Items where Community is "Hammell M. lab"

Paper

O'Neill, Kathryn, Shaw, Regina, Bolger, Isobel, NYGC ALS Consortium, Tam, Oliver H, Phatnani, Hemali, Gale Hammell, Molly (March 2025) ALS molecular subtypes are a combination of cellular and pathological features learned by deep multiomics classifiers. Cell Reports, 44 (3). p. 115402. ISSN 2211-1247 (Public Dataset)

Elhussein, Ahmed, Baymuradov, Ulugbek, NYGC ALS Consortium, Elhadad, Noémie, Natarajan, Karthik, Gürsoy, Gamze (September 2024) A framework for sharing of clinical and genetic data for precision medicine applications. Nature Medicine. ISSN 1078-8956 (Public Dataset)

Tonelli, Claudia, Yordanov, Georgi N, Hao, Yuan, Deschênes, Astrid, Hinds, Juliene, Belleau, Pascal, Klingbeil, Olaf, Brosnan, Erin, Doshi, Abhishek, Park, Youngkyu, Hruban, Ralph H, Vakoc, Christopher R, Dobin, Alexander, Preall, Jonathan, Tuveson, David A (January 2024) A mucus production programme promotes classical pancreatic ductal adenocarcinoma. Gut. ISSN 0017-5749

Torre, Denis, Fstkchyan, Yesai S, Ho, Jessica Sook Yuin, Cheon, Youngseo, Patel, Roosheel S, Degrace, Emma J, Mzoughi, Slim, Schwarz, Megan, Mohammed, Kevin, Seo, Ji-Seon, Romero-Bueno, Raquel, Demircioglu, Deniz, Hasson, Dan, Tang, Weijing, Mahajani, Sameehan U, Campisi, Laura, Zheng, Simin, Song, Won-Suk, Wang, Ying-Chih, Shah, Hardik, Francoeur, Nancy, Soto, Juan, Salfati, Zelda, Weirauch, Matthew T, Warburton, Peter, Beaumont, Kristin, Smith, Melissa L, Mulder, Lubbertus, Villalta, S Armando, Kessenbrock, Kai, Jang, Cholsoon, Lee, Daeyoup, De Rubeis, Silvia, Cobos, Inma, Tam, Oliver, Hammell, Molly Gale, Seldin, Marcus, Shi, Yongsheng, Basu, Uttiya, Sebastiano, Vittorio, Byun, Minji, Sebra, Robert, Rosenberg, Brad R, Benner, Chris, Guccione, Ernesto, Marazzi, Ivan (December 2023) Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Molecular Cell, 83 (23). 4255-4271.e9. ISSN 1097-2765 (Public Dataset)

Mou, Haiwei, Eskiocak, Onur, Özler, Kadir A, Gorman, Megan, Yue, Junjiayu, Jin, Ying, Wang, Zhikai, Gao, Ya, Janowitz, Tobias, Meyer, Hannah V, Yu, Tianxiong, Wilkinson, John E, Kucukural, Alper, Ozata, Deniz M, Beyaz, Semir (January 2023) CRISPR-induced exon skipping of β-catenin reveals tumorigenic mutants driving distinct subtypes of liver cancer. Journal of Pathology. ISSN 0022-3417

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

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

Šušnjar, Urša, Škrabar, Neva, Brown, Anna-Leigh, Abbassi, Yasmine, Phatnani, Hemali, NYGC ALS Consortium, Cortese, Andrea, Cereda, Cristina, Bugiardini, Enrico, Cardani, Rosanna, Meola, Giovanni, Ripolone, Michela, Moggio, Maurizio, Romano, Maurizio, Secrier, Maria, Fratta, Pietro, Buratti, Emanuele (April 2022) Cell environment shapes TDP-43 function with implications in neuronal and muscle disease. Communications Biology, 5 (1). p. 314. ISSN 2399-3642

Brown, Anna-Leigh, Wilkins, Oscar G, Keuss, Matthew J, Hill, Sarah E, Zanovello, Matteo, Lee, Weaverly Colleen, Bampton, Alexander, Lee, Flora CY, Masino, Laura, Qi, Yue A, Bryce-Smith, Sam, Gatt, Ariana, Hallegger, Martina, Fagegaltier, Delphine, Phatnani, Hemali, NYGC ALS Consortium, Newcombe, Jia, Gustavsson, Emil K, Seddighi, Sahba, Reyes, Joel F, Coon, Steven L, Ramos, Daniel, Schiavo, Giampietro, Fisher, Elizabeth MC, Raj, Towfique, Secrier, Maria, Lashley, Tammaryn, Ule, Jernej, Buratti, Emanuele, Humphrey, Jack, Ward, Michael E, Fratta, Pietro (February 2022) TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A. Nature, 603 (7899). pp. 131-137. ISSN 0028-0836

Phatnani, H, Kwan, J, Sareen, D, Broach, JR, Simmons, Z, Arcila-Londono, X, Lee, EB, Van Deerlin, VM, Shneider, NA, Fraenkel, E, Ostrow, LW, Baas, F, Zaitlen, N, Berry, JD, Malaspina, A, Fratta, P, Cox, GA, Thompson, LM, Finkbeiner, S, Dardiotis, E, Miller, TM, Chandran, S, Pal, S, Hornstein, E, MacGowan, DJ, Heiman-Patterson, T, Hammell, MG, Patsopoulos, NA, Butovsky, O, Dubnau, J, Nath, A, Bowser, R, Harms, M, Poss, M, Phillips-Cremins, J, Crary, J, Atassi, N, Lange, DJ, Adams, DJ, Stefanis, L, Gotkine, M, Baloh, RH, Babu, S, Raj, T, Paganoni, S, Shalem, O, Smith, C, Zhang, B, Harris, B, Broce, I, Drory, V, Ravits, J, McMillan, C, Menon, V, Wu, L, Altschuler, S, Li, J, Lim, RG, Kaye, JA, Dardov, V, Coyne, AN, Wu, J, Milani, P, Cheng, A, Thompson, TG, Ornelas, L, Frank, A, Adam, M, Banuelos, MG, Casale, M, Cox, V, Escalante-Chong, R, Daigle, JG, Gomez, E, Hayes, L, Holewenski, R, Lei, S, Lenail, A, Lima, L, Mandefro, B, Matlock, A, Panther, L, Patel-Murray, NL, Pham, J, Ramamoorthy, D, Sachs, K, Shelley, B, Stocksdale, J, Trost, H, Wilhelm, M, Venkatraman, V, Wassie, BT, Wyman, S, Yang, S, Van Eyk, JE, Lloyd, TE, Finkbeiner, S, Rothstein, JD, Svendsen, CN (November 2021) An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients. iScience, 24 (11). p. 103221. ISSN 2589-0042

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

Dewan, R, Chia, R, Ding, J, Hickman, RA, Stein, TD, Abramzon, Y, Ahmed, S, Sabir, MS, Portley, MK, Tucci, A, Ibáñez, K, Shankaracharya, FNU, Keagle, P, Rossi, G, Caroppo, P, Tagliavini, F, Waldo, ML, Johansson, PM, Nilsson, CF, Adeleye, A, Alba, C, Bacikova, D, Hupalo, DN, Martinez, EMG, Pollard, HB, Sukumar, G, Soltis, AR, Tuck, M, Zhang, X, Wilkerson, MD, Smith, BN, Ticozzi, N, Fallini, C, Gkazi, AS, Topp, SD, Kost, J, Scotter, EL, Kenna, KP, Miller, JW, Tiloca, C, Vance, C, Danielson, EW, Troakes, C, Colombrita, C, Al-Sarraj, S, Lewis, EA, King, A, Calini, D, Pensato, V, Castellotti, B, de Belleroche, J, Baas, F, ten Asbroek, ALMA, Sapp, PC, McKenna-Yasek, D, McLaughlin, RL, Polak, M, Asress, S, Esteban-Pérez, J, Muñoz-Blanco, JL, Stevic, Z, D'Alfonso, S, Mazzini, L, Comi, GP, Del Bo, R, Ceroni, M, Gagliardi, S, Querin, G, Bertolin, C, van Rheenen, W, Diekstra, FP, Rademakers, R, van Blitterswijk, M, Boylan, KB, Lauria, G, Duga, S, Corti, S, Cereda, C, Corrado, L, Sorarù, G, Williams, KL, Nicholson, GA, Blair, IP, Leblond-Manry, C, Rouleau, GA, Hardiman, O, Morrison, KE, Veldink, JH, van den Berg, LH, Al-Chalabi, A, Pall, H, Shaw, PJ, Turner, MR, Talbot, K, Taroni, F, García-Redondo, A, Wu, Z, Gellera, C, Ratti, A, Brown, RH (February 2021) Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis. Neuron, 109 (3). 448-460.e4. ISSN 0896-6273

Rupert, D.D., Nowlan, A.C., Tam, O. H., Hammell, M. G. (May 2020) Ten Simple Rules for Running a Successful women-in-STEM Organization on an Academic Campus. PLoS Comput Biol, 16 (5). e1007754. ISSN 1553-734x

O'Neill, K., Brocks, D., Hammell, M. G. (March 2020) Mobile Genomics: Tools and Techniques for Tackling Transposons. Philos Trans R Soc Lond B Biol Sci, 375 (1795). ISSN 0962-8436

Rupert, Deborah, Nowlan, Alexandra, Tam, Oliver, Hammell, Molly Gale (February 2020) Methods for Running a Successful Women-in-STEM Organization on an Academic Campus. bioRxiv. (Unpublished)

Okamura, Eiichi, Tam, Oliver H, Posfai, Eszter, Li, Lingyu, Cockburn, Katie, Lee, Cheryl QE, Garner, Jodi, Rossant, Janet (November 2019) Esrrb function is required for proper primordial germ cell development in presomite stage mouse embryos. Developmental Biology, 455 (2). pp. 382-392. ISSN 0012-1606

Tam, O. H., Rozhkov, N. V., Shaw, R., Kim, D., Hubbard, I., Fennessey, S., Propp, N., Fagegaltier, D., Harris, B. T., Ostrow, L. W., Phatnani, H., Ravits, J., Dubnau, J., Gale Hammell, M. (October 2019) Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia. Cell Rep, 29 (5). 1164-1177.e5.

Lee, C. H., Yu, J. R., Granat, J., Saldana-Meyer, R., Andrade, J., LeRoy, G., Jin, Y., Lund, P., Stafford, J. M., Garcia, B. A., Ueberheide, B., Reinberg, D. (September 2019) Automethylation of PRC2 promotes H3K27 methylation and is impaired in H3K27M pediatric glioma. Genes Dev, 33 (19-20). pp. 1428-1440. ISSN 0890-9369

Tam, O. H., Ostrow, L. W., Hammell, M. G. (July 2019) Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease. Mob DNA, 10. p. 32. ISSN 1759-8753 (Print)

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

Utama, Raditya, Bastian, Anja, Sadagopan, Narayanan, Jin, Ying, Antoniou, Eric, Gao, Qing, Huang, Yinghui J, Gopalakrishna-Pillai, Sailesh, Lee, Peter P, Atwal, Gurinder S (February 2019) Cell non-autonomous interactions during non-immune stromal progression in the breast tumor microenvironment. BioRxiv. (Unpublished)

Anaparthy, N., Ho, Y. J., Martelotto, L., Hammell, M., Hicks, J. (January 2019) Single-Cell Applications of Next-Generation Sequencing. Cold Spring Harb Perspect Med, 9 (10). ISSN 2157-1422

Bourque, G., Burns, K. H., Gehring, M., Gorbunova, V., Seluanov, A., Hammell, M., Imbeault, M., Izsvak, Z., Levin, H. L., Macfarlan, T. S., Mager, D. L., Feschotte, C. (November 2018) Ten things you should know about transposable elements. Genome Biol, 19 (1). p. 199. ISSN 1474-7596

O'Neill, K., Liao, W. W., Patel, A., Hammell, M. G. (October 2018) TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma. Frontiers in Genetics, 9. Article Number: 461 . ISSN 1664-8021

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

Ho, Y. J., Anaparthy, N., Molik, D., Mathew, G., Aicher, T., Patel, A., Hicks, J., Gale Hammell, M. (July 2018) Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations. Genome Res, 28 (9). pp. 1353-1363. ISSN 1088-9051

Conlon, E. G., Fagegaltier, D., Agius, P., Davis-Porada, J., Gregory, J., Hubbard, I., Kang, K., Kim, D., Phatnani, H., Shneider, N. A., Manley, J. L., Kwan, J., Sareen, D., Broach, J. R., Simmons, Z., Arcila-Londono, X., Lee, E. B., Van Deerlin, V. M., Fraenkel, E., Ostrow, L. W., Baas, F., Zaitlen, N., Berry, J. D., Malaspina, A., Fratta, P., Cox, G. A., Thompson, L. M., Finkbeiner, S., Dardiotis, E., Miller, T. M., Chandran, S., Pal, S., Hornstein, E., Macgowan, D. J., Heiman-Patterson, T., Hammell, M. G., Patsopoulos, N. A., Dubnau, J., Nath, A., Phatnani, H., Shneider, N. A., Manley, J. L. (July 2018) Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism. eLife, 7. ISSN 2050084X (ISSN)

O’Neill, Kathryn, Liao, Wen-Wei, Patel, Ami, Hammell, Molly Gale (June 2018) TEsmall identifies small RNAs associated with targeted inhibitor resistance in melanoma. bioRxiv.

Tam, O. H., Pennisi, D., Wilkinson, L., Little, M. H., Wazin, F., Wan, V. L., Lovicu, F. J. (May 2018) Crim1 is required for maintenance of the ocular lens epithelium. Exp Eye Res, 170. pp. 58-66. ISSN 0014-4835

Lee, Chul-Hwan, Yu, Jia-Ray, Kumar, Sunil, Jin, Ying, LeRoy, Gary, Bhanu, Natarajan, Kaneko, Syuzo, Garcia, Benjamin A., Hamilton, Andrew D., Reinberg, Danny (May 2018) Allosteric Activation Dictates PRC2 Activity Independent of Its Recruitment to Chromatin. Molecular Cell, 70 (3). pp. 422-434. ISSN 1097-2765

Nicolas, Aude, Kenna, Kevin P, Renton, Alan E, Ticozzi, Nicola, Faghri, Faraz, Chia, Ruth, Dominov, Janice A, Kenna, Brendan J, Nalls, Mike A, Keagle, Pamela, Rivera, Alberto M, van Rheenen, Wouter, Murphy, Natalie A, van Vugt, Joke JFA, Geiger, Joshua T, Van der Spek, Rick A, Pliner, Hannah A, Shankaracharya, Smith, Bradley N, Marangi, Giuseppe, Topp, Simon D, Abramzon, Yevgeniya, Gkazi, Athina Soragia, Eicher, John D, Kenna, Aoife, ITALSGEN Consortium, Mora, Gabriele, Calvo, Andrea, Mazzini, Letizia, Riva, Nilo, Mandrioli, Jessica, Caponnetto, Claudia, Battistini, Stefania, Volanti, Paolo, La Bella, Vincenzo, Conforti, Francesca L, Borghero, Giuseppe, Messina, Sonia, Simone, Isabella L, Trojsi, Francesca, Salvi, Fabrizio, Logullo, Francesco O, D'Alfonso, Sandra, Corrado, Lucia, Capasso, Margherita, Ferrucci, Luigi, Genomic Translation for ALS Care (GTAC) Consortium, Moreno, Cristiane de Araujo Martins, Kamalakaran, Sitharthan, Goldstein, David B, ALS Sequencing Consortium, Gitler, Aaron D, Harris, Tim, Myers, Richard M, NYGC ALS Consortium, Phatnani, Hemali, Musunuri, Rajeeva Lochan, Evani, Uday Shankar, Abhyankar, Avinash, Zody, Michael C, Answer ALS Foundation, Kaye, Julia, Finkbeiner, Steven, Wyman, Stacia K, LeNail, Alex, Lima, Leandro, Fraenkel, Ernest, Svendsen, Clive N, Thompson, Leslie M, Van Eyk, Jennifer E, Berry, James D, Miller, Timothy M, Kolb, Stephen J, Cudkowicz, Merit, Baxi, Emily, Clinical Research in ALS and Related Disorders for Therapeutic D, Benatar, Michael, Taylor, J Paul, Rampersaud, Evadnie, Wu, Gang, Wuu, Joanne, SLAGEN Consortium, Lauria, Giuseppe, Verde, Federico, Fogh, Isabella, Tiloca, Cinzia, Comi, Giacomo P, Sorarù, Gianni, Cereda, Cristina, French ALS Consortium, Corcia, Philippe, Laaksovirta, Hannu, Myllykangas, Liisa, Jansson, Lilja, Valori, Miko, Ealing, John, Hamdalla, Hisham, Rollinson, Sara, Pickering-Brown, Stuart, Orrell, Richard W, Sidle, Katie C, Malaspina, Andrea, Hardy, John, Singleton, Andrew B, Johnson, Janel O, Arepalli, Sampath, Sapp, Peter C, McKenna-Yasek, Diane, Polak, Meraida, Asress, Seneshaw, Al-Sarraj, Safa, King, Andrew, Troakes, Claire, Vance, Caroline, de Belleroche, Jacqueline, Baas, Frank, Ten Asbroek, Anneloor LMA, Muñoz-Blanco, José Luis, Hernandez, Dena G, Ding, Jinhui, Gibbs, J Raphael, Scholz, Sonja W, Floeter, Mary Kay, Campbell, Roy H, Landi, Francesco, Bowser, Robert, Pulst, Stefan M, Ravits, John M, MacGowan, Daniel JL, Kirby, Janine, Pioro, Erik P, Pamphlett, Roger, Broach, James, Gerhard, Glenn, Dunckley, Travis L, Brady, Christopher B, Kowall, Neil W, Troncoso, Juan C, Le Ber, Isabelle, Mouzat, Kevin, Lumbroso, Serge, Heiman-Patterson, Terry D, Kamel, Freya, Van Den Bosch, Ludo, Baloh, Robert H, Strom, Tim M, Meitinger, Thomas, Shatunov, Aleksey, Van Eijk, Kristel R, de Carvalho, Mamede, Kooyman, Maarten, Middelkoop, Bas, Moisse, Matthieu, McLaughlin, Russell L, Van Es, Michael A, Weber, Markus, Boylan, Kevin B, Van Blitterswijk, Marka, Rademakers, Rosa, Morrison, Karen E, Basak, A Nazli, Mora, Jesús S, Drory, Vivian E, Shaw, Pamela J, Turner, Martin R, Talbot, Kevin, Hardiman, Orla, Williams, Kelly L, Fifita, Jennifer A, Nicholson, Garth A, Blair, Ian P, Rouleau, Guy A, Esteban-Pérez, Jesús, García-Redondo, Alberto, Al-Chalabi, Ammar, Project MinE ALS Sequencing Consortium, Rogaeva, Ekaterina, Zinman, Lorne, Ostrow, Lyle W, Maragakis, Nicholas J, Rothstein, Jeffrey D, Simmons, Zachary, Cooper-Knock, Johnathan, Brice, Alexis, Goutman, Stephen A, Feldman, Eva L, Gibson, Summer B, Taroni, Franco, Ratti, Antonia, Gellera, Cinzia, Van Damme, Philip, Robberecht, Wim, Fratta, Pietro, Sabatelli, Mario, Lunetta, Christian, Ludolph, Albert C, Andersen, Peter M, Weishaupt, Jochen H, Camu, William, Trojanowski, John Q, Van Deerlin, Vivianna M, Brown, Robert H, van den Berg, Leonard H, Veldink, Jan H, Harms, Matthew B, Glass, Jonathan D, Stone, David J, Tienari, Pentti, Silani, Vincenzo, Chiò, Adriano, Shaw, Christopher E, Traynor, Bryan J, Landers, John E (March 2018) Genome-wide Analyses Identify KIF5A as a Novel ALS Gene. Neuron, 97 (6). 1268-1283.e6. ISSN 0896-6273

Jin, Y., Hammell, M. (February 2018) Analysis of RNA-Seq Data Using TEtranscripts. Methods Mol Biol, 1751. pp. 153-167. ISSN 1064-3745

Ho, Yu-Jui, Anaparthy, Naishitha, Molik, David, Aicher, Toby, Patel, Ami, Hicks, James, Hammell, Molly (December 2017) SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations. bioRxiv. (Unpublished)

Zhang, S., Fan, G., Hao, Y., Hammell, M., Wilkinson, J. E., Tonks, N. K. (October 2017) Suppression of protein tyrosine phosphatase N23 predisposes to breast tumorigenesis via activation of FYN kinase. Genes Dev, 31 (19). pp. 1939-57. ISSN 0890-9369

Kumar, Vijay, Rosenbaum, Julie, Wang, Zihua, Forcier, Talitha, Ronemus, Michael, Wigler, Michael, Levy, Dan (June 2017) Mutational sequencing for accurate count and long-range assembly. bioRxiv.

Krug, L., Chatterjee, N., Borges-Monroy, R., Hearn, S., Liao, W. W., Morrill, K., Prazak, L., Rozhkov, N., Theodorou, D., Hammell, M., Dubnau, J. (March 2017) Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS. PLoS Genet, 13 (3). e1006635. ISSN 1553-7390 (Public Dataset)

Chio, I. I. C., Jafarnejad, S. M., Ponz-Sarvise, M., Park, Y., Rivera, K., Palm, W., Ohlund, D., Hammell, M., Crawford, H., Schmidt, E., Thompson, C., Pappin, D., Sonenberg, N., Tuveson, D. (March 2017) NRF2 promotes tumor maintenance by modulating mRNA translation in pancreatic cancer. Cancer Research, 77 (Supple). ISSN 0008-54721538-7445

Chio, Iok In Christine, Jafarnejad, Seyed Mehdi, Ponz-Sarvise, Mariano, Park, Youngkyu, Rivera, Keith, Palm, Wilhelm, Wilson, John, Sangar, Vineet, Hao, Yuan, Öhlund, Daniel, Wright, Kevin, Filippini, Dea, Lee, Eun Jung, Da Silva, Brandon, Schoepfer, Christina, Wilkinson, John Erby, Buscaglia, Jonathan M, DeNicola, Gina M, Tiriac, Herve, Hammell, Molly, Crawford, Howard C, Schmidt, Edward E, Thompson, Craig B, Pappin, Darryl J, Sonenberg, Nahum, Tuveson, David A (August 2016) NRF2 Promotes Tumor Maintenance by Modulating mRNA Translation in Pancreatic Cancer. Cell, 166 (4). pp. 963-976. ISSN 0092-8674

Vareslija, D., McBryan, J., Fagan, A., Redmond, A. M., Hao, Y., Sims, A. H., Turnbull, A. K., Dixon, J. M., P, O. Gaora, Hudson, L., Purcell, S., Hill, A. D., Young, L. (June 2016) Adaptation to AI therapy in breast cancer can induce dynamic alterations in ER activity resulting in estrogen independent metastatic tumours. Clin Cancer Res, 22 (11). pp. 2765-77. ISSN 1078-0432 (Electronic)1078-0432 (Linking)

Popescu, G. V., Noutsos, C., Popescu, S. C. (April 2016) Big Data in Plant Science: Resources and Data Mining Tools for Plant Genomics and Proteomics. Methods Mol Biol, 1415. pp. 533-547. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Jin, Y., Tam, O. H., Paniagua, E., Hammell, M. (November 2015) TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics, 31 (22). pp. 3593-3599. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

Tajima, K., Yae, T., Javaid, S., Tam, O., Comaills, V., Morris, R., Wittner, B. S., Liu, M., Engstrom, A., Takahashi, F., Black, J. C., Ramaswamy, S., Shioda, T., Hammell, M., Haber, D. A., Whetstine, J. R., Maheswaran, S. (September 2015) SETD1A modulates cell cycle progression through a miRNA network that regulates p53 target genes. Nat Commun, 6. p. 8257. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

Dong, J., Panchakshari, R. A., Zhang, T., Zhang, Y., Hu, J., Volpi, S. A., Meyers, R. M., Ho, Y. J., Du, Z., Robbiani, D. F., Meng, F., Gostissa, M., Nussenzweig, M. C., Manis, J. P., Alt, F. W. (September 2015) Orientation-specific joining of AID-initiated DNA breaks promotes antibody class switching. Nature, 525 (7567). pp. 134-9. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Rozhkov, N. V. (September 2015) Global Run-On Sequencing (GRO-seq) Library Preparation from Drosophila Ovaries. Methods Mol Biol, 1328. pp. 217-30. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Petsch, K., Manzotti, P. S., Tam, O. H., Meeley, R., Hammell, M., Consonni, G., Timmermans, M. C. (August 2015) Novel DICER-LIKE1 siRNAs Bypass the Requirement for DICER-LIKE4 in Maize Development. Plant Cell, 27 (8). pp. 2163-2177. ISSN 1532-298X (Electronic)1040-4651 (Linking)

Burke, S. L., Hammell, M., Ambros, V. (August 2015) Robust Distal Tip Cell Pathfinding in the Face of Temperature Stress Is Ensured by Two Conserved microRNAS in Caenorhabditis elegans. Genetics, 200 (4). pp. 1201-18. ISSN 1943-2631 (Electronic)0016-6731 (Linking)

Wasik, K. A., Tam, O. H., Knott, S. R., Falciatori, I., Hammell, M., Vagin, V. V., Hannon, G. J. (June 2015) RNF17 blocks promiscuous activity of PIWI proteins in mouse testes. Genes Dev, 29 (13). pp. 1403-1415. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Vareslija, D., McBryan, J., Fagan, A., Redmond, A., Hao, Y., Hill, A. D. K., Young, L. S. (May 2015) Adaptation to AI therapy in breast cancer can induce dynamic alterations in ER activity resulting in estrogen independent metastatic tumours. Cancer Research, 75 (9 supp). Abstract nr P3-05. ISSN 0008-5472

Goh, W. S., Falciatori, I., Tam, O. H., Burgess, R., Meikar, O., Kotaja, N., Hammell, M., Hannon, G. J. (May 2015) piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis. Genes Dev, 29 (10). pp. 1032-44. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Yu, J. R., Tai, Y., Jin, Y., Hammell, M. C., Wilkinson, J. E., Roe, J. S., Vakoc, C. R., Van Aelst, L. (February 2015) TGF-beta/Smad signaling through DOCK4 facilitates lung adenocarcinoma metastasis. Genes Dev, 29 (3). pp. 250-61. ISSN 0890-9369

Boj, Sylvia F, Hwang, Chang-Il, Baker, Lindsey A, Chio, Iok In Christine, Engle, Dannielle D, Corbo, Vincenzo, Jager, Myrthe, Ponz-Sarvise, Mariano, Tiriac, Hervé, Spector, Mona S, Gracanin, Ana, Oni, Tobiloba, Yu, Kenneth H, van Boxtel, Ruben, Huch, Meritxell, Rivera, Keith D, Wilson, John P, Feigin, Michael E, Öhlund, Daniel, Handly-Santana, Abram, Ardito-Abraham, Christine M, Ludwig, Michael, Elyada, Ela, Alagesan, Brinda, Biffi, Giulia, Yordanov, Georgi N, Delcuze, Bethany, Creighton, Brianna, Wright, Kevin, Park, Youngkyu, Morsink, Folkert H M., Molenaar, I.  Quintus, Borel Rinkes, Inne H, Cuppen, Edwin, Hao, Yuan, Jin, Ying, Nijman, Isaac J, Iacobuzio-Donahue, Christine, Leach, Steven D, Pappin, Darryl J, Hammell, Molly, Klimstra, David S, Basturk, Olca, Hruban, Ralph H, Offerhaus, George Johan, Vries, Robert G J., Clevers, Hans, Tuveson, David A (January 2015) Organoid Models of Human and Mouse Ductal Pancreatic Cancer. Cell, 160 (1-2). pp. 324-338. ISSN 0092-8674

Dotto, M. C., Petsch, K. A., Aukerman, M. J., Beatty, M., Hammell, M., Timmermans, M. C. (December 2014) Genome-Wide Analysis of leafbladeless1-Regulated and Phased Small RNAs Underscores the Importance of the TAS3 ta-siRNA Pathway to Maize Development. PLoS Genetics, 10 (12). e1004826. ISSN 1553-7390

Sun, J., Ramos, A., Chapman, B., Johnnidis, J. B., Le, L., Ho, Y. J., Klein, A., Hofmann, O., Camargo, F. D. (October 2014) Clonal dynamics of native haematopoiesis. Nature, 514. pp. 322-327. ISSN 0028-0836

Kojima, Y., Tam, O. H., Tam, P. P. (June 2014) Timing of developmental events in the early mouse embryo. Seminars in Cell & Developmental Biology, 34. pp. 65-75. ISSN 1084-9521

Meikar, O., Vagin, V. V., Chalmel, F., Sostar, K., Lardenois, A., Hammell, M., Jin, Y., Da Ros, M., Wasik, K. A., Toppari, J., Hannon, G. J., Kotaja, N. (April 2014) An atlas of chromatoid body components. RNA, 20 (4). pp. 483-95. ISSN 1355-8382

Feigin, M. E., Xue, B., Hammell, M. C., Muthuswamy, S. K. (March 2014) G-protein-coupled receptor GPR161 is overexpressed in breast cancer and is a promoter of cell proliferation and invasion. Proceedings of the National Academy of Sciences of the United States of America, 111 (11). pp. 4191-6. ISSN 0027-8424

Kojima, Yoji, Kaufman-Francis, Keren, Studdert, Joshua B, Steiner, Kirsten A, Power, Melinda D, Loebel, David AF, Jones, Vanessa, Hor, Angelyn, de Alencastro, Gustavo, Logan, Grant J, Teber, Erdahl T, Tam, Oliver H, Stutz, Michael D, Alexander, Ian E, Pickett, Hilda A, Tam, Patrick PL (January 2014) The transcriptional and functional properties of mouse epiblast stem cells resemble the anterior primitive streak. Cell Stem Cell, 14 (1). pp. 107-120. ISSN 1934-5909

McKay, S. J., Skidmore, E. J., LaRose, C. J., Mercer, A. W., Noutsos, C. (October 2013) Cloud Computing with iPlant Atmosphere. Curr Protoc Bioinformatics, 43. 9 15 1-20. ISSN 1934-340X (Electronic)1934-3396 (Linking)

Rozhkov, N. V., Hammell, M., Hannon, G. J. (February 2013) Multiple roles for Piwi in silencing Drosophila transposons. Genes and Development, 27 (4). pp. 400-412. ISSN 08909369 (ISSN)

Paul, S., Kuo, A., Schalch, T., Vogel, H., Joshua-Tor, L., McCombie, W. R., Gozani, O., Hammell, M., Mills, A. A. (January 2013) Chd5 Requires PHD-Mediated Histone 3 Binding for Tumor Suppression. Cell Reports, 3 (1). pp. 92-102. ISSN 2211-1247 (Public Dataset)

Li, W. H., Jin, Y., Prazak, L., Hammell, M., Dubnau, J. (September 2012) Transposable Elements in TDP-43-Mediated Neurodegenerative Disorders. PLoS ONE, 7 (9). ISSN 1932-6203

Fesen, R. A., Zastrow, J. A., Hammell, M. C., Shull, J. M., Silvia, D. W. (August 2011) Ejecta Knot Flickering, Mass Ablation, and Fragmentation in Cassiopeia A. Astrophysical Journal, 736 (2). p. 13. ISSN 0004-637X

Karp, X., Hammell, M., Ow, M. C., Ambros, V. (April 2011) Effect of life history on microRNA expression during C. elegans development. RNA, 17 (4). pp. 639-651. ISSN 13558382 (ISSN)

Hammell, M. (September 2010) Computational methods to identify miRNA targets. Seminars in Cell & Developmental Biology, 21 (7). pp. 738-44. ISSN 1084-9521

Hong, X., Hammell, M., Ambros, V., Cohen, S. M. (September 2009) Immunopurification of Ago1 miRNPs selects for a distinct class of microRNA targets. Proceedings of the National Academy of Sciences of the United States of America, 106 (35). pp. 15085-90. ISSN 0027-8424

Zhang, L., Hammell, M., Kudlow, B. A., Ambros, V., Han, M. (September 2009) Systematic analysis of dynamic miRNA-target interactions during C. elegans development. Development, 136 (18). pp. 3043-55. ISSN 0950-1991

Hammell, M. C., Fesen, R. A. (November 2008) A Catalog of Outer Ejecta Knots in the Cassiopeia A Supernova Remnant. Astrophysical Journal Supplement Series, 179 (1). pp. 195-208. ISSN 0067-0049

Martinez, N. J., Ow, M. C., Barrasa, M. I., Hammell, M., Sequerra, R., Doucette-Stamm, L., Roth, F. P., Ambros, V. R., Walhout, A. J. (September 2008) A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes & Development, 22 (18). pp. 2535-49. ISSN 0890-9369 (Print)0890-9369

Hammell, M., Long, D., Zhang, L., Lee, A., Carmack, C. S., Han, M., Ding, Y., Ambros, V. (September 2008) mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nature Methods, 5 (9). pp. 813-9. ISSN 1548-7091 (Print)1548-7091

Fesen, R. A., Hoflich, P. A., Hamilton, A. J. S., Hammell, M. C., Gerardy, C. L., Khokhlov, A. M., Wheeler, J. C. (March 2007) The chemical distribution in a subluminous type Ia supernova: Hubble Space Telescope images of the SN 1885 remnant. Astrophysical Journal, 658 (1). pp. 396-409. ISSN 0004-637X

Fesen, R. A., Hammell, M. C., Morse, J., Chevalier, R. A., Borkowski, K. J., Dopita, M. A., Gerardy, C. L., Lawrence, S. S., Raymond, J. C., van den Bergh, S. (July 2006) The expansion asymmetry and age of the Cassiopeia A supernova remnant. Astrophysical Journal, 645 (1). pp. 283-292. ISSN 0004-637X

Fesen, R. A., Hammell, M. C., Morse, J., Chevalier, R. A., Borkowski, K. J., Dopita, M. A., Gerardy, C. L., Lawrence, S. S., Raymond, J. C., van den Bergh, S. (January 2006) Discovery of outlying high-velocity oxygen-rich ejecta in Cassiopeia A. Astrophysical Journal, 636 (2). pp. 859-872. ISSN 0004-637X

Immler, S., Fesen, R. A., Van Dyk, S. D., Weiler, K. W., Petre, R., Lewin, W. H. G., Pooley, D., Pietsch, W., Aschenbach, B., Hammell, M. C., Rudie, G. C. (October 2005) Late-time X-ray, UV, and optical monitoring of supernova 1979C. Astrophysical Journal, 632 (1). pp. 283-293. ISSN 0004-637X

MacDonald, E. C., Allen, P., Dalton, G., Moustakas, L. A., Heymans, C., Edmondson, E., Blake, C., Clewley, L., Hammell, M. C., Olding, E., Miller, L., Rawlings, S., Wall, J., Wegner, G., Wolf, C. (August 2004) The Oxford-Dartmouth Thirty Degree Survey - I. Observations and calibration of a wide-field multiband survey. Monthly Notices of the Royal Astronomical Society, 352 (4). pp. 1255-1272. ISSN 0035-8711

Book Section

Cumming, G. P., French, T., Hogg, J., McKendrick, D., Gilstad, H., Molik, D., Luciano, J. S. (2017) Trust and provenance in communication to ehealth consumers. In: The Digitization of Healthcare: New Challenges and Opportunities. UNSPECIFIED, pp. 189-203. ISBN 9781349951734 (ISBN); 9781349951727 (ISBN)

Conference or Workshop Item

Tonelli, Claudia, Yordanov, Georgi N, Hao, Yuan, Deschenes, Astrid, Brosnan, Erin, Doshi, Abishek, Park, Youngkyu, Preall, Jonathan, Tuveson, David A (2022) The transcription factor SPDEF promotes the survival of mucinous pancreatic ductal adenocarcinoma of the classical subtype. In: American Association for Cancer Research Annual Meeting 2022, 2022 Apr 8-13, Philadelphia, PA.

Steele, Nina G, Biffi, Giulia, Kemp, Samantha, Zhang, Yaqing, Drouillard, Donovan, Syu, LiJyun, Hao, Yuan, Oni, Tobiloba, Brosnan, Erin, Elyada, Ela, Doshi, Abhishek, Hansma, Christa, Espinoza, Carlos, Abbas, Ahmed, The, Stephanie, Irizarry-Negron, Valerie, Halbrook, Christopher, Franks, Nicole, Hoffman, Megan, Carpenter, Eileen, Nwosu, Zeribe, Park, Youngkyu, Crawford, Howard, Lyssiotis, Costas, Frankel, Timothy, Rao, Arvind, Bednar, Filip, Dlugosz, Andrzej, Preall, Jonathan, Tuveson, David, Allen, Benjamin, Di Magliano, Marina Pasca (July 2021) Inhibition of Hedgehog signaling alters fibroblast composition in pancreatic cancer. In: AACR Annual Meeting 2021.

Thesis

Wunderlich, Cole (September 2023) Quantifying Transposable Element Expression in Single-Cell RNA Sequencing Data. PhD thesis, Cold Spring Harbor Laboratory.

O’Neill, Kathryn Shea (June 2022) Investigations into the contribution of retrotransposon activation in neurodegenerative disease. PhD thesis, Cold Spring Harbor Laboratory.

Video

Hammell, M. (November 2011) Talk from Molly Hammell at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Dataset

Krug, L., Chatterjee, N., Borges-Monroy, R., Hearn, S., Liao, W., Morrill, K., Prazak, L., Rozhkov, N., Theodorou, D., Hammell, M., Dubnau, J. (2017) Datasets from "Krug, L., Chatterjee, N., Borges-Monroy, R., Hearn, S., Liao, W. W., Morrill, K., Prazak, L., Rozhkov, N., Theodorou, D., Hammell, M., Dubnau, J. (2017) Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS. PLoS Genet". [Dataset]