemically modifies tRNAs and regulates tRNA fragment levels. Nature Structural and Molecular Biology, 28 (1). pp. 62-70. ISSN 1545-9993

Michael, Todd P, Ernst, Evan, Hartwick, Nolan, Chu, Philomena, Bryant, Douglas, Gilbert, Sarah, Ortleb, Stefan, Baggs, Erin L, Sree, K Sowjanya, Appenroth, Klaus J, Fuchs, Joerg, Jupe, Florian, Sandoval, Justin P, Krasileva, Ksenia V, Borisjuk, Ljudmylla, Mockler, Todd C, Ecker, Joseph R, Martienssen, Robert A, Lam, Eric (December 2020) Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. Genome Research, 31 (2). pp. 225-238. ISSN 1088-9051

Chang, K. C., Diermeier, S. D., Yu, A. T., Brine, L. D., Russo, S., Bhatia, S., Alsudani, H., Kostroff, K., Bhuiya, T., Brogi, E., Pappin, D. J., Bennett, C. F., Rigo, F., Spector, D. L. (December 2020) MaTAR25 lncRNA regulates the Tensin1 gene to impact breast cancer progression. Nat Commun, 11 (1). p. 6438. ISSN 2041-1723

Stec, N., Doerfel, K., Hills-Muckey, K., Ettorre, V. M., Ercan, S., Keil, W., Hammell, C. M. (December 2020) An Epigenetic Priming Mechanism Mediated by Nutrient Sensing Regulates Transcriptional Output during C. elegans Development. Curr Biol. ISSN 0960-9822

Borges, F., Donoghue, M. T. A., LeBlanc, C., Wear, E. E., Tanurdžić, M., Berube, B., Brooks, A., Thompson, W. F., Hanley-Bowdoin, L., Martienssen, R. A. (November 2020) Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation. Curr Biol, 31 (3). pp. 591-600. ISSN 0960-9822

Ciccone, M. F., Trousdell, M. C., Dos Santos, C. O. (November 2020) Characterization of Organoid Cultures to Study the Effects of Pregnancy Hormones on the Epigenome and Transcriptional Output of Mammary Epithelial Cells. J Mammary Gland Biol Neoplasia, 25 (4). pp. 351-366. ISSN 1083-3021

Hu, Y, Tareen, A., Sheu, Y. J., Ireland, W. T., Speck, C., Li, H., Joshua-Tor, L., Kinney, J. B., Stillman, B. (October 2020) Evolution of DNA replication origin specification and gene silencing mechanisms. Nature Communications, 11 (1). p. 5175. ISSN 2041-1723

Fein, Miriam R, He, Xue-Yan, Almeida, Ana S, Bružas, Emilis, Pommier, Arnaud, Yan, Ran, Eberhardt, Anaïs, Fearon, Douglas T, Van Aelst, Linda, Wilkinson, John Erby, Dos Santos, Camila O, Egeblad, Mikala (October 2020) Cancer cell CCR2 orchestrates suppression of the adaptive immune response. Journal of Experimental Medicine, 217 (10). ISSN 0022-1007

Miyabayashi, Koji, Baker, Lindsey A, Deschênes, Astrid, Traub, Benno, Caligiuri, Giuseppina, Plenker, Dennis, Alagesan, Brinda, Belleau, Pascal, Li, Siran, Kendall, Jude, Jang, Gun Ho, Kawaguchi, Risa Karakida, Somerville, Tim DD, Tiriac, Hervé, Hwang, Chang-Il, Burkhart, Richard A, Roberts, Nicholas J, Wood, Laura D, Hruban, Ralph H, Gillis, Jesse, Krasnitz, Alexander, Vakoc, Christopher R, Wigler, Michael, Notta, Faiyaz, Gallinger, Steven, Park, Youngkyu, Tuveson, David A (October 2020) Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes. Cancer Discovery, 10 (10). pp. 1566-1589. ISSN 2159-8274

Fisher, M. L., Balinth, S., Mills, A. A. (September 2020) p63-related signaling at a glance. J Cell Sci, 133 (17). ISSN 0021-9533 (Print)0021-9533

Aganezov, S., Goodwin, S., Sherman, R. M., Sedlazeck, F. J., Arun, G., Bhatia, S., Lee, I., Kirsche, M., Wappel, R., Kramer, M., Kostroff, K., Spector, D. L., Timp, W., McCombie, W. R., Schatz, M. C. (September 2020) Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. Genome Res, 30 (9). pp. 1258-1273. ISSN 1088-9051 (Print)1088-9051

Jaremko, M. J., On, K. F., Thomas, D. R., Stillman, B., Joshua-Tor, L. (August 2020) The dynamic nature of the human origin recognition complex revealed through five cryoEM structures. Elife, 9. e58622. ISSN 2050-084x

Yuan, Zuanning, Schneider, Sarah, Dodd, Thomas, Riera, A., Bai, Lin, Yan, Chunli, Magdalou, Indiana, Ivanov, Ivaylo, Stillman, Bruce, Li, Huilin, Speck, C. (July 2020) Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6. Proceedings of the National Academy of Sciences of the United States of America, 117 (30). pp. 17747-17756. ISSN 0027-8424

Breschi, A., Muñoz-Aguirre, M., Wucher, V., Davis, C. A., Garrido-Martín, D., Djebali, S., Gillis, J., Pervouchine, D. D., Vlasova, A., Dobin, A., Zaleski, C., Drenkow, J., Danyko, C., Scavelli, A., Reverter, F., Snyder, M. P., Gingeras, T. R., Guigó, R. (July 2020) A limited set of transcriptional programs define major cell types. Genome Res, 30 (7). pp. 1047-1059. ISSN 1088-9051 (Print)1088-9051

Arun, G., Aggarwal, D., Spector, D. L. (June 2020) MALAT1 Long Non-Coding RNA: Functional Implications. Noncoding RNA, 6 (2). E22.

Somerville, T. D. D., Xu, Y., Wu, X. S., Maia-Silva, D., Hur, S. K., de Almeida, L. M. N., Preall, J. B., Koo, P. K., Vakoc, C. R. (May 2020) ZBED2 is an antagonist of interferon regulatory factor 1 and modifies cell identity in pancreatic cancer. Proc Natl Acad Sci U S A, 117 (21). pp. 11471-11482. ISSN 0027-8424 (Print)0027-8424

Lee, J., Shah, M., Ballouz, S., Crow, M., Gillis, J. (May 2020) CoCoCoNet: conserved and comparative co-expression across a diverse set of species. Nucleic Acids Research. ISSN 0305-1048

Gutbrod, M. J., Martienssen, R. A. (May 2020) Conserved chromosomal functions of RNA interference. Nat Rev Genet, 21 (5). pp. 311-331. ISSN 1471-0056

Somerville, T. D. D., Biffi, G., DaBler-Plenker, J., Hur, S.K., He, X.-Y., Vance, K.E., Miyabayashi, K., Xu, Y., Maia-Silva, D., Klingbeil, O., Demerdash, O. E., Preall, J. B., Hollingsworth, M. A., Egeblad, M., Tuveson, D. A., Vakoc, C. R. (April 2020) Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation. Elife, 9. e53381. ISSN 2050-084x (Public Dataset)

Lee, S.C., Ernst, E., Berube, B., Borges, F., Parent, J. S., Ledon, P., Schorn, A., Martienssen, R. A. (April 2020) Arabidopsis Retrotransposon Virus-Like Particles and Their Regulation by Epigenetically Activated Small RNA. Genome Research, 30 (4). pp. 576-588. ISSN 1088-9051

Sheng, L., Rigo, F., Bennett, C. F., Krainer, A. R., Hua, Y. (April 2020) Comparison of the Efficacy of MOE and PMO Modifications of Systemic Antisense Oligonucleotides in a Severe SMA Mouse Model. Nucleic Acids Research, 6 (48). pp. 2853-2865. ISSN 0305-1048 (Public Dataset)

Wheeler, E., Brooks, A.M., Concia, L., Vera, D., Wear, E. E., LeBlanc, C., Ramu, U., Vaughn, M. W., Bass, H., Martienssen, R. A., Thompson, W.F., Hanley-Bowdoin, L. (March 2020) Arabidopsis DNA Replication Initiates in Intergenic, AT-rich Open Chromatin. Plant Physiology. ISSN 0032-0889 (Public Dataset)

Rahman, M. A., Lin, K. T., Bradley, R. K., Abdel-Wahab, O., Krainer, A. R. (March 2020) Recurrent SRSF2 mutations in MDS affect both splicing and NMD. Genes Dev, 34 (5-6). pp. 413-427. ISSN 0890-9369

Sinnakannu, J. R., Lee, K. L., Cheng, S., Li, J., Yu, M., Tan, S. P., Ong, C. C. H., Li, H., Than, H., Anczukow-Camarda, O., Krainer, A. R., Roca, X., Rozen, S. G., Iqbal, J., Yang, H., Chuah, C., Ong, S. T. (February 2020) SRSF1 mediates cytokine-induced impaired imatinib sensitivity in chronic myeloid leukemia. Leukemia, 34 (7). pp. 1787-1798. ISSN 0887-6924

Chang, K. C., Diermeier, S. D., Yu, A. T., Brine, L. D., Russo, S., Bhatia, S., Alsudani, H., Kostroff, K., Bhuiya, T., Brogi, E., Bennett, C. F., Rigo, F., Spector, D. L. (February 2020) MaTAR25 LncRNA Regulates the Tensin1 Gene to Impact Breast Cancer Progression. BioRxiv. (Unpublished)

Koo, PK, Ploenzke, M (February 2020) Deep learning for inferring transcription factor binding sites. Current Opinion in Systems Biology, 19. pp. 16-23. ISSN 2452-3100

Rey-Suarez, Ivan, Wheatley, Brittany A, Koo, Peter, Bhanja, Anshuman, Shu, Zhou, Mochrie, Simon, Song, Wenxia, Shroff, Hari, Upadhyaya, Arpita (January 2020) WASP family proteins regulate the mobility of the B cell receptor during signaling activation. Nature Communications, 11 (1). p. 439. ISSN 2041-1723

Chen, C. C., Li, B., Millman, S. E., Chen, C., Li, X., Morris, J. P. Iv, Mayle, A., Ho, Y. J., Loizou, E., Liu, H., Qin, W., Shah, H., Violante, S., Cross, J. R., Lowe, S. W., Zhang, L. (January 2020) Vitamin B6 Addiction in Acute Myeloid Leukemia. Cancer Cell, 37 (1). pp. 71-84. ISSN 15356108 (ISSN) (Public Dataset)

Rahman, M. A., Krainer, A. R., Abdel-Wahab, O. (January 2020) SnapShot: Splicing Alterations in Cancer. Cell, 180 (1). 208-208.e1. ISSN 0092-8674

Martinez, M. A. Q., Kinney, B. A., Medwig-Kinney, T. N., Ashley, G., Ragle, J. M., Johnson, L., Aguilera, J., Hammell, C. M., Ward, J. D., Matus, D. Q. (January 2020) Rapid Degradation of Caenorhabditis elegans Proteins at Single-Cell Resolution with a Synthetic Auxin. G3 (Bethesda, Md.), 10 (1). pp. 267-280. ISSN 21601836 (ISSN) (Public Dataset)

Tareen, A., Kinney, J. B. (December 2019) Logomaker: beautiful sequence logos in Python. Bioinformatics. ISSN 1367-4803 (Public Dataset)

Scharner, J., Ma, W. K., Zhang, Q., Lin, K. T., Rigo, F., Bennett, C. F., Krainer, A. R. (December 2019) Hybridization-mediated off-target effects of splice-switching antisense oligonucleotides. Nucleic Acids Res, 48 (2). ISSN 0305-1048 (Public Dataset)

Hershlag, A., Peyser, A., Bristow, S. L., Puig, O., Pollock, A., Niknazar, M., Mills, A. A. (December 2019) The potential impact of tumor suppressor genes on human gametogenesis: a case-control study. J Assist Reprod Genet. ISSN 1058-0468

Park, S., Brugiolo, M., Akerman, M., Das, S., Urbanski, L., Geier, A., Kesarwani, A. K., Fan, M., Leclair, N., Lin, K. T., Hu, L., Hua, I., George, J., Muthuswamy, S. K., Krainer, A. R., Anczukow, O. (November 2019) Differential Functions of Splicing Factors in Mammary Transformation and Breast Cancer Metastasis. Cell Rep, 29 (9). 2672-2688.e7. ISSN 2211-1247 (Public Dataset)

Li, S., Kendall, J., Park, S., Wang, Z., Alexander, J., Moffitt, A., Ranade, N., Danyko, C., Gegenhuber, B., Fischer, S., Robinson, B. D., Lepor, H., Tollkuhn, J., Gillis, J., Brouzes, E., Krasnitz, A., Levy, D., Wigler, M. (November 2019) Copolymerization of single-cell nucleic acids into balls of acrylamide gel. Genome Res, 30 (1). pp. 49-61. ISSN 1088-9051 (Public Dataset)

Carter, J. A., Preall, J. B., Atwal, G. S. (October 2019) Bayesian Inference of Allelic Inclusion Rates in the Human T Cell Receptor Repertoire. Cell Syst, 9 (5). pp. 475-482. ISSN 2405-4712 (Public Dataset)

Chen, X., Sun, Y. C., Zhan, H., Kebschull, J. M., Fischer, S., Matho, K., Huang, Z. J., Gillis, J., Zador, A. M. (October 2019) High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing. Cell, 179 (3). 772-786.e19. ISSN 0092-8674 (Public Dataset)

Yoshimi, A., Lin, K. T., Wiseman, D. H., Rahman, M. A., Pastore, A., Wang, B., Lee, S. C., Micol, J. B., Zhang, X. J., de Botton, S., Penard-Lacronique, V., Stein, E. M., Cho, H., Miles, R. E., Inoue, D., Albrecht, T. R., Somervaille, T. C. P., Batta, K., Amaral, F., Simeoni, F., Wilks, D. P., Cargo, C., Intlekofer, A. M., Levine, R. L., Dvinge, H., Bradley, R. K., Wagner, E. J., Krainer, A. R., Abdel-Wahab, O. (October 2019) Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis. Nature, 574 (7777). pp. 273-277. ISSN 0028-0836

Kneuss, E., Munafo, M., Eastwood, E. L., Deumer, U. S., Preall, J. B., Hannon, G. J., Czech, B. (August 2019) Specialization of the Drosophila nuclear export family protein Nxf3 for piRNA precursor export. Genes Dev, 33 (17-18). pp. 1208-1220. ISSN 0890-9369

Carter, J. A., Preall, J. B., Grigaityte, K., Goldfless, S. J., Jeffery, E., Briggs, A. W., Vigneault, F., Atwal, G. S. (July 2019) Single T Cell Sequencing Demonstrates the Functional Role alpha beta TCR Pairing in Cell Lineage and Antigen Specificity. Frontiers in Immunology, 10. Article Number:1516. ISSN 1664-3224

Jung, J., Grant, T., Thomas, D. R., Diehnelt, C. W., Grigorieff, N., Joshua-Tor, L. (June 2019) High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations. Proc Natl Acad Sci U S A, 116 (26). pp. 12828-12832. ISSN 0027-8424

Feng, H., Bao, S., Rahman, M. A., Weyn-Vanhentenryck, S. M., Khan, A., Wong, J., Shah, A., Flynn, E. D., Krainer, A. R., Zhang, C. (June 2019) Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites. Mol Cell, 74 (6). 1189-1204.e6. ISSN 1097-2765

Elyada, E., Bolisetty, M., Laise, P., Flynn, W. F., Courtois, E. T., Burkhart, R. A., Teinor, J. A., Belleau, P., Biffi, G., Lucito, M. S., Sivajothi, S., Armstrong, T. D., Engle, D. D., Yu, K. H., Hao, Y., Wolfgang, C. L., Park, Y., Preall, J., Jaffee, E. M., Califano, A., Robson, P., Tuveson, D. A. (June 2019) Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts. Cancer Discov, 9 (8). pp. 1102-1123. ISSN 2159-8274

Lin, K. T., Krainer, A. R. (May 2019) PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis. Bioinformatics, 35 (23). pp. 5048-5054. ISSN 1367-4803

Kinney, J. B., McCandlish, D. M. (May 2019) Massively Parallel Assays and Quantitative Sequence-Function Relationships. Annu Rev Genomics Hum Genet, 20. pp. 99-127. ISSN 1527-8204

Schorn, A. J., Martienssen, R. (May 2019) Getting in LINE with Replication. Molecular Cell, 74 (3). pp. 415-417. ISSN 10972765 (ISSN)

Arun, G., Spector, D. L. (March 2019) MALAT1 Long Non-Coding RNA and Breast Cancer. RNA Biol, 16 (6). pp. 860-863. ISSN 1547-6286

Scharner, J., Qi, S., Rigo, F., Bennett, C. F., Krainer, A. R. (March 2019) Delivery of GalNAc-Conjugated Splice-Switching ASOs to Non-hepatic Cells through Ectopic Expression of Asialoglycoprotein Receptor. Mol Ther Nucleic Acids, 16. pp. 313-325. ISSN 2162-2531 (Print)

Crow, M., Lim, N., Ballouz, S., Pavlidis, P., Gillis, J. (March 2019) Predictability of human differential gene expression. Proc Natl Acad Sci U S A. ISSN 0027-8424

Stein, C. B., Genzor, P., Mitra, S., Elchert, A. R., Ipsaro, J. J., Benner, L., Sobti, S., Su, Y., Hammell, M., Joshua-Tor, L., Haase, A. D. (February 2019) Decoding the 5' nucleotide bias of PIWI-interacting RNAs. Nat Commun, 10 (1). p. 828. ISSN 2041-1723

Abulwerdi, F. A., Xu, W., Ageeli, A. A., Yonkunas, M. J., Arun, G., Nam, H., Schneekloth, J. S., Dayie, T. K., Spector, D., Baird, N., Le Grice, S. F. J. (February 2019) Selective Small-Molecule Targeting of a Triple Helix Encoded by the Long Noncoding RNA, MALAT1. ACS Chemical Biology, 14 (2). pp. 223-235. ISSN 15548929 (ISSN) (Public Dataset)

Barnes, S. L., Belliveau, N. M., Ireland, W. T., Kinney, J. B., Phillips, R. (February 2019) Mapping DNA sequence to transcription factor binding energy in vivo. PLoS Comput Biol, 15 (2). e1006226. ISSN 1553-734x

Wang, E., Lu, S. X., Pastore, A., Chen, X., Imig, J., Chun-Wei Lee, S., Hockemeyer, K., Ghebrechristos, Y. E., Yoshimi, A., Inoue, D., Ki, M., Cho, H., Bitner, L., Kloetgen, A., Lin, K. T., Uehara, T., Owa, T., Tibes, R., Krainer, A. R., Abdel-Wahab, O., Aifantis, I. (February 2019) Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia. Cancer Cell, 35 (3). 359-384.e7. ISSN 1535-6108

Ando, Y., Elkayam, E., McPherson, R. L., Dasovich, M., Cheng, S. J., Voorneveld, J., Filippov, D. V., Ong, S. E., Joshua-Tor, L., Leung, A. K. L. (January 2019) ELTA: Enzymatic Labeling of Terminal ADP-Ribose. Mol Cell, 73 (4). 845-856 e5. ISSN 1097-2765

Trivedi, Gaurang, Inoue, Daichi, Chen, Cynthia, Bitner, Lillian, Chung, Young Rock, Taylor, Justin, Gönen, Mithat, Wess, Jürgen, Abdel-Wahab, Omar, Zhang, Lingbo (2019) Muscarinic acetylcholine receptor regulates self-renewal of early erythroid progenitors. Science Translational Medicine, 11 (511).

Adams, R. M., Kinney, J. B., Walczak, A. M., Mora, T. (December 2018) Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy. Cell Syst, 8 (1). pp. 86-93. ISSN 2405-4712 (Print)2405-4712

Forcier, T. L., Ayaz, A., Gill, M. S., Jones, D., Phillips, R., Kinney, J. B. (December 2018) Measuring cis-regulatory energetics in living cells using allelic manifolds. eLife, 7. ISSN 2050084X (ISSN)

Lu, H. C., Pollack, H., Lefante, J. J., Mills, A. A., Tian, D. (December 2018) Altered sleep architecture, rapid eye movement (REM) sleep, and neural oscillation in a mouse model of human chromosome 16p11.2 microdeletion. Sleep, 42 (3). ISSN 0161-8105

On, Kin Fan, Jaremko, Matt, Stillman, Bruce, Joshua-Tor, Leemor (December 2018) A structural view of the initiators for chromosome replication. Current Opinion in Structural Biology, 53. pp. 131-139. ISSN 0959-440X

Lu, B., Klingbeil, O., Tarumoto, Y., Somerville, T. D. D., Huang, Y. H., Wei, Y., Wai, D. C., Low, J. K. K., Milazzo, J. P., Wu, X. S., Cao, Z., Yan, X., Demerdash, O. E., Huang, G., Mackay, J. P., Kinney, J. B., Shi, J., Vakoc, C. R. (November 2018) A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence. Cancer Cell, 34 (6). pp. 970-981. ISSN 1535-6108

Biffi, G., Oni, T. E., Spielman, B., Hao, Y., Elyada, E., Park, Y., Preall, J., Tuveson, D. A. (October 2018) IL-1-induced JAK/STAT signaling is antagonized by TGF-beta to shape CAF heterogeneity in pancreatic ductal adenocarcinoma. Cancer Discov, 9 (2). pp. 282-301. ISSN 2159-8274

Chen, W. C., Tareen, A., Kinney, J. B. (October 2018) Density Estimation on Small Data Sets. Physical Review Letters, 121 (16). p. 160605. ISSN 00319007 (ISSN)

Hwang, D. W., Jaganathan, A., Shrestha, P., Jin, Y., El-Amine, N., Wang, S. H., Hammell, M., Mills, A. A. (August 2018) Chromatin-mediated translational control is essential for neural cell fate specification. Life Sci Alliance, 1 (4). e201700016. ISSN 2575-1077

Crow, M., Gillis, J. (August 2018) Co-expression in Single-Cell Analysis: Saving Grace or Original Sin? Trends Genet, 34 (11). pp. 823-831. ISSN 0168-9525 (Print)0168-9525

Posfai, A., Zhou, J., Plotkin, J. B., Kinney, J. B., McCandlish, D. M. (August 2018) Selection for Protein Stability Enriches for Epistatic Interactions. Genes (Basel), 9 (9). ISSN 2073-4425 (Print)2073-4425

Wong, M. S., Kinney, J. B., Krainer, A. R. (August 2018) Quantitative Activity Profile and Context Dependence of All Human 5' Splice Sites. Mol Cell, 71 (6). 1012-1026.e3. ISSN 1097-2765

Tramentozzi, E., Ferraro, P., Hossain, M., Stillman, B., Bianchi, V., Pontarin, G. (July 2018) The dNTP triphosphohydrolase activity of SAMHD1 persists during S-phase when the enzyme is phosphorylated at T592. Cell Cycle, 17 (9). pp. 1102-1114. ISSN 1551-4005

Huang, Y. H., Klingbeil, O., He, X. Y., Wu, X. S., Arun, G., Lu, B., Somerville, T. D. D., Milazzo, J. P., Wilkinson, J. E., Demerdash, O. E., Spector, D. L., Egeblad, M., Shi, J., Vakoc, C. R. (July 2018) POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer. Genes Dev, 32 (13-14). pp. 915-928. ISSN 0890-9369

Aznarez, Isabel, Nomakuchi, Tomoki T., Tetenbaum-Novatt, Jaclyn, Rahman, Mohammad Alinoor, Fregoso, Oliver, Rees, Holly, Krainer, Adrian R. (May 2018) Mechanism of Nonsense-Mediated mRNA Decay Stimulation by Splicing Factor SRSF1. Cell Reports, 23 (7). pp. 2186-2198. ISSN 2211-1247

Ballouz, S., Dobin, A., Gingeras, T. R., Gillis, J. (May 2018) The fractured landscape of RNA-seq alignment: the default in our STARs. Nucleic Acids Res. ISSN 0305-1048

Zhang, T., Wu, Y. C., Mullane, P., Ji, Y. J., Liu, H., He, L., Arora, A., Hwang, H. Y., Alessi, A. F., Niaki, A. G., Periz, G., Guo, L., Wang, H., Elkayam, E., Joshua-Tor, L., Myong, S., Kim, J. K., Shorter, J., Ong, S. E., Leung, A. K. L., Wang, J. (March 2018) FUS Regulates Activity of MicroRNA-Mediated Gene Silencing. Mol Cell, 69 (5). 787-801.e8. ISSN 1097-2765 (Public Dataset)

Crow, M., Paul, A., Ballouz, S., Huang, Z. J., Gillis, J. (February 2018) Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Nat Commun, 9 (1). p. 884. ISSN 2041-1723

Lin, K. T., Ma, W. K., Scharner, J., Liu, Y. R., Krainer, A. R. (February 2018) A human-specific switch of alternatively spliced AFMID isoforms contributes to TP53 mutations and tumor recurrence in hepatocellular carcinoma. Genome Res, 28 (3). pp. 275-284. ISSN 1088-9051

Arun, G., Diermeier, S. D., Spector, D. L. (February 2018) Therapeutic Targeting of Long Non-Coding RNAs in Cancer. Trends Mol Med, 24 (3). pp. 257-277. ISSN 1471-4914

Li, J., Wu, C., Wang, W., He, Y., Elkayam, E., Joshua-Tor, L., Hammond, P. T. (February 2018) Structurally modulated codelivery of siRNA and Argonaute 2 for enhanced RNA interference. Proc Natl Acad Sci U S A, 115 (12). E2696-E2705. ISSN 0027-8424

Krishnan, N., Bonham, C. A., Rus, I. A., Shrestha, O. K., Gauss, C. M., Haque, A., Tocilj, A., Joshua-Tor, L., Tonks, N. K. (January 2018) Harnessing insulin- and leptin-induced oxidation of PTP1B for therapeutic development. Nat Commun, 9 (1). p. 283. ISSN 2041-1723

Noguchi, Y., Yuan, Z., Bai, L., Schneider, S., Zhao, G., Stillman, B., Speck, C., Li, H. (November 2017) Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model. Proc Natl Acad Sci U S A, 114 (45). E9529-9538. ISSN 0027-8424

He, H., Li, Y., Dong, Q., Chang, A. Y., Gao, F., Chi, Z., Su, M., Zhang, F., Ban, H., Martienssen, R., Chen, Y. H., Li, F. (November 2017) Coordinated regulation of heterochromatin inheritance by Dpb3-Dpb4 complex. Proc Natl Acad Sci U S A. ISSN 0027-8424

Roche, B., Arcangioli, B., Martienssen, R. (September 2017) New roles for Dicer in the nucleolus and its relevance to cancer. Cell Cycle, 16 (18). pp. 1643-1653. ISSN 1551-4005

Diermeier, S. D., Spector, D. L. (August 2017) Antisense Oligonucleotide-mediated Knockdown in Mammary Tumor Organoids. Bio Protoc, 7 (16). ISSN 2331-8325 (Print)2331-8325

Li, M. A., Amaral, P. P., Cheung, P., Bergmann, J. H., Kinoshita, M., Kalkan, T., Ralser, M., Robson, S., Meyenn, F. V., Paramor, M., Yang, F., Chen, C., Nichols, J., Spector, D. L., Kouzarides, T., He, L., Smith, A. (August 2017) A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation. Elife, 6. ISSN 2050-084x

Elkayam, Elad, Faehnle, Christopher R., Morales, Marjorie, Sun, Jingchuan, Li, Huilin, Joshua-Tor, Leemor (August 2017) Multivalent Recruitment of Human Argonaute by GW182. Molecular Cell, 67 (4). pp. 646-658. ISSN 1097-2765 (Public Dataset)

Faehnle, C. R., Walleshauser, J., Joshua-Tor, L. (August 2017) Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis. Nat Struct Mol Biol, 24 (8). pp. 658-665. ISSN 1545-9985 (Public Dataset)

Roche, B., Arcangioli, B., Martienssen, R. A. (July 2017) Transcriptional reprogramming in cellular quiescence. RNA Biol, 14 (7). pp. 843-853. ISSN 1547-6286

Schorn, A. J., Gutbrod, M. J., LeBlanc, C., Martienssen, R. (June 2017) LTR-Retrotransposon Control by tRNA-Derived Small RNAs. Cell, 170 (1). pp. 61-71. ISSN 0092-8674 (Public Dataset)

Chang, An-Yun, Castel, Stephane E., Ernst, Evan, Kim, Hyun Soo, Martienssen, Robert A. (June 2017) The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly. Cell Reports, 19 (12). pp. 2477-2489. ISSN 2211-1247

Elkayam, E., Parmar, R., Brown, C. R., Willoughby, J. L., Theile, C. S., Manoharan, M., Joshua-Tor, L. (April 2017) siRNA carrying an (E)-vinylphosphonate moiety at the 5' end of the guide strand augments gene silencing by enhanced binding to human Argonaute-2. Nucleic Acids Res, 45 (6). pp. 3528-3536. ISSN 1362-4962 (Electronic)0305-1048 (Linking) (Public Dataset)

Taniguchi, Y., Kawata, M., Ho Chang, S., Mori, D., Okada, K., Kobayashi, H., Sugita, S., Hosaka, Y., Inui, H., Taketomi, S., Yano, F., Ikeda, T., Akiyama, H., Mills, A. A., Chung, U. I., Tanaka, S., Kawaguchi, H., Saito, T. (March 2017) Regulation of Chondrocyte Survival in Mouse Articular Cartilage by p63. Arthritis and Rheumatology, 69 (3). pp. 598-609. ISSN 2326-5205

Yuan, Z., Riera, A., Bai, L., Sun, J., Nandi, S., Spanos, C., Chen, Z. A., Barbon, M., Rappsilber, J., Stillman, B., Speck, C., Li, H. (March 2017) Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1. Nat Struct Mol Biol, 24 (3). pp. 316-324. ISSN 1545-9985 (Public Dataset)

Ipsaro, J. J., Shen, C., Arai, E., Xu, Y., Kinney, J. B., Joshua-Tor, L., Vakoc, C. R., Shi, J. (February 2017) Rapid generation of drug-resistance alleles at endogenous loci using CRISPR-Cas9 indel mutagenesis. PLoS One, 12 (2). e0172177. ISSN 1932-6203

Senturk, S., Shirole, N. H., Nowak, D. G., Corbo, V., Pal, D., Vaughan, A., Tuveson, D. A., Trotman, L. C., Kinney, J. B., Sordella, R. (February 2017) Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization. Nat Commun, 8. p. 14370. ISSN 2041-1723 (Public Dataset)

Tocilj, A., On, K. F., Yuan, Z., Sun, J., Elkayam, E., Li, H., Stillman, B., Joshua-Tor, L. (January 2017) Structure of the active form of human Origin Recognition Complex and its ATPase motor module. Elife, 6. ISSN 2050-084X (Electronic)2050-084X (Linking) (Public Dataset)

Mills, A. A. (January 2017) The Chromodomain Helicase DNA-Binding Chromatin Remodelers: Family Traits that Protect from and Promote Cancer. Cold Spring Harb Perspect Med. ISSN 2157-1422 (Electronic)2157-1422 (Linking)

Kawata, M., Taniguchi, Y., Mori, D., Yano, F., Ohba, S., Chung, U. I., Shimogori, T., Mills, A. A., Tanaka, S., Saito, T. (2017) Different regulation of limb development by p63 transcript variants. PLoS One, 12 (3). e0174122. ISSN 1932-6203

Zhang, Bin, Mao, Yuntao S., Diermeier, Sarah D., Novikova, Irina V., Nawrocki, Eric P., Jones, Tom A., Lazar, Zsolt, Tung, Chang-Shung, Luo, Weijun, Eddy, Sean R., Sanbonmatsu, Karissa Y., Spector, David L. (2017) Identification and Characterization of a Class of MALAT1-like Genomic Loci. Cell Reports, 19 (8). pp. 1723-1738. ISSN 2211-1247 (Public Dataset)

Adams, R. M., Mora, T., Walczak, A. M., Kinney, J. B. (December 2016) Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. Elife, 5. ISSN 2050-084X (Electronic)2050-084X (Linking) (Public Dataset)

Roche, B., Arcangioli, B., Martienssen, R. A. (October 2016) RNA interference is essential for cellular quiescence. Science, 354 (6313). ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Diermeier, Sarah D, Chang, Kung-Chi, Freier, Susan M, Song, Junyan, El Demerdash, Osama, Krasnitz, Alexander, Rigo, Frank, Bennett, C.  Frank, Spector, David L (September 2016) Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration. Cell Reports, 17 (1). pp. 261-274. ISSN 2211-1247 (Public Dataset)

Allemand, E., Myers, M. P., Garcia-Bernardo, J., Harel-Bellan, A., Krainer, A. R., Muchardt, C. (September 2016) A Broad Set of Chromatin Factors Influences Splicing. PLoS Genet, 12 (9). e1006318. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Anczukow, O., Krainer, A. R. (September 2016) Splicing-factor alterations in cancers. RNA, 22 (9). pp. 1285-301. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

Hossain, M., Stillman, B. (July 2016) Opposing roles for DNA replication initiator proteins ORC1 and CDC6 in control of Cyclin E gene transcription. Elife, 5. ISSN 2050-084X (Electronic)2050-084X (Linking) (Public Dataset)

Bruun, G. H., Doktor, T. K., Borch-Jensen, J., Masuda, A., Krainer, A. R., Ohno, K., Andresen, B. S. (July 2016) Global identification of hnRNP A1 binding sites for SSO-based splicing modulation. BMC Biol, 14 (1). p. 54. ISSN 1741-7007 (Electronic)1741-7007 (Linking)

MacDiarmid, J. A., Langova, V., Bailey, D., Pattison, S. T., Pattison, S. L., Christensen, N., Armstrong, L. R., Brahmbhatt, V. N., Smolarczyk, K., Harrison, M. T., Costa, M., Mugridge, N. B., Sedliarou, I., Grimes, N. A., Kiss, D. L., Stillman, B., Hann, C. L., Gallia, G. L., Graham, R. M., Brahmbhatt, H. (April 2016) Targeted Doxorubicin Delivery to Brain Tumors via Minicells: Proof of Principle Using Dogs with Spontaneously Occurring Tumors as a Model. PLoS One, 11 (4). e0151832. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Liu, Y., Chen, C., Xu, Z., Scuoppo, C., Rillahan, C. D., Gao, J., Spitzer, B., Bosbach, B., Kastenhuber, E. R., Baslan, T., Ackermann, S., Cheng, L., Wang, Q., Niu, T., Schultz, N., Levine, R. L., Mills, A. A., Lowe, S. W. (March 2016) Deletions linked to TP53 loss drive cancer through p53-independent mechanisms. Nature, 531 (7595). pp. 471-475. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Sheu, Y. J., Kinney, J. B., Stillman, B. (March 2016) Concerted activities of Mcm4, Sld3 and Dbf4 in control of origin activation and DNA replication fork progression. Genome Res, 26 (3). pp. 315-330. ISSN 1549-5469 (Electronic)1088-9051 (Linking) (Public Dataset)

Atwal, G. S., Kinney, J. B. (March 2016) Learning Quantitative Sequence–Function Relationships from Massively Parallel Experiments. Journal of Statistical Physics, 162 (5). pp. 1203-1243. ISSN 00224715

Nomakuchi, T. T., Rigo, F., Aznarez, I., Krainer, A. R. (February 2016) Antisense oligonucleotide-directed inhibition of nonsense-mediated mRNA decay. Nat Biotechnol, 34 (2). pp. 164-166. ISSN 1546-1696 (Electronic)1087-0156 (Linking)

Pichugina, T., Sugawara, T., Kaykov, A., Schierding, W., Masuda, K., Uewaki, J., Grand, R. S., Allison, J. R., Martienssen, R. A., Nurse, P., Ueno, M., O'Sullivan, J. M. (January 2016) A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe. Sci Rep, 6. p. 18757. ISSN 2045-2322 (Electronic)2045-2322 (Linking)

Hammell, Christopher M, Hannon, Gregory J (January 2016) Inducing RNAi in Caenorhabditis elegans by Injection of dsRNA. Cold Spring Harbor protocols, 2016 (1). pdb.prot086306. ISSN 1940-3402

Arun, G., Diermeier, S., Akerman, M., Chang, K. C., Wilkinson, J. E., Hearn, S., Kim, Y., MacLeod, A. R., Krainer, A. R., Norton, L., Brogi, E., Egeblad, M., Spector, D. L. (January 2016) Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss. Genes Dev, 30 (1). pp. 34-51. ISSN 1549-5477 (Electronic)0890-9369 (Linking) (Public Dataset)

Breschi, A., Djebali, S., Gillis, J., Pervouchine, D. D., Dobin, A., Davis, C. A., Gingeras, T. R., Guigo, R. (2016) Gene-specific patterns of expression variation across organs and species. Genome Biol, 17 (1). p. 151. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Shen, Chen, Ipsaro, Jonathan J, Shi, Junwei, Milazzo, Joseph P, Wang, Eric, Roe, Jae-Seok, Suzuki, Yutaka, Pappin, Darryl J, Joshua-Tor, Leemor, Vakoc, Christopher R (December 2015) NSD3-Short Is an Adaptor Protein that Couples BRD4 to the CHD8 Chromatin Remodeler. Molecular Cell, 60 (6). pp. 847-859. ISSN 1097-2765

Sanchez, Carlos G, Teixeira, Felipe Karam, Czech, Benjamin, Preall, Jonathan B, Zamparini, Andrea L, Seifert, Jessica R K., Malone, Colin D, Hannon, Gregory J, Lehmann, Ruth (December 2015) Regulation of Ribosome Biogenesis and Protein Synthesis Controls Germline Stem Cell Differentiation. Cell Stem Cell, 18 (2). pp. 276-290. ISSN 1934-5909

Zepeda-Mendoza, C. J., Mukhopadhyay, S., Wong, E. S., Harder, N., Splinter, E., de Wit, E., Eckersley-Maslin, M. A., Ried, T., Eils, R., Rohr, K., Mills, A., de Laat, W., Flicek, P., Sengupta, A. M., Spector, D. L. (November 2015) Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. BMC Genomics, 16 (1). p. 982. ISSN 1471-2164 (Electronic)1471-2164 (Linking)

Anczukow, O., Krainer, A. R. (October 2015) The spliceosome, a potential Achilles heel of MYC-driven tumors. Genome Med, 7 (1). p. 107. ISSN 1756-994X (Electronic)1756-994X (Linking)

Yu, Y., Gu, J., Jin, Y., Luo, Y., Preall, J. B., Ma, J., Czech, B., Hannon, G. J. (October 2015) Panoramix enforces piRNA-dependent cotranscriptional silencing. Science, 350 (6258). pp. 339-42. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Anczukow, O., Akerman, M., Clery, A., Wu, J., Shen, C., Shirole, N. H., Raimer, A., Sun, S., Jensen, M. A., Hua, Y., Allain, F. H., Krainer, A. R. (October 2015) SRSF1-Regulated Alternative Splicing in Breast Cancer. Mol Cell, 60 (1). pp. 105-17. ISSN 1097-4164 (Electronic)1097-2765 (Linking)

Stillman, B. (July 2015) Reconsidering DNA Polymerases at the Replication Fork in Eukaryotes. Molecular Cell, 59 (2). pp. 139-141. ISSN 1097-2765

Ren, J., Castel, S. E., Martienssen, R. A. (July 2015) Dicer in action at replication-transcription collisions. Mol Cell Oncol, 2 (3). e991224. ISSN 2372-3556 (Electronic)2372-3556 (Linking)

Tian, D., Stoppel, L. J., Heynen, A. J., Lindemann, L., Jaeschke, G., Mills, A. A., Bear, M. F. (January 2015) Contribution of mGluR5 to pathophysiology in a mouse model of human chromosome 16p11.2 microdeletion. Nature Neuroscience, 18. pp. 182-184. ISSN 1097-6256

Guo, Ya, Xu, Quan, Canzio, Daniele, Shou, Jia, Li, Jinhuan, Gorkin, David U, Jung, Inkyung, Wu, Haiyang, Zhai, Yanan, Tang, Yuanxiao, Lu, Yichao, Wu, Yonghu, Jia, Zhilian, Li, Wei, Zhang, Michael Q, Ren, Bing, Krainer, Adrian R, Maniatis, Tom, Wu, Qiang (2015) CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell, 162 (4). pp. 900-910. ISSN 0092-8674

This list was generated on Fri Jul 12 07:17:29 2024 EDT.
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving