Items where Community is "Publications"

Paper

Tang, Ziqi, Koo, Peter K (March 2024) Evaluating the representational power of pre-trained DNA language models for regulatory genomics. bioRxiv. (Public Dataset) (Submitted)

Satterlee, James W, Alonso, David, Gramazio, Pietro, Jenike, Katharine M, He, Jia, Arrones, Andrea, Villanueva, Gloria, Plazas, Mariola, Ramakrishnan, Srividya, Benoit, Matthias, Gentile, Iacopo, Hendelman, Anat, Shohat, Hagai, Fitzgerald, Blaine, Robitaille, Gina M, Green, Yumi, Swartwood, Kerry, Passalacqua, Michael J, Gagnon, Edeline, Hilgenhof, Rebecca, Huggins, Trevis D, Eizenga, Georgia C, Gur, Amit, Rutten, Twan, Stein, Nils, Yao, Shengrui, Bellot, Clement, Bendahmane, Mohammed, Frary, Amy, Knapp, Sandra, Särkinen, Tiina, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Eshed, Yuval, Prohens, Jaime, Vilanova, Santiago, Lippman, Zachary B (February 2024) Convergent evolution of plant prickles is driven by repeated gene co-option over deep time. bioRxiv. (Submitted)

Ortiz, Jenelys Ruiz, Lewis, Steven M, Ciccone, Michael, Chatterjee, Deeptiman, Henry, Samantha, Siepel, Adam, Dos Santos, Camila O (January 2024) Single-Cell Transcription Mapping of Murine and Human Mammary Organoids Responses to Female Hormones. Journal of Mammary Gland Biology and Neoplasia, 29 (1). p. 3. ISSN 1083-3021 (Public Dataset)

Amor, Corina, Fernández-Maestre, Inés, Chowdhury, Saria, Ho, Yu-Jui, Nadella, Sandeep, Graham, Courtenay, Carrasco, Sebastian E, Nnuji-John, Emmanuella, Feucht, Judith, Hinterleitner, Clemens, Barthet, Valentin JA, Boyer, Jacob A, Mezzadra, Riccardo, Wereski, Matthew G, Tuveson, David A, Levine, Ross L, Jones, Lee W, Sadelain, Michel, Lowe, Scott W (January 2024) Prophylactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction. Nature Aging. ISSN 2662-8465 (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

Kotagama, Kasuen, Grimme, Acadia L, Braviner, Leah, Yang, Bing, Sakhawala, Rima M, Yu, Guoyun, Benner, Lars Kristian, Joshua-Tor, Leemor, McJunkin, Katherine (January 2024) The catalytic activity of microRNA Argonautes plays a modest role in microRNA star strand destabilization in C. elegans. bioRxiv. (Submitted)

Wang, Julia H, Tsin, Dexter, Engel, Tatiana A (December 2023) Predictive variational autoencoder for learning robust representations of time-series data. arXiv. (Submitted)

Wang, Julia Huiming, Tsin, Dexter, Engel, Tatiana (December 2023) Predictive variational autoencoder for learning robust representations of time-series data. arXiv. (Submitted)

Loh, Liyen, Carcy, Salomé, Krovi, Harsha S, Domenico, Joanne, Spengler, Andrea, Lin, Yong, Torres, Joshua, Palmer, William, Norman, Paul J, Stone, Matthew, Brunetti, Tonya, Meyer, Hannah V, Gapin, Laurent (December 2023) Unraveling the Phenotypic States of Human innate-like T Cells: Comparative Insights with Conventional T Cells and Mouse Models. bioRxiv. (Submitted)

Tang, Ziqi, Toneyan, Shushan, Koo, Peter K (December 2023) Current approaches to genomic deep learning struggle to fully capture human genetic variation. Nature Genetics, 55 (12). pp. 2021-2022. ISSN 1061-4036

Zhang, Anqi, Zador, Anthony M (December 2023) Neurons in the primary visual cortex of freely moving rats encode both sensory and non-sensory task variables. PLoS Biology, 21 (12). e3002384. ISSN 1545-7885

Passalacqua, Michael John, Gillis, Jesse (November 2023) Coexpression enhances cross-species integration of scRNA-seq across diverse plant species. bioRxiv. (Submitted)

Staklinski, Stephen J, Scheben, Armin, Siepel, Adam, Kilberg, Michael S (November 2023) Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification. bioRxiv. (Submitted)

Maia-Silva, Diogo, Schier, Allison C, Skopelitis, Damianos, Kechejian, Vahag, Alpsoy, Aktan, Liverpool, Jynelle, Taatjes, Dylan J, Vakoc, Christopher R (October 2023) Marker-based CRISPR screening reveals a MED12-p63 interaction that activates basal identity in pancreatic ductal adenocarcinoma. bioRxiv. (Submitted)

Funamizu, A, Marbach, F, Zador, AM (October 2023) Stable sound decoding despite modulated sound representation in the auditory cortex. Current Biology, 33 (20). 4470-4483.e7. ISSN 0960-9822

Aguirre, Lyndsey, Hendelman, Anat, Hutton, Samuel F, McCandlish, David M, Lippman, Zachary B (October 2023) Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science, 382 (6668). pp. 315-320. ISSN 0036-8075

Ortiz, Jenelys Ruiz, Lewis, Steven M, Ciccone, Michael F, Chatterjee, Deeptiman, Henry, Samantha, Siepel, Adam, Dos Santos, Camila O (September 2023) Single-cell transcription mapping of murine and human mammary organoids responses to female hormones. bioRxiv. (Public Dataset) (Submitted)

Amor, Corina, Fernández-Maestre, Inés, Chowdhury, Saria, Ho, Yu-Jui, Nadella, Sandeep, Graham, Courtenay, Carrasco, Sebastian E, Nnuji-John, Emmanuella, Feucht, Judith, Hinterleitner, Clemens, Barthet, Valentin JA, Boyer, Jacob A, Mezzadra, Riccardo, Wereski, Matthew G, Tuveson, David A, Levine, Ross L, Jones, Lee W, Sadelain, Michel, Lowe, Scott W (September 2023) Prophylactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction. Research Square. (Submitted)

Iohannes, Sessen Daniel, Jackson, David (September 2023) Tackling redundancy: genetic mechanisms underlying paralog compensation in plants. New Phytologist. ISSN 0028-646X

Funamizu, Akihiro, Marbach, Fred, Zador, Anthony M (September 2023) Stable sound decoding despite modulated sound representation in the auditory cortex. bioRxiv. (Submitted)

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)

Lei, Pin-Ji, Pereira, Ethel R, Andersson, Patrik, Amoozgar, Zohreh, Van Wijnbergen, Jan Willem, O'Melia, Meghan J, Zhou, Hengbo, Chatterjee, Sampurna, Ho, William W, Posada, Jessica M, Kumar, Ashwin S, Morita, Satoru, Menzel, Lutz, Chung, Charlie, Ergin, Ilgin, Jones, Dennis, Huang, Peigen, Beyaz, Semir, Padera, Timothy P (September 2023) Cancer cell plasticity and MHC-II-mediated immune tolerance promote breast cancer metastasis to lymph nodes. Journal of Experimental Medicine, 220 (9). e20221847. ISSN 0022-1007 (Public Dataset)

de Ruiter Swain, Jed, Michalopoulou, Evdokia, Noch, Evan K, Lukey, Michael J, Van Aelst, Linda (August 2023) Metabolic partitioning in the brain and its hijacking by glioblastoma. Genes and Development, 37. pp. 681-702. ISSN 0890-9369

Kahng, Jessica A, Xavier, Andre M, Ferro, Austin, Auguste, Yohan SS, Cheadle, Lucas (August 2023) Integrated high-confidence and high-throughput approaches for quantifying synapse engulfment by oligodendrocyte precursor cells. bioRxiv. (Submitted)

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)

Rupert, Deborah D, Pagliaro, Alexa, Choe, Jane, Shea, Stephen D (August 2023) Selective deletion of Methyl CpG binding protein 2 from parvalbumin interneurons in the auditory cortex delays the onset of maternal retrieval in mice. The Journal of Neuroscience. JN-RM-0838-23. ISSN 0270-6474

Wiberg, Akira, Lucey, Maria A, Kleeman, Sam, Kang, Youngjoo, Ng, Mike, Furniss, Dominic (August 2023) Genetic correlations between migraine and carpal tunnel syndrome. Plastic and Reconstructive Surgery. ISSN 0032-1052

Kleeman, Sam O, Thakir, Tuba Mansoor, Demestichas, Breanna, Mourikis, Nicholas, Loiero, Dominik, Ferrer, Miriam, Bankier, Sean, Riazat-Kesh, Yosef JRA, Lee, Hassal, Chantzichristos, Dimitrios, Regan, Claire, Preall, Jonathan, Sinha, Sarthak, Rosin, Nicole, Yipp, Bryan, de Almeida, Luiz GN, Biernaskie, Jeff, Dufour, Antoine, Tober-Lau, Pinkus, Ruusalepp, Arno, Bjorkegren, Johan LM, Ralser, Markus, Kurth, Florian, Demichev, Vadim, Heywood, Todd, Gao, Qing, Johannsson, Gudmundur, Koelzer, Viktor H, Walker, Brian R, Meyer, Hannah V, Janowitz, Tobias (August 2023) Cystatin C is glucocorticoid responsive, directs recruitment of Trem2+ macrophages, and predicts failure of cancer immunotherapy. Cell Genomics, 3 (8). p. 100347. ISSN 2666-979X

Berube, Benjamin, Ernst, Evan, Cahn, Jonathan, Roche, Benjamin, de Santis Alves, Cristiane, Lynn, Jason, Scheben, Armin, Siepel, Adam, Ross-Ibarra, Jeffrey, Kermicle, Jerry, Martienssen, Robert A (August 2023) Teosinte Pollen Drive guides maize domestication and evolution by RNAi. bioRxiv. (Public Dataset) (Submitted)

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 underlies epigenetic inheritance of DNA methylation. bioRxiv. (Submitted)

Corona, Alberto, Choe, Jane, Muñoz-Castañeda, Rodrigo, Osten, Pavel, Shea, Stephen D (July 2023) A circuit from the locus coeruleus to the anterior cingulate cortex modulates offspring interactions in mice. Cell Reports, 42 (7). p. 112771. ISSN 2211-1247

Ferrer, Miriam, Mourikis, Nicholas, Davidson, Emma E, Kleeman, Sam O, Zaccaria, Marta, Habel, Jill, Rubino, Rachel, Gao, Qing, Flint, Thomas R, Young, Lisa, Connell, Claire M, Lukey, Michael J, Goncalves, Marcus D, White, Eileen P, Venkitaraman, Ashok R, Janowitz, Tobias (July 2023) Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia. Cell Metabolism, 35 (7). 1147-1162.e7. ISSN 1550-4131

Findling, Charles, Hubert, Felix, Acerbi, Luigi, Benson, Brandon, Benson, Julius, Birman, Daniel, Bonacchi, Niccolò, Carandini, Matteo, Catarino, Joana A, Chapuis, Gaelle A, Churchland, Anne K, Dan, Yang, DeWitt, Eric EJ, Engel, Tatiana A, Fabbri, Michele, Faulkner, Mayo, Fiete, Ila Rani, Freitas-Silva, Laura, Gerçek, Berk, Harris, Kenneth D, Häusser, Michael, Hofer, Sonja B, Hu, Fei, Huntenburg, Julia M, Khanal, Anup, Krasniak, Chris, Langdon, Christopher, Latham, Peter E, P Lau, Petrina Y, Mainen, Zach, Meijer, Guido T, Miska, Nathaniel J, Mrsic-Flogel, Thomas D, Noel, Jean-Paul, Nylund, Kai, Pan-Vazquez, Alejandro, Paninski, Liam, Pillow, Jonathan, Rossant, Cyrille, Roth, Noam, Schaeffer, Rylan, Schartner, Michael, Shi, Yanliang, Socha, Karolina Z, Steinmetz, Nicholas A, Svoboda, Karel, Tessereau, Charline, Urai, Anne E, Wells, Miles J, West, Steven Jon, Whiteway, Matthew R, Winter, Olivier, Witten, Ilana B, Zador, Anthony, Dayan, Peter, Pouget, Alexandre (July 2023) Brain-wide representations of prior information in mouse decision-making. bioRxiv. (Submitted)

Toneyan, Shushan, Koo, Peter K (July 2023) Interpreting Cis -Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics. bioRxiv. (Submitted)

Yan, Ran, Moresco, Philip, Gegenhuber, Bruno, Fearon, Douglas T (June 2023) T cell-Mediated Development of Stromal Fibroblasts with an Immune-Enhancing Chemokine Profile. Cancer Immunology Research. OF1-OF11. ISSN 2326-6066

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

Guillotin, Bruno, Rahni, Ramin, Passalacqua, Michael, Mohammed, Mohammed Ateequr, Xu, Xiaosa, Raju, Sunil Kenchanmane, Ramírez, Carlos Ortiz, Jackson, David, Groen, Simon C, Gillis, Jesse, Birnbaum, Kenneth D (May 2023) A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature, 617 (7962). pp. 785-791. ISSN 0028-0836

Hur, Stella K, Somerville, Tim DD, Wu, Xiaoli S, Maia-Silva, Diogo, Demerdash, Osama E, Tuveson, David A, Notta, Faiyaz, Vakoc, Christopher R (April 2023) p73 activates transcriptional signatures of basal lineage identity and ciliogenesis in pancreatic ductal adenocarcinoma. bioRxiv. (Submitted)

Chang, Mario C, Staklinski, Stephen J, Malut, Vinay R, Pierre, Geraldine L, Kilberg, Michael S, Merritt, Matthew E (April 2023) Metabolomic Profiling of Asparagine Deprivation in Asparagine Synthetase Deficiency Patient-Derived Cells. Nutrients, 15 (8). p. 1938. ISSN 2072-6643

Staklinski, Stephen J, Chang, Mario C, Ahrens-Nicklas, Rebecca C, Kaur, Shagun, Stefanatos, Arianna K, Dudenhausen, Elizabeth E, Merritt, Matthew E, Kilberg, Michael S (March 2023) Characterizing asparagine synthetase deficiency variants in lymphoblastoid cell lines. JIMD Reports, 64 (2). pp. 167-179. ISSN 2192-8304

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)

Ferrer, Miriam, Mourikis, Nicholas, Davidson, Emma E, Kleeman, Sam O, Zaccaria, Marta, Habel, Jill, Rubino, Rachel, Flint, Thomas R, Connell, Claire M, Lukey, Michael J, White, Eileen P, Coll, Anthony P, Venkitaraman, Ashok R, Janowitz, Tobias (February 2023) Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia. bioRxiv. (Submitted)

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)

Girish, Vishruth, Lakhani, Asad A, Scaduto, Christine M, Thompson, Sarah L, Brown, Leanne M, Hagenson, Ryan A, Sausville, Erin L, Mendelson, Brianna E, Lukow, Devon A, Yuan, Monet Lou, Kandikuppa, Pranav K, Stevens, Eric C, Lee, Sophia N, Salovska, Barbora, Li, Wenxue, Smith, Joan C, Taylor, Alison M, Martienssen, Robert A, Liu, Yansheng, Sun, Ruping, Sheltzer, Jason M (January 2023) Oncogene-like addiction to aneuploidy in human cancers. bioRxiv. (Public Dataset) (Submitted)

Acerbi, L, Aguillon-Rodriguez, V, Ahmadi, M, Amjad, J, Angelaki, D, Arlandis, J, Ashwood, ZC, Banga, K, Barrell, H, Bayer, HM, Benson, J, Benson, B, Bhagat, J, Birman, D, Bougrova, K, Boussard, J, Bruijns, SA, Carandini, M, Catarino, J, Cazettes, F, Dan, Y, Davatolagh, F, Dayan, P, Denève, S, Dong, LL, Engel, T, Fabbri, M, Fiete, I, Findling, C, Freitas-Silva, L, Ganguli, S, Gercek, B, Ghani, N, Gordeliy, I, Haetzel, LM, Hausser, M, Hiratani, N, Hofer, S, Hu, F, Huber, F, Hurwitz, C, Khanal, A, Krasniak, CS, Krishnagopal, S, Krumin, M, Langdon, C, Latham, P, Lau, P, Lee, H, Liu, A, Mainen, ZF, Vergara, HM, Mcgrory, C, McMannon, B, Meijer, GT, Melin, M, Meshulam, L, Miska, NJ, Mitelut, C, Mohammadi, Z, Mrsic-Flogel, T, Murakami, M, Noel, JP, Nylund, K, Vazquez, AP, Paninski, L, Pezzotta, A, Picard, S, Pillow, JW, Pouget, A, Roth, N, Roy, NA, Saniee, K, Schaeffer, R, Shi, Y, Socha, KZ, Soitu, C, Svoboda, K, Taheri, M, Tessereau, C, Urai, AE, Varol, E, Wells, MJ, Whiteway, MR, Windolf, C, Witten, I, Wool, LE, Zador, AM, Bonacchi, N, Chapuis, GA, Churchland, AK, DeWitt, EEJ, Faulkner, M, Harris, KD, Huntenburg, JM, Hunter, M, Laranjeira, IC, Rossant, C, Sasaki, M, Schartner, MM (January 2023) A modular architecture for organizing, processing and sharing neurophysiology data. Nature Methods, 20 (3). pp. 403-407. ISSN 1548-7091 (Public Dataset)

Chang, Mario C, Staklinski, Stephen J, Merritt, Matthew E, Kilberg, Michael S (2023) A method for measurement of human asparagine synthetase (ASNS) activity and application to ASNS protein variants associated with ASNS deficiency. Biology Methods and Protocols, 8 (1). bpad026. ISSN 2396-8923

Karakida Kawaguchi, Risa, Tang, Ziqi, Fischer, Stephan, Rajesh, Chandana, Tripathy, Rohit, Koo, Peter K, Gillis, Jesse (December 2022) Learning single-cell chromatin accessibility profiles using meta-analytic marker genes. Briefings in Bioinformatics. bbac541. ISSN 1467-5463

Xie, Yunyao, Huang, Longwen, Corona, Alberto, Pagliaro, Alexa H, Shea, Stephen D (December 2022) A dopaminergic reward prediction error signal shapes maternal behavior in mice. Neuron. S0896-6273(22)01073. ISSN 0896-6273

Toneyan, Shushan, Tang, Ziqi, Koo, Peter K (December 2022) Evaluating deep learning for predicting epigenomic profiles. Nature Machine Intelligence, 4 (12). pp. 1088-1100. ISSN 2522-5839

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

Hashimoto, Taiki, Takayanagi, Daisuke, Yonemaru, Junpei, Naka, Tomoaki, Nagashima, Kengo, Yatabe, Yasushi, Shida, Dai, Hamamoto, Ryuji, Kleeman, Sam O, Leedham, Simon J, Maughan, Timothy, Takashima, Atsuo, Shiraishi, Kouya, Sekine, Shigeki (October 2022) Clinicopathological and molecular characteristics of RSPO fusion-positive colorectal cancer. British Journal of Cancer, 127 (6). pp. 1043-1050. ISSN 0007-0920

Kleeman, Sam O, Cordioli, Mattia, Timmers, Paul RHJ, Khan, Atlas, Tober-Lau, Pinkus, Kurth, Florian, Demichev, Vadim, Meyer, Hannah V, Wilson, James F, Ralser, Markus, Kiryluk, Krzysztof, Ganna, Andrea, Baillie, Kenneth, Janowitz, Tobias (October 2022) Cystatin C is associated with adverse COVID-19 outcomes in diverse populations. iScience, 25 (10). p. 105040. ISSN 2589-0042 (In Press)

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

Chae, Honggoo, Banerjee, Arkarup, Dussauze, Marie, Albeanu, Dinu F (September 2022) Long-range functional loops in the mouse olfactory system and their roles in computing odor identity. Neuron. S0896-6273(22)00810. ISSN 0896-6273

Carter, Jason A, Strömich, Léonie, Peacey, Matthew, Chapin, Sarah R, Velten, Lars, Steinmetz, Lars M, Brors, Benedikt, Pinto, Sheena, Meyer, Hannah V (August 2022) Transcriptomic diversity in human medullary thymic epithelial cells. Nature Communications, 13 (1). p. 4296. ISSN 2041-1723

Patel, B, Kleeman, SO, Neavin, D, Powell, J, Baskozos, G, Ng, M, Ahmed, WUR, Bennett, DL, Schmid, AB, Furniss, D, Wiberg, A (August 2022) Shared genetic susceptibility between trigger finger and carpal tunnel syndrome: a genome-wide association study. The Lancet Rheumatology, 4 (8). e556-e565. ISSN 2665-9913

Gegenhuber, Bruno, Tollkuhn, Jessica (July 2022) Epigenetic Mechanisms of Brain Sexual Differentiation. Cold Spring Harbor Perspectives in Biology. a039099. ISSN 1943-0264

Zhang, Anqi, Zador, Anthony M (July 2022) Diversity and task-dependence of task representations in V1 during freely-moving decisions. bioRxiv. (Submitted)

Ahmed, Waheed-Ul-Rahman, Kleeman, Sam, Ng, Michael, Wang, Wei, Auton, Adam, 23andMe Research Team, Lee, Regent, Handa, Ashok, Zondervan, Krina T, Wiberg, Akira, Furniss, Dominic (June 2022) Genome-wide association analysis and replication in 810,625 individuals with varicose veins. Nature Communications, 13 (1). p. 3065. ISSN 2041-1723

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

Luo, Pei X, Zakharenkov, Hannah Cortez, Torres, Lisette Y, Rios, Roberto A, Gegenhuber, Bruno, Black, Alexis M, Xu, Christine K, Minie, Vanessa A, Tran, Amy M, Tollkuhn, Jessica, Trainor, Brian C (May 2022) Oxytocin receptor behavioral effects and cell types in the bed nucleus of the stria terminalis. Hormones and Behaviour, 143. p. 105203. ISSN 0018-506X

Gegenhuber, B, Wu, MV, Bronstein, R, Tollkuhn, J (May 2022) Gene regulation by gonadal hormone receptors underlies brain sex differences. Nature. ISSN 0028-0836

Toneyan, Shushan, Tang, Ziqi, Koo, Peter K (May 2022) Evaluating deep learning for predicting epigenomic profiles. bioRxiv. (Unpublished)

Kwon, Choon-Tak, Tang, Lingli, Wang, Xingang, Gentile, Iacopo, Hendelman, Anat, Robitaille, Gina, Van Eck, Joyce, Xu, Cao, Lippman, Zachary B (March 2022) Dynamic evolution of small signalling peptide compensation in plant stem cell control. Nature Plants. ISSN 2055-0278

Xie, Yunyao, Huang, Longwen, Corona, Alberto, Pagliaro, Alexa H, Shea, Stephen D (March 2022) A reinforcement learning algorithm shapes maternal care in mice. bioRxiv. (Unpublished)

Czégel, Dániel, Giaffar, Hamza, Tenenbaum, Joshua B, Szathmáry, Eörs (February 2022) Bayes and Darwin: How replicator populations implement Bayesian computations. BioEssays : news and reviews in molecular, cellular and developmental biology. e2100255. ISSN 1521-1878

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

Nowlan, Alexandra C, Kelahan, Clancy, Shea, Stephen D (February 2022) Multisensory integration of social signals by a pathway from the basal amygdala to the auditory cortex in maternal mice. bioRxiv. (Unpublished)

Brennan, Christina M, Nadella, Sandeep, Zhao, Xiang, Dima, Richard J, Jordan-Martin, Nicole, Demestichas, Breanna R, Kleeman, Sam O, Ferrer, Miriam, von Gablenz, Eva Carlotta, Mourikis, Nicholas, Rubin, Michael E, Adnani, Harsha, Lee, Hassal, Ha, Taehoon, Prum, Soma, Schleicher, Cheryl B, Fox, Sharon S, Ryan, Michael G, Pili, Christina, Goldberg, Gary, Crawford, James M, Goodwin, Sara, Zhang, Xiaoyue, Preall, Jonathan B, Costa, Ana SH, Conigliaro, Joseph, Masci, Joseph R, Yang, Jie, Tuveson, David A, Tracey, Kevin J, Janowitz, Tobias (February 2022) Oral famotidine versus placebo in non-hospitalised patients with COVID-19: a randomised, double-blind, data-intense, phase 2 clinical trial. Gut. ISSN 0017-5749

Petruzzelli, M, Ferrer, M, Schuijs, MJ, Kleeman, SO, Mourikis, N, Hall, Z, Perera, D, Raghunathan, S, Vacca, M, Gaude, E, Lukey, MJ, Jodrell, DI, Frezza, C, Wagner, EF, Venkitaraman, AR, Halim, TYF, Janowitz, T (February 2022) Early Neutrophilia Marked by Aerobic Glycolysis Sustains Host Metabolism and Delays Cancer Cachexia. Cancers, 14 (4). p. 963. ISSN 2072-6694

Wang, Zhikai, Moresco, Philip, Yan, Ran, Li, Jiayun, Gao, Ya, Biasci, Daniele, Yao, Min, Pearson, Jordan, Hechtman, Jaclyn F, Janowitz, Tobias, Zaidi, Raza M, Weiss, Matthew J, Fearon, Douglas T (January 2022) Carcinomas assemble a filamentous CXCL12-keratin-19 coating that suppresses T cell-mediated immune attack. Proceedings of the National Academy of Sciences of USA, 119 (4). e2119463119-e2119463119. ISSN 0027-8424

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Kepple, Daniel, Cazakoff, Brittany, Demmer, Heike, Eckmeier, Dennis, Shea, Stephen, Koulakov, Alexei (June 2018) Computational algorithms and neural circuitry for compressed sensing in the mammalian main olfactory bulb. bioRxiv. (Unpublished)

Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., Schatz, M. C. (June 2018) Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods, 15 (6). pp. 461-468. ISSN 1548-7091

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Bružas, Emilis, Egeblad, Mikala (March 2018) Bone Talk: Activated Osteoblasts Promote Lung Cancer Growth. Trends in Molecular Medicine, 24 (3). pp. 237-239. ISSN 1471-4914

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Kumar, V., Rosenbaum, J., Wang, Z., Forcier, T., Ronemus, M., Wigler, M., Levy, D. (January 2018) Partial bisulfite conversion for unique template sequencing. Nucleic Acids Res, 46 (2). e10. ISSN 0305-1048

Alexander, J., Kendall, J., McIndoo, J., Rodgers, L., Aboukhalil, R., Levy, D., Stepansky, A., Sun, G., Chobadjiev, L., Riggs, M., Cox, H., Hakker, I., Nowak, D. G., Laze, J., Llukani, E., Srivastava, A., Gruschow, S., Yadav, S. S., Robinson, B. D., Atwal, G., Trotman, L. C., Lepor, H., Hicks, J. B., Wigler, M., Krasnitz, A. (January 2018) Utility of single cell genomics in diagnostic evaluation of prostate cancer. Cancer Res, 78 (2). pp. 348-358. ISSN 0008-5472

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)

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Shuvaev, Sergey, Giaffar, Hamza, Koulakov, Alexei A (December 2017) Representations of Sound in Deep Learning of Audio Features from Music. arXiv. (Submitted)

Lee, M., Naguib, A., Trotman, L. C., El-Amine, N. (December 2017) Endocytosis and PTEN in Tumor Suppression. Molecular Biology of the Cell, 28 (26 ASC). Abstract M257. ISSN 1059-15241939-4586

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Banerjee, Arkarup, Marbach, F., Anselmi, Francesca, Koh, Matthew S, Davis, Martin B, Garcia da Silva, P., Delevich, K., Oyibo, Hassana K., Gupta, Priyanka, Li, Bo, Albeanu, Dinu F (July 2017) Long-range interactions between short axon cells and external tufted cells gate glomerular output in the mouse olfactory bulb. Neuron, 87 (1). pp. 193-207. ISSN 0896-6273

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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

Chalk, M., Masset, P., Gutkin, B., Deneve, S. (June 2017) Sensory noise predicts divisive reshaping of receptive fields. PLoS Comput Biol, 13 (6). e1005582. ISSN 1553-734x

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.

Soyk, Sebastian, Lemmon, Zachary H., Oved, Matan, Fisher, Josef, Liberatore, Katie L., Park, Soon Ju, Goren, Anna, Jiang, Ke, Ramos, Alexis, van der Knaap, Esther, Van Eck, Joyce, Zamir, Dani, Eshed, Yuval, Lippman, Zachary B. (June 2017) Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene. Cell, 169 (6). pp. 1142-1155. ISSN 0092-8674

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Peikon, I. D., Kebschull, J. M., Vagin, V. V., Ravens, D. I., Sun, Y. C., Brouzes, E., Correa, I. R., Bressan, D., Zador, A. M. (April 2017) Using high-throughput barcode sequencing to efficiently map connectomes. Nucleic Acids Res. ISSN 0305-1048

Underwood, Charles J., Henderson, Ian R., Martienssen, Robert A. (April 2017) Genetic and epigenetic variation of transposable elements in Arabidopsis. Current Opinion in Plant Biology, 36. pp. 135-141. ISSN 1369-5266

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Sarkar, Bidyut, Das, Anand Kant, Arumugam, Senthil, Kaushalya, Sanjeev Kumar, Bandyopadhyay, Arkarup, Balaji, Jayaprakash, Maiti, Sudipta (2012) The dynamics of somatic exocytosis in monoaminergic neurons. Frontiers in Physiology, 3. p. 414. ISSN 1664-042X

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Azumi, Y., Liu, D. H., Zhao, D. Z., Li, W. X., Wang, G. F., Hu, Y., Ma, H. (June 2002) Homolog interaction during meiotic prophase I in Arabidopsis requires the SOLO DANCERS gene encoding a novel cyclin-like protein. Embo Journal, 21 (12). pp. 3081-3095. ISSN 0261-4189

Bjerling, P., Silverstein, R. A., Thon, G., Caudy, A., Grewal, S., Ekwall, K. (April 2002) Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity. Molecular and Cellular Biology, 22 (7). pp. 2170-2181. ISSN 0270-7306

Kim, J. Y., Yuan, Z. A., Cilia, M., Khalfan-Jagani, Z., Jackson, D. P. (March 2002) Intercellular trafficking of a KNOTTED1 green fluorescent protein fusion in the leaf and shoot meristem of Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 99 (6). pp. 4103-4108. ISSN 0027-8424

Ejkova, Elena, Tansey, William P. (March 2002) Old dogs and new tricks: meeting on mechanisms of eukaryotic transcription. Embo Reports, 3 (3). pp. 219-23. ISSN 1469-221X

van der Knaap, E., Lippman, Z. B., Tanksley, S. D. (February 2002) Extremely elongated tomato fruit controlled by four quantitative trait loci with epistatic interactions. Theoretical and Applied Genetics, 104 (2-3). pp. 241-247. ISSN 0040-5752

Cilia, M., Cantrill, L., van Bel, A. (January 2002) Plasmodesma 2001: on safari through the symplast. Plant Cell, 14 (1). pp. 7-10. ISSN 1040-4651 (Print)

Caudy, A. A., Myers, M., Hannon, G. J., Hammond, S. M. (2002) Fragile X-related protein and VIG associate with the RNA interference machinery. Genes and Development, 16 (19). pp. 2491-2496. ISSN 08909369 (ISSN)

Muratani, M., Gerlich, D., Janicki, S. M., Gebhard, M., Eils, R., Spector, D. L. (2002) Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nature Cell Biology, 4. pp. 106-110. ISSN 1465-7392

Paddison, P. J., Hannon, G. J. (2002) RNA interference: The new somatic cell genetics? Cancer Cell, 2 (1). pp. 17-23. ISSN 15356108 (ISSN)

Paddison, P. J., Caudy, A. A., Bernstein, E., Hannon, G. J., Conklin, D. S. (2002) Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes and Development, 16 (8). pp. 948-958. ISSN 08909369 (ISSN)

Paddison, P. J., Caudy, A. A., Hannon, G. J. (2002) Stable suppression of gene expression by RNAi in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America, 99 (3). pp. 1443-1448. ISSN 00278424 (ISSN)

Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R., Hannon, G. J. (August 2001) Argonaute2, a link between genetic and biochemical analyses of RNAi. Science, 293 (5532). pp. 1146-1150. ISSN 0036-8075

Salghetti, S. E., Caudy, A. A., Chenoweth, J. G., Tansey, W. P. (August 2001) Regulation of transcriptional activation domain function by ubiquitin. Science, 293 (5535). pp. 1651-1653. ISSN 0036-8075

Hammond, S. M., Caudy, A. A., Hannon, G. J. (2001) Post-transcriptional gene silencing by double-stranded RNA. Nature Reviews Genetics, 2 (2). pp. 110-119. ISSN 14710056 (ISSN)

Bernstein, E., Caudy, A. A., Hammond, S. M., Hannon, G. J. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409 (6818). pp. 363-366. ISSN 00280836 (ISSN)

Bernstein, E., Denli, A. M., Hannon, G. J. (2001) The rest is silence. RNA, 7 (11). pp. 1509-1521. ISSN 13558382 (ISSN)

Piano, F., Schetter, A. J., Mangone, M., Stein, L., Kemphues, K. J. (December 2000) RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans. Current Biology, 10 (24). pp. 1619-1622. ISSN 0960-9822

Gaasterland, T., Sczyrba, A., Thomas, E., Aytekin-Kurban, G., Gordon, P., Sensen, C. W. (April 2000) MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh region. Genome Research, 10 (4). pp. 502-510. ISSN 1088-9051

Salghetti, S. E., Muratani, M., Wijnen, H., Futcher, B., Tansey, W. P. (March 2000) Functional overlap of sequences that activate transcription and signal ubiquitin-mediated proteolysis. Proceedings of the National Academy of Sciences of the United States of America, 97 (7). pp. 3118-3123. ISSN 0027-8424

Book Section

Xu, M., Ergin, I., Beyaz, S. (April 2020) Advances in Diagnostic Procedures and Their Applications in the Era of Cancer Immunotherapy. In: Immunotherapy. Springer, pp. 37-50.

Campbell, R. A. A., Honegger, K. S., Gruntman, E., Turner, G. C. (2012) Two-Photon Imaging of Population Activity with Genetically Encoded Calcium Indicators in Living Flies. In: Genetically Encoded Functional Indicators. Neuromethods, 72 . Humana Press, pp. 113-124. ISBN 978-1-62703-013-7

Paddison, P. J., Caudy, A. A., Sachidanandam, R., Hannon, G. J. (2004) Short hairpin activated gene silencing in mammalian cells. In: RNA Interference, Editing and Modification: methods and protocols. Methods Mol Biol, 265 . Springer, pp. 85-100.

Hall, I. M., Grewal, S. I. S. (2003) Structure and function of heterochromatin: implications for epigenetic gene silencing and genome organization. In: RNAi : a guide to gene silencing. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. , pp. 205-232. ISBN 978-087969641-2

Dataset

Pisupati, S., Chartarifsky, L., Khanal, A., Churchland, A. K. (February 2020) Dataset from: Lapses in perceptual decisions reflect exploration. [Dataset]