Items where Community is "CSHL Post Doctoral Fellows"

Paper

Olson, Andrew, Kumari, Sunita, Wei, Xuehong, Chougule, Kapeel, Lu, Zhenyuan, Tello-Ruiz, Marcela Karey, Kumar, Vivek, Van Buren, Peter, Olson, Audra, Kim, Catherine, Braynen, Janeen, Zhang, Lifang, Dyer, Sarah, Alvarez-Jarreta, Jorge, Saraf, Shradha, Contreras-Moreira, Bruno, Naamati, Guy, Ernst, Christina, Papatheodorou, Irene, George, Nancy, Jaiswal, Pankaj, Naithani, Sushma, Gupta, Parul, Elser, Justin, D'Eustachio, Peter, Assmann, Sarah M, Ferrero-Serrano, Ángel, Pasha, Asher, Provart, Nicholas, Gladman, Nicholas, Ware, Doreen (December 2025) Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research. Nucleic Acids Research (NAR). ISSN 0305-1048

Nore, Alexandre, Roselletti, Elena, Chakraborty, Tanmoy, Särkkä, Nicha, Perera, Rajika L, Wilson, Duncan, Syrjänen, Johanna L (November 2025) Structural insights into mechanisms of zinc scavenging by the Candida albicans zincophore Pra1. Nature Communications, 16 (1). ISSN 2041-1723

Eskiocak, Onur, Gewolb, Joseph, Shah, Vyom, Rouse, James A, Chowdhury, Saria, Akyildiz, Erdogan O, Fernández-Maestre, Inés, Boyer, Jacob A, Filliol, Aveline, Harris, Alexander S, Utama, Raditya, Guo, Guangran, Castro-Hernández, Carolina, Nnuji-John, Emmanuella, Chung, Charlie, Anderson, Arianna, Flowers, Sara, Habel, Jill, Romesser, Paul B, Levine, Ross L, Lowe, Scott W, Sadelain, Michel, Beyaz, Semir, Amor, Corina (November 2025) Anti-uPAR CAR T cells reverse and prevent aging-associated defects in intestinal regeneration and fitness. Nature Aging. ISSN 2662-8465

Long, Yuexuan, Ni, Xiaolin, Chen, Tingwei, Huang, Xianzhe, Hong, Qiyang, Wang, Jixin, Wang, Cong, Huang, Zigeng, Xu, Haiqing, Sun, Mengyi, Pang, Junling, Choi, Jiyeon, Zhang, Tongwu, Long, Erping (November 2025) Genetic determinants of gene expression noise and its role in complex trait variation. Cell Reports, 44 (12). p. 116612. ISSN 2211-1247

Clausen, Thomas Mandel, Weiss, Ryan J, Tremblay, Jacob R, Kellman, Benjamin P, Coker, Joanna, Dworkin, Leo A, Rodriguez, Jessica P, Chang, Ivy M, Chen, Timothy, Padala, Vikram, Karlsson, Richard, Song, Hyemin, Peck, Kristina L, Ogawa, Satoshi, Sandoval, Daniel R, Joshi, Hiren J, Wang, Gaowei, Ferguson, L Paige, Bhalerao, Nikita, Moores, Allison, Reya, Tannishtha, Sander, Maike, Caffrey, Thomas C, Grem, Jean L, Aicher, Alexandra, Heeschen, Christopher, Le, Dzung, Lewis, Nathan E, Hollingsworth, Michael A, Grandgenett, Paul M, Bellis, Susan L, Miller, Rebecca L, Fuster, Mark M, Dawson, David W, Engle, Dannielle D, Esko, Jeffrey D (November 2025) Antithrombin-binding heparan sulfate is ubiquitously expressed in epithelial cells and suppresses pancreatic tumorigenesis. Journal of Clinical Investigation, 135 (22). ISSN 1558-8238

Cunniff, Patrick J, Sivetz, Nicole, Skopelitis, Damianos, Klingbeil, Olaf, Toobian, Daniel, Maia-Silva, Diogo, Egeblad, Mikala, Vakoc, Christopher R (November 2025) KLF5 enables dichotomous lineage programs in pancreatic cancer via the AAA+ ATPase coactivators RUVBL1 and RUVBL2. Nature Communications, 16 (1). p. 9996. ISSN 2041-1723

Qi, Xiaoli, Muñoz-Castañeda, Rodrigo, Yue, Yuanlei, Xiao, Sheng, Ding, Liya, Narasimhan, Arun, Chen, Xin, Wang, Wei, Li, Yuanyuan, Elowsky, Corey, Palmer, Jason, Drewes, Rhonda, Sun, Jianjun, Wu, Jinglei, Qu, Lei, Wu, Zhuhao, Peng, Hanchuan, Osten, Pavel (November 2025) Confocal Airy beam oblique light-sheet tomography for brain-wide cell type distribution and morphology. Nature Methods. ISSN 1548-7091

Gentile, Iacopo, Santo Domingo, Miguel, Zebell, Sophia G, Fitzgerald, Blaine, Lippman, Zachary B (November 2025) Pan-angiosperm analysis of the CLE signaling peptide gene family unveils paths, patterns, and predictions of paralog diversification. Molecular Biology and Evolution (MBE), 42 (11). msaf294. ISSN 0737-4038

Kang, Hyunook, Steigerwald, Ruben, Ullman, Elijah Z, Epstein, Max, Paladugu, Srinu, Liotta, Dennis C, Traynelis, Stephen F, Furukawa, Hiro (October 2025) Mechanism of conductance control and neurosteroid binding in NMDA receptors. Nature. ISSN 0028-0836

Cheng, Teri, Roche, Benjamin, Abderahmane, Farida, Touat-Todeschini, Leila, Fréon, Karine, Lakhani, Asad A, Bhattacharjee, Sonali, Spielmann, Liam G, Jenen, Emerson, Choi, Christine, Ren, Jie, Verdel, André, Lambert, Sarah AE, Martienssen, Robert A (October 2025) Transcription-replication conflict resolution by nuclear RNA interference. Molecular Cell. ISSN 1097-2765 (Public Dataset)

Bencze, Gyula, Venkataramani, Prabhadevi, Elkayam, Elad, Rivera, Keith D, Garg, Ankur, Szabadkai, Istvan, Orfi, Laszlo, Joshua-Tor, Leemor, Pappin, Darryl, Tonks, Nicholas K (October 2025) Identification and Validation of an inhibitor of the protein kinases PIM and DYRK. bioRxiv. ISSN 2692-8205 (Submitted)

Dantas, Ezequiel, Murthy, Anirudh, Kim, Jeshua, Ahmed, Tanvir, Ahmed, Mujmmail, Perrier, Tiffany, Ramsamooj, Shakti, Nathoo, Isaac, Kniess Debarba, Lucas, Lima Queiroz, Andre, Li, Shiri, Ersoy, Baran, Ferrer, Miriam, Goldstein, Ido, Gao, Jonathan, Lam, Tiffany, Nagler, Matthew, Malbari, Murtaza, Altorki, Nasser, Cararo Lopes, Eduardo, Gomez Jenkins, Maria, Das, Trishna, Jamal-Hanjani, Mariam, White, Eileen, Janowitz, Tobias, Goncalves, Marcus D (October 2025) JAK1/2 Inhibition Delays Cachexia and Improves Survival through Increased Food Intake. bioRxiv. ISSN 2692-8205 (Submitted)

O’Neil, Shawn T, Schilder, Brian M, Schaper, Kevin, Cox, Corey, Korn, Daniel, Gehrke, Sarah, Mungall, Christopher J, Haendel, Melissa A (October 2025) monarchr: an R package for querying biomedical knowledge graphs. Bioinformatics, 41 (10). ISSN 1367-4803

Chorbadjiev, Liubomir, Cokol, Murat, Weinstein, Zohar, Shi, Kevin, Fleisch, Christopher, Dimitrov, Nikolay, Mladenov, Svetlin, Todorov, Ivo, Ivanov, Iordan, Xu, Simon, Ford, Steven, Lee, Yoon-Ha, Yamrom, Boris, Marks, Steven, Munoz, Adriana, Lash, Alex, Volfovsky, Natalia, Iossifov, Ivan (September 2025) Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform. Genome Research. ISSN 1088-9051

Staklinski, Stephen, Scheben, Armin, Brault, Lise, Hassett, Rebecca, Serio, Ryan, Xing, Jiawei, Nowak, Dawid, Siepel, Adam (September 2025) Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data. bioRxiv. ISSN 2692-8205 (Submitted)

Xu, Xiaosa, Passalacqua, Michael, Rice, Brian, Demesa-Arevalo, Edgar, Kojima, Mikiko, Takebayashi, Yumiko, Yu, Xingyao, Harris, Benjamin, Liu, Yuchen, Gallavotti, Andrea, Sakakibara, Hitoshi, Gillis, Jesse, Jackson, David (August 2025) Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variation. Developmental Cell. S1534-5807(25)00500. ISSN 1534-5807

Tran, Thu M, Claeys, Hannes, Abraham-Juárez, María Jazmín, Vi, Son L, Xu, Xiaosa, Michalski, Kevin, Chou, Tsung Han, Iohannes, Sessen D, Boumpas, Panagiotis, Williams, Z'Dhanne P, Sheppard, Samatha, Griffiths, Cara, Paul, Matthew J, Furukawa, Hiro, Jackson, David (August 2025) Non-catalytic and catalytic TREHALOSE-6-PHOSPHATE SYNTHASES interact with RAMOSA3 to control maize development. bioRxiv. ISSN 2692-8205

Julian, Linda, Crozier, Lisa, Lukow, Devon, Mishra, Sanat, Swamy, Aditi, Hagenson, Ryan A, Sennhenn, Peter, Sausville, Erin L, Mendelson, Brianna, Chuaqui, Claudio, Qiao, Lu, Vasudevan, Anand, Lin, Kuan-Ting, Bhatia, Sonam, Bertomeu, Thierry, Chatr-Aryamontri, Andrew, Zhang, Li, Rees, Matthew G, Ronan, Melissa M, Roth, Jennifer A, Nottoli, Timothy, Bai, Suxia, Lakshmipathi, Jayalakshmi, Muthusamy, Viswanathan, Van Vranken, Jonathan G, Gygi, Steven P, Thompson, Sarah L, Smith, Joan C, Anderson, Kendall, Shah, Sanjana, Bindra, Ranjit S, Akerman, Martin, Spector, David L, Krainer, Adrian R, Sheltzer, Jason M (August 2025) On-target toxicity limits the efficacy of CDK11 inhibition against cancers with 1p36 deletions. bioRxiv. ISSN 2692-8205 (Submitted)

Adrover, Jose M, Han, Xiao, Sun, Lijuan, Fujii, Takeo, Sivetz, Nicole, Daßler-Plenker, Juliane, Evans, Clary, Peters, Jessica, He, Xue-Yan, Cannon, Courtney D, Ho, Won Jin, Raptis, George, Powers, R Scott, Egeblad, Mikala (July 2025) Neutrophils drive vascular occlusion, tumour necrosis and metastasis. Nature. ISSN 0028-0836 (Public Dataset)

Zebell, Sophia G, Martí-Gómez, Carlos, Fitzgerald, Blaine, Cunha, Camila P, Lach, Michael, Seman, Brooke M, Hendelman, Anat, Sretenovic, Simon, Qi, Yiping, Bartlett, Madelaine, Eshed, Yuval, McCandlish, David M, Lippman, Zachary B (July 2025) Cryptic variation fuels plant phenotypic change through hierarchical epistasis. Nature. ISSN 0028-0836 (Public Dataset)

Reid, Ashlan P, Neophytou, Demetrios, Levy, Robert, Pham, Cody, Oviedo, Hysell V (April 2025) Asynchronous development of the mouse auditory cortex is driven by hemispheric identity and sex. Nature Communications, 16 (1). p. 3654. ISSN 2041-1723

Zhu, Xiaoyue Aelita, Starosta, Sarah, Ferrer, Miriam, Hou, Junxiao, Chevy, Quentin, Lucantonio, Federica, Muñoz-Castañeda, Rodrigo, Zhang, Fengrui, Zang, Kaikai, Zhao, Xiang, Fiocchi, Francesca R, Bergstrom, Mason, Siebels, Aubrey A, Upin, Thomas, Wulf, Michael, Evans, Sarah, Kravitz, Alexxai V, Osten, Pavel, Janowitz, Tobias, Pignatelli, Marco, Kepecs, Adam (April 2025) A neuroimmune circuit mediates cancer cachexia-associated apathy. Science, 388 (6743). eadm8857. ISSN 0036-8075

Koh, Matthew, Anselmi, Francesca, Kaushalya, Sanjeev K, Hernandez, Diego E, Bast, Walter Germán, Villar, Pablo S, Chae, Honggoo, Davis, Martin B, Teja, Sadhu Sai, Qu, Zhe, Gradinaru, Viviana, Gupta, Priyanka, Banerjee, Arkarup, Albeanu, Dinu F (March 2025) Axially decoupled photo-stimulation and two photon readout (ADePT) for mapping functional connectivity of neural circuits. bioRxiv. ISSN 2692-8205 (Submitted)

Benoit, Matthias, Jenike, Katharine M, Satterlee, James W, Ramakrishnan, Srividya, Gentile, Iacopo, Hendelman, Anat, Passalacqua, Michael J, Suresh, Hamsini, Shohat, Hagai, Robitaille, Gina M, Fitzgerald, Blaine, Alonge, Michael, Wang, Xingang, Santos, Ryan, He, Jia, Ou, Shujun, Golan, Hezi, Green, Yumi, Swartwood, Kerry, Karavolias, Nicholas G, Sierra, Gina P, Orejuela, Andres, Roda, Federico, Goodwin, Sara, McCombie, W Richard, Kizito, Elizabeth B, Gagnon, Edeline, Knapp, Sandra, Särkinen, Tiina E, Frary, Amy, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Lippman, Zachary B (March 2025) Solanum pan-genetics reveals paralogues as contingencies in crop engineering. Nature. ISSN 0028-0836 (Public Dataset)

Lanctot, Amy, Hendelman, Anat, Udilovich, Peter, Robitaille, Gina M, Lippman, Zachary B (February 2025) Antagonizing cis-regulatory elements of a conserved flowering gene mediate developmental robustness. Proceedings of the National Academy of Sciences of the United States of America, 122 (8). e2421990122. ISSN 0027-8424

Zebell, Sophia G, Martí-Gómez, Carlos, Fitzgerald, Blaine, Pinto Da Cunha, Camila, Lach, Michael, Seman, Brooke M, Hendelman, Anat, Sretenovic, Simon, Qi, Yiping, Bartlett, Madelaine, Eshed, Yuval, McCandlish, David M, Lippman, Zachary B (February 2025) Cryptic variation fuels plant phenotypic change through hierarchical epistasis. bioRxiv. ISSN 2692-8205 (Public Dataset) (Submitted)

Hernandez, Diego E, Ciuparu, Andrei, Garcia da Silva, Pedro, Velasquez, Cristina M, Rebouillat, Benjamin, Gross, Michael D, Davis, Martin B, Chae, Honggoo, Muresan, Raul C, Albeanu, Dinu F (January 2025) Fast updating feedback from piriform cortex to the olfactory bulb relays multimodal identity and reward contingency signals during rule-reversal. Nature Communications, 16 (1). p. 937. ISSN 2041-1723 (Public Dataset)

Garg, Ankur, On, Kin Fan, Xiao, Yang, Elkayam, Elad, Cifani, Paolo, David, Yael, Joshua-Tor, Leemor (January 2025) The molecular basis of Human FN3K mediated phosphorylation of glycated substrates. Nature Communications, 16 (1). p. 941. ISSN 2041-1723 (Public Dataset)

Cahn, Jonathan, Regulski, Michael, Lynn, Jason, Ernst, Evan, de Santis Alves, Cristiane, Ramakrishnan, Srividya, Chougule, Kapeel, Wei, Sharon, Lu, Zhenyuan, Xu, Xiaosa, Ramu, Umamaheswari, Drenkow, Jorg, Kramer, Melissa, Seetharam, Arun, Hufford, Matthew B, McCombie, W Richard, Ware, Doreen, Jackson, David, Schatz, Michael C, Gingeras, Thomas R, Martienssen, Robert A (December 2024) MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. Nature Communications, 15 (1). p. 10854. ISSN 2041-1723 (Public Dataset)

Liang, Heng, Fisher, Matthew L, Wu, Caizhi, Ballon, Carlos, Sun, Xueqin, Mills, Alea A (November 2024) PRMT5/WDR77 Enhances the Proliferation of Squamous Cell Carcinoma via the ΔNp63α-p21 Axis. Cancers, 16 (22). p. 3789. ISSN 2072-6694 (Public Dataset)

Lanctot, Amy, Hendelman, Anat, Udilovich, Peter, Robitaille, Gina M, Lippman, Zachary (November 2024) Antagonizing cis-regulatory elements of a conserved flowering gene mediate developmental robustness. bioRxiv. ISSN 2692-8205 (Submitted)

Swamynathan, Manojit M, Kuang, Shan, Watrud, Kaitlin E, Doherty, Mary R, Gineste, Charlotte, Mathew, Grinu, Gong, Grace Q, Cox, Hilary, Cheng, Eileen, Reiss, David, Kendall, Jude, Ghosh, Diya, Reczek, Colleen R, Zhao, Xiang, Herzka, Tali, Špokaitė, Saulė, Dessus, Antoine N, Kim, Seung Tea, Klingbeil, Olaf, Liu, Juan, Nowak, Dawid G, Alsudani, Habeeb, Wee, Tse-Luen, Park, Youngkyu, Minicozzi, Francesca, Rivera, Keith, Almeida, Ana S, Chang, Kenneth, Chakrabarty, Ram P, Wilkinson, John E, Gimotty, Phyllis A, Diermeier, Sarah D, Egeblad, Mikala, Vakoc, Christopher R, Locasale, Jason W, Chandel, Navdeep S, Janowitz, Tobias, Hicks, James B, Wigler, Michael, Pappin, Darryl J, Williams, Roger L, Cifani, Paolo, Tuveson, David A, Laporte, Jocelyn, Trotman, Lloyd C (October 2024) Dietary pro-oxidant therapy by a vitamin K precursor targets PI 3-kinase VPS34 function. Science, 386 (6720). eadk9167. ISSN 0036-8075

Chen, Qian, Wang, Saisai, Zhang, Juqing, Xie, Min, Lu, Bin, He, Jie, Zhen, Zhuoran, Li, Jing, Zhu, Jiajun, Li, Rong, Li, Pilong, Wang, Haifeng, Vakoc, Christopher, Roeder, Robert G, Chen, Mo (October 2024) JMJD1C forms condensates to facilitate a RUNX1-dependent gene expression program shared by multiple types of AML cells. Protein and Cell. pwae059. ISSN 1674-800X (Public Dataset)

Kelberman, Michael A, Rodberg, Ellen, Arabzadeh, Ehsan, Bair-Marshall, Chloe J, Berridge, Craig W, Berrocoso, Esther, Breton-Provencher, Vincent, Chandler, Daniel J, Che, Alicia, Davy, Oscar, Devilbiss, David M, Downs, Anthony M, Drummond, Gabrielle, Dvorkin, Roman, Fazlali, Zeinab, Froemke, Robert C, Glennon, Erin, Gold, Joshua I, Ito, Hiroki, Jiang, Xiaolong, Johansen, Joshua P, Kaye, Alfred P, Kim, Jenny R, Kuo, Chao-Cheng, Liu, Rong-Jian, Liu, Yang, Llorca-Torralba, Meritxell, McCall, Jordan G, McElligott, Zoe A, McKinney, Andrew M, Miguelez, Cristina, Min, Ming-Yuan, Nowlan, Alexandra C, Omrani, Mohsen, Poe, Gina R, Pickering, Anthony Edward, Ranjbar-Slamloo, Yadollah, Razquin, Jone, Rodenkirch, Charles, Sales, Anna C, Satyasambit, Rath, Shea, Stephen D, Sur, Mriganka, Tkaczynski, John Arthur, Torres-Sanchez, Sonia, Uematsu, Akira, Vazquez, Chayla R, Vreven, Amelien, Wang, Qi, Waterhouse, Barry D, Yang, Hsiu-Wen, Yang, Jen-Hau, Zhao, Liping, Zouridis, Ioannis S, Weinshenker, David, Vazey, Elena, Totah, Nelson K (October 2024) Diversity of ancestral brainstem noradrenergic neurons across species and multiple biological factors. bioRxiv. ISSN 2692-8205 (Submitted)

Yuan, Li, Chen, Xiaoyin, Zhan, Huiqing, Henry, Gilbert L, Zador, Anthony M (September 2024) Massive multiplexing of spatially resolved single neuron projections with axonal BARseq. Nature Communications, 15 (1). p. 8371. ISSN 2041-1723 (Public Dataset)

Benoit, Matthias, Jenike, Katharine M, Satterlee, James W, Ramakrishnan, Srividya, Gentile, Iacopo, Hendelman, Anat, Passalacqua, Michael J, Suresh, Hamsini, Shohat, Hagai, Robitaille, Gina M, Fitzgerald, Blaine, Alonge, Michael M, Wang, Xingang, Santos, Ryan, He, Jia, Ou, Shujun, Golan, Hezi, Green, Yumi, Swartwood, Kerry, Sierra, Gina P, Orejuela, Andres, Fornaguera, Federico, Goodwin, Sara, McCombie, William Richard, Kizito, Elizabeth Balyejusa, Gagnon, Edeline, Knapp, Sandra, Sarkinen, Tiina, Frary, Amy, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Lippman, Zachary B (September 2024) Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering. bioRxiv. ISSN 2692-8205 (Submitted)

Shimada, Atsushi, Cahn, Jonathan, Ernst, Evan, Lynn, Jason, Grimanelli, Daniel, Henderson, Ian, Kakutani, Tetsuji, Martienssen, Robert A (September 2024) Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs. Nature Plants. ISSN 2055-0278 (Public Dataset)

Wang, Bo, Chougule, Kapeel, Jiao, Yinping, Olson, Andrew, Kumar, Vivek, Gladman, Nicholas, Huang, Jian, Llaca, Victor, Fengler, Kevin, Wei, Xuehong, Wang, Liya, Wang, Xiaofei, Regulski, Michael, Drenkow, Jorg, Gingeras, Thomas, Hayes, Chad, Armstrong, J Scott, Huang, Yinghua, Xin, Zhanguo, Ware, Doreen (September 2024) High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436. NAR Genomics and Bioinformatics, 6 (3). lqae097. ISSN 2631-9268 (Public Dataset)

Garg, Ankur, On, Kin Fan, Xiao, Yang, Elkayam, Elad, Cifani, Paolo, David, Yael, Joshua-Tor, Leemor (August 2024) The molecular basis of Human FN3K mediated phosphorylation of glycated substrate. 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, Poncet, Adrien, Bellot, Clement, Frary, Amy, Knapp, Sandra, Bendahmane, Mohammed, Särkinen, Tiina, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Eshed, Yuval, Prohens, Jaime, Vilanova, Santiago, Lippman, Zachary B (August 2024) Convergent evolution of plant prickles by repeated gene co-option over deep time. Science, 385 (6708). eado1663. ISSN 0036-8075 (Public Dataset)

Klingbeil, Olaf, Skopelitis, Damianos, Tonelli, Claudia, Yoshimoto, Toyoki, Alpsoy, Aktan, Panepinto, Maria C, Minicozzi, Francesca, Merrill, Joseph R, Cafiero, Amanda M, Aggarwal, Disha, Russo, Suzanne, Ha, Taehoon, Demerdash, Osama E, Wee, Tse-Luen, Spector, David L, Lyons, Scott K, Tuveson, David A, Cifani, Paolo, Vakoc, Christopher R (July 2024) MARK2/MARK3 kinases are catalytic co-dependencies of YAP/TAZ in human cancer. Cancer Discovery. ISSN 2159-8274 (Public Dataset)

Li, Jiayun, Moresco, Philip, Fearon, Douglas T (July 2024) Intratumoral NKT cell accumulation promotes antitumor immunity in pancreatic cancer. Proceedings of the National Academy of Sciences of the United States of America, 121 (29). e2403917121. ISSN 0027-8424 (Public Dataset)

He, Tongchen, Xiao, Lanbo, Qiao, Yuanyuan, Klingbeil, Olaf, Young, Eleanor, Wu, Xiaoli S, Mannan, Rahul, Mahapatra, Somnath, Redin, Esther, Cho, Hanbyul, Bao, Yi, Kandarpa, Malathi, Ching-Yi Tien, Jean, Wang, Xiaoju, Eyunni, Sanjana, Zheng, Yang, Kim, NamHoon, Zheng, Heng, Hou, Siyu, Su, Fengyun, Miner, Stephanie J, Mehra, Rohit, Cao, Xuhong, Abbineni, Chandrasekhar, Samajdar, Susanta, Ramachandra, Murali, Dhanasekaran, Saravana M, Talpaz, Moshe, Parolia, Abhijit, Rudin, Charles M, Vakoc, Christopher R, Chinnaiyan, Arul M (June 2024) Targeting the mSWI/SNF complex in POU2F-POU2AF transcription factor-driven malignancies. Cancer Cell. S1535-6108(24)00231. ISSN 1535-6108 (Public Dataset)

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

Seo, Myeong-Gyun, Lim, Yoonseo, Hendelman, Anat, Robitaille, Gina, Beak, Hong Kwan, Hong, Woo-Jong, Park, Soon Ju, Lippman, Zachary B, Park, Young-Joon, Kwon, Choon-Tak (June 2024) Evolutionary conservation of receptor compensation for stem cell homeostasis in Solanaceae plants. Horticulture Research, 11 (6). uhae126. ISSN 2662-6810 (Public Dataset)

Throesch, Benjamin T, Bin Imtiaz, Muhammad Khadeesh, Muñoz-Castañeda, Rodrigo, Sakurai, Masahiro, Hartzell, Andrea L, James, Kiely N, Rodriguez, Alberto R, Martin, Greg, Lippi, Giordano, Kupriyanov, Sergey, Wu, Zhuhao, Osten, Pavel, Izpisua Belmonte, Juan Carlos, Wu, Jun, Baldwin, Kristin K (April 2024) Functional sensory circuits built from neurons of two species. Cell, 187 (9). 2143-2157.e15. ISSN 0092-8674

Homer, Joshua A, Koelln, Rebecca A, Barrow, Andrew S, Gialelis, Timothy L, Boiarska, Zlata, Steinohrt, Nikita S, Lee, Erinna F, Yang, Wen-Hsuan, Johnson, Robert M, Chung, Taemoon, Habowski, Amber N, Vishwakarma, Dharmendra S, Bhunia, Debmalya, Avanzi, Charlotte, Moorhouse, Adam D, Jackson, Mary, Tuveson, David A, Lyons, Scott K, Lukey, Michael J, Fairlie, W Douglas, Haider, Shozeb M, Steinmetz, Michel O, Prota, Andrea E, Moses, John E (March 2024) Modular synthesis of functional libraries by accelerated SuFEx click chemistry. Chemical Science, 15 (11). pp. 3879-3892. ISSN 2041-6520 (Public Dataset)

Klingbeil, Olaf, Skopelitis, Damianos, Tonelli, Claudia, Alpsoy, Aktan, Minicozzi, Francesca, Aggarwal, Disha, Russo, Suzanne, Ha, Taehoon, Demerdash, Osama E, Spector, David L, Tuveson, David A, Cifani, Paolo, Vakoc, Christopher R (February 2024) MARK2/MARK3 kinases are catalytic co-dependencies of YAP/TAZ in human cancer. bioRxiv. (Submitted)

Cahn, Jonathan, Regulski, Michael, Lynn, Jason, Ernst, Evan, Alves, Cristiane de Santis, Ramakrishnan, Srividya, Chougule, Kapeel, Wei, Sharon, Lu, Zhenyuan, Xu, Xiaosa, Drenkow, Jorg, Kramer, Melissa, Seetharam, Arun, Hufford, Matthew, McCombie, Richard, Ware, Doreen, Jackson, David, Schatz, Michael, Gingeras, Thomas, Martienssen, Robert (February 2024) MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. bioRxiv. (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)

Gustison, Morgan L, Muñoz-Castañeda, Rodrigo, Osten, Pavel, Phelps, Steven M (February 2024) Sexual coordination in a whole-brain map of prairie vole pair bonding. eLife, 12. RP87029. ISSN 2050-084X (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

Chorbadjiev, Liubomir, Cokol, Murat, Weinstein, Zohar, Shi, Kevin, Fleisch, Chris, Dimitrov, Nikolay, Mladenov, Svetlin, Xu, Simon, Hall, Jake, Ford, Steven, Lee, Yoon-Ha, Yamrom, Boris, Marks, Steven, Munoz, Adriana, Lash, Alex, Volfovsky, Natalia, Iossifov, Ivan (February 2024) The Genotype and Phenotypes in Families (GPF) platform manages the large and complex data at SFARI. bioRxiv. (Submitted)

He, Tongchen, Xiao, Lanbo, Qiao, Yuanyuan, Klingbeil, Olaf, Young, Eleanor, Wu, Xiaoli S, Mannan, Rahul, Mahapatra, Somnath, Eyunni, Sanjana, Tien, Jean Ching-Yi, Wang, Xiaoju, Zheng, Yang, Kim, NamHoon, Zheng, Heng, Hou, Siyu, Su, Fengyun, Miner, Stephanie J, Mehra, Rohit, Cao, Xuhong, Sekhar, A Chandra, Samajdar, Susanta, Ramachandra, Murali, Parolia, Abhijit, Vakoc, Christopher R, Chinnaiyan, Arul M (January 2024) Targeting the mSWI/SNF Complex in POU2F-POU2AF Transcription Factor-Driven Malignancies. bioRxiv. (Submitted)

Alpsoy, Aktan, Wu, Xiaoli S, Pal, Sujay, Klingbeil, Olaf, Kumar, Pramod, El Demerdash, Osama, Nalbant, Benan, Vakoc, Christopher R (January 2024) IκBζ is a dual-use coactivator of NF-κB and POU transcription factors. Molecular Cell. S1097-2765(24)00008. ISSN 1097-2765 (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

Swamynathan, Manojit, Mathew, Grinu, Aziz, Andrei, Gordon, Chris, Hillowe, Andrew, Wang, Hehe, Jhaveri, Aashna, Kendall, Jude, Cox, Hilary, Giarrizzo, Michael, Azabdaftari, Gissou, Rizzo, Robert C, Diermeier, Sarah D, Ojima, Iwao, Bialkowska, Agnieszka B, Kaczocha, Martin, Trotman, Lloyd C (2024) FABP5 Inhibition against PTEN-Mutant Therapy Resistant Prostate Cancer. Cancers, 16 (1). p. 60. ISSN 2072-6694

Xu, Jihao, Roe, Jae-Seok, Lee, EunJung, Tonelli, Claudia, Ji, Keely Y, Younis, Omar W, Somervile, Tim DD, Yao, Melissa, Milazzo, Joseph P, Tiriac, Herve, Kolarzyk, Anna M, Lee, Esak, Grem, Jean L, Lazenby, Audrey J, Grunkemeyer, James A, Hollingsworth, Michael A, Grandgenett, Paul M, Borowsky, Alexander D, Park, Youngkyu, Vakoc, Christopher R, Tuveson, David A, Hwang, Chang-Il (December 2023) Engrailed-1 Promotes Pancreatic Cancer Metastasis. Advanced Science. e2308537. ISSN 2198-3844

Balasooriya, Gayan I, Wee, Tse-Luen, Spector, David L (October 2023) A sub-set of guanine- and cytosine-rich genes are actively transcribed at the nuclear Lamin B1 region. bioRxiv. (Public Dataset) (Submitted)

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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

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

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

Scheben, Armin, Mendivil Ramos, Olivia, Kramer, Melissa, Goodwin, Sara, Oppenheim, Sara, Becker, Daniel J, Schatz, Michael C, Simmons, Nancy B, Siepel, Adam, McCombie, W Richard (September 2023) Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biology and Evolution, 15 (9). ISSN 1759-6653 (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)

Stevenson, Dennis Wm, Ramakrishnan, Srividya, Alves, Cristiane de Santis, Coelho, Laís Araujo, Kramer, Melissa, Goodwin, Sara, Ramos, Olivia Mendevil, Eshel, Gil, Sondervan, Veronica M, Frangos, Samantha, Zumajo-Cardona, Cecilia, Jenike, Katherine, Ou, Shujun, Wang, Xiaojin, Lee, Yin Peng, Loke, Stella, Rossetto, Maurizio, McPherson, Hannah, Nigris, Sebastiano, Moschin, Silvia, Little, Damon P, Katari, Manpreet S, Varala, Kranthi, Kolokotronis, Sergios-Orestis, Ambrose, Barbara, Croft, Larry J, Coruzzi, Gloria M, Schatz, Michael, McCombie, W Richard, Martienssen, Robert A (August 2023) The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. bioRxiv. (Public Dataset) (Submitted)

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

Merrill, Joseph R, Inguscio, Alessandra, Chung, Taemoon, Demestichas, Breanna, Garcia, Libia A, Habel, Jill, Lewis, David Y, Janowitz, Tobias, Lyons, Scott K (August 2023) Sensitive, non-immunogenic in vivo imaging of cancer metastases and immunotherapy response. Cell Stress, 7 (8). pp. 59-68. ISSN 2523-0204

Shimada, Atsushi, Cahn, Jonathan, Ernst, Evan, Lynn, Jason, Grimanelli, Daniel, Henderson, Ian, Kakutani, Tetsuji, Martienssen, Robert A (August 2023) Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs. (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)

Brina, Daniela, Ponzoni, Adele, Troiani, Martina, Calì, Bianca, Pasquini, Emiliano, Attanasio, Giuseppe, Mosole, Simone, Mirenda, Michela, D'Ambrosio, Mariantonietta, Colucci, Manuel, Guccini, Ilaria, Revandkar, Ajinkya, Alajati, Abdullah, Tebaldi, Toma, Donzel, Deborah, Lauria, Fabio, Parhizgari, Nahjme, Valdata, Aurora, Maddalena, Martino, Calcinotto, Arianna, Bolis, Marco, Rinaldi, Andrea, Barry, Simon, Rüschoff, Jan Hendrik, Sabbadin, Marianna, Sumanasuriya, Semini, Crespo, Mateus, Sharp, Adam, Yuan, Wei, Grinu, Mathew, Boyle, Alexandra, Miller, Cynthia, Trotman, Lloyd, Delaleu, Nicolas, Fassan, Matteo, Moch, Holger, Viero, Gabriella, de Bono, Johann, Alimonti, Andrea (August 2023) The Akt/mTOR and MNK/eIF4E pathways rewire the prostate cancer translatome to secrete HGF, SPP1 and BGN and recruit suppressive myeloid cells. Nature Cancer, 4 (8). pp. 1102-1121. ISSN 2662-1347 (Public Dataset)

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

Costa, Iris Munhoz, Effer, Brian, Costa-Silva, Tales Alexandre, Chen, Chen, Ciccone, Michael F, Pessoa, Adalberto, Dos Santos, Camila O, Monteiro, Gisele (July 2023) Cathepsin B Is Not an Intrinsic Factor Related to Asparaginase Resistance of the Acute Lymphoblastic Leukemia REH Cell Line. International Journal of Molecular Sciences, 24 (13). p. 11215. ISSN 1661-6596

Syrjänen, Johanna L, Epstein, Max, Gómez, Ricardo, Furukawa, Hiro (June 2023) Structure of human CALHM1 reveals key locations for channel regulation and blockade by ruthenium red. Nature Communications, 14 (1). p. 3821. ISSN 2041-1723 (Public Dataset)

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

Gialelis, Timothy L, Wang, Zifei, Homer, Joshua A, Yang, Wen-Hsuan, Chung, Taemoon, Hu, Qingting, Smedley, Christopher J, Pawar, Nitin J, Upadhyay, Nitinkumar S, Tuveson, David A, Lyons, Scott K, Lukey, Michael J, Moses, John E (April 2023) Inhibition of mitochondrial metabolism by (-)-jerantinine A: synthesis and biological studies in triple-negative breast cancer cells. MedChemComm, 14 (4). pp. 710-714. ISSN 2632-8682

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)

Mousset, Alexandra, Lecorgne, Enora, Bourget, Isabelle, Lopez, Pascal, Jenovai, Kitti, Cherfils-Vicini, Julien, Dominici, Chloé, Rios, Géraldine, Girard-Riboulleau, Cédric, Liu, Bodu, Spector, David L, Ehmsen, Sidse, Renault, Shufang, Hego, Caroline, Mechta-Grigoriou, Fatima, Bidard, François-Clément, Terp, Mikkel Green, Egeblad, Mikala, Gaggioli, Cédric, Albrengues, Jean (April 2023) Neutrophil extracellular traps formed during chemotherapy confer treatment resistance via TGF-β activation. Cancer Cell, 41 (4). 757-775.e10. ISSN 1535-6108 (Public Dataset)

Balasooriya, Gayan I, Spector, David L (April 2023) Allele pairing at Sun1-enriched domains at the nuclear periphery via T1A3 tandem DNA repeats. bioRxiv. (Public Dataset) (Submitted)

Chung, Taemoon, Garcia, Libia, Swamynathan, Manojit M, Froeling, Fieke EM, Trotman, Lloyd C, Tuveson, David A, Lyons, Scott K (April 2023) Internally Controlled and Dynamic Optical Measures of Functional Tumor Biology. Analytical Chemistry, 95 (13). pp. 5661-5670. ISSN 0003-2700

Hirschhorn, Daniel, Budhu, Sadna, Kraehenbuehl, Lukas, Gigoux, Mathieu, Schröder, David, Chow, Andrew, Ricca, Jacob M, Gasmi, Billel, De Henau, Olivier, Mangarin, Levi Mark B, Li, Yanyun, Hamadene, Linda, Flamar, Anne-Laure, Choi, Hyejin, Cortez, Czrina A, Liu, Cailian, Holland, Aliya, Schad, Sara, Schulze, Isabell, Betof Warner, Allison, Hollmann, Travis J, Arora, Arshi, Panageas, Katherine S, Rizzuto, Gabrielle A, Duhen, Rebekka, Weinberg, Andrew D, Spencer, Christine N, Ng, David, He, Xue-Yan, Albrengues, Jean, Redmond, David, Egeblad, Mikala, Wolchok, Jedd D, Merghoub, Taha (March 2023) T cell immunotherapies engage neutrophils to eliminate tumor antigen escape variants. Cell, 186 (7). 1432-1447.e17. ISSN 0092-8674 (Public Dataset)

Bonham, ChristopherA, Mandati, Vinay, Singh, RakeshK, Pappin, DarrylJ, Tonks, NicholasK (March 2023) Coupling substrate-trapping with proximity-labeling to identify protein tyrosine phosphatase PTP1B signaling networks. Journal of Biological Chemistry. p. 104582. ISSN 0021-9258

Adrover, Jose M, McDowell, Sheri AC, He, Xue-Yan, Quail, Daniela F, Egeblad, Mikala (February 2023) NETworking with cancer: The bidirectional interplay between cancer and neutrophil extracellular traps. Cancer Cell. ISSN 1535-6108

Hazra, Rasmani, Utama, Raditya, Naik, Payal, Dobin, Alexander, Spector, David L (January 2023) Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA-sequencing datasets. 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)

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

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

Xu, Xiaosa, Jackson, David (December 2022) Single-cell analysis opens a goldmine for plant functional studies. Current Opinion in Biotechnology, 79. p. 102858. ISSN 0958-1669

Szadai, Zoltán, Pi, Hyun-Jae, Chevy, Quentin, Ócsai, Katalin, Albeanu, Dinu F, Chiovini, Balázs, Szalay, Gergely, Katona, Gergely, Kepecs, Adam, Rózsa, Balázs (November 2022) Cortex-wide response mode of VIP-expressing inhibitory neurons by reward and punishment. eLife, 11. e78815. ISSN 2050-084X

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

Chen, Yushu, Chen, Xiaoyin, Baserdem, Batuhan, Zhan, Huiqing, Li, Yan, Davis, Martin B, Kebschull, Justus M, Zador, Anthony M, Koulakov, Alexei A, Albeanu, Dinu F (October 2022) High-throughput sequencing of single neuron projections reveals spatial organization in the olfactory cortex. Cell, 185 (22). 4117-4134.e28. ISSN 0092-8674

He, Jia, Alonge, Michael, Ramakrishnan, Srividya, Benoit, Matthias, Soyk, Sebastian, Reem, Nathan T, Hendelman, Anat, Van Eck, Joyce, Schatz, Michael C, Lippman, Zachary B (October 2022) Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. The Plant Cell, 35 (1). pp. 351-368. ISSN 1532-298X

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

Qian, Yongjun, Li, Jiayun, Zhao, Shengli, Matthews, Elizabeth A, Adoff, Michael, Zhong, Weixin, An, Xu, Yeo, Michele, Park, Christine, Yang, Xiaolu, Wang, Bor-Shuen, Southwell, Derek G, Huang, Z Josh (October 2022) Programmable RNA sensing for cell monitoring and manipulation. Nature. ISSN 0028-0836

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

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

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

Doepner, Miriam, Lee, Inyoung, Natale, Christopher A, Brathwaite, Roderick, Venkat, Swati, Kim, Sung Hoon, Wei, Yiliang, Vakoc, Christopher R, Capell, Brian C, Katzenellenbogen, John A, Katzenellenbogen, Benita S, Feigin, Michael E, Ridky, Todd W (September 2022) Endogenous DOPA inhibits melanoma through suppression of CHRM1 signaling. Science Advances, 8 (35). eabn4007. ISSN 2375-2548

Olsen, Timothy, Caruana, Dennis, Cheslack-Postava, Keely, Szema, Austin, Thieme, Juergen, Kiss, Andrew, Singh, Malvika, Smith, Gregory, McClain, Steven, Glotch, Timothy, Esposito, Michael, Promisloff, Robert, Ng, David, He, Xueyan, Egeblad, Mikala, Kew, Richard, Szema, Anthony (August 2022) Iraq/Afghanistan war lung injury reflects burn pits exposure. Scientific Reports, 12 (1). p. 14671. ISSN 2045-2322

Goodwin, Daniel R, Vaughan, Alex, Leible, Daniel, Alon, Shahar, Henry, Gilbert L, Cheng, Anne, Chen, Xiaoyin, Zhang, Ruihan, Xue, Andrew G, Wassie, Asmamaw T, Sinha, Anubhav, Bando, Yosuke, Kajita, Atsushi, Marblestone, Adam H, Zador, Anthony M, Boyden, Edward S, Church, George M, Kohman, Richie E (July 2022) Expansion Sequencing of RNA Barcoded Neurons in the Mammalian Brain: Progress and Implications for Molecularly Annotated Connectomics. bioRxiv. (Submitted)

Werner, Jonathan M, Ballouz, Sara, Hover, John, Gillis, Jesse (July 2022) Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events. Developmental Cell, 57 (16). S1534-5807(22)00496. ISSN 1534-5807

Song, Dongyan, Adrover, Jose M, Felice, Christy, Christensen, Lisa N, He, Xue-Yan, Merrill, Joseph R, Wilkinson, John E, Janowitz, Tobias, Lyons, Scott K, Egeblad, Mikala, Tonks, Nicholas K (July 2022) PTP1B inhibitors protect against acute lung injury and regulate CXCR4 signaling in neutrophils. JCI Insight, 7 (14). e158199. ISSN 2379-3708

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)

Orstad, Grace, Fort, Gabriela, Parnell, Timothy J, Jones, Alex, Stubben, Chris, Lohman, Brian, Gillis, Katherine L, Orellana, Walter, Tariq, Rushmeen, Klingbeil, Olaf, Kaestner, Klaus, Vakoc, Christopher R, Spike, Benjamin T, Snyder, Eric L (July 2022) FoxA1 and FoxA2 control growth and cellular identity in NKX2-1-positive lung adenocarcinoma. Developmental Cell. ISSN 1534-5807

Barnes, Allison C, Rodríguez-Zapata, Fausto, Juárez-Núñez, Karla A, Gates, Daniel J, Janzen, Garrett M, Kur, Andi, Wang, Li, Jensen, Sarah E, Estévez-Palmas, Juan M, Crow, Taylor M, Kavi, Heli S, Pil, Hannah D, Stokes, Ruthie L, Knizner, Kevan T, Aguilar-Rangel, Maria R, Demesa-Arévalo, Edgar, Skopelitis, Tara, Pérez-Limón, Sergio, Stutts, Whitney L, Thompson, Peter, Chiu, Yu-Chun, Jackson, David, Muddiman, David C, Fiehn, Oliver, Runcie, Daniel, Buckler, Edward S, Ross-Ibarra, Jeffrey, Hufford, Matthew B, Sawers, Ruairidh JH, Rellán-Álvarez, Rubén (July 2022) An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time. Proceedings of the National Academy of Sciences of USA, 119 (27). e2100036119. ISSN 0027-8424

Wu, Yuan-Ting, Bennett, Hannah C, Chon, Uree, Vanselow, Daniel J, Zhang, Qingguang, Muñoz-Castañeda, Rodrigo, Cheng, Keith C, Osten, Pavel, Drew, Patrick J, Kim, Yongsoo (June 2022) Quantitative relationship between cerebrovascular network and neuronal cell types in mice. Cell Reports, 39 (12). p. 110978. ISSN 2211-1247

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

Li, Ruitong, Klingbeil, Olaf, Monducci, Davide, Young, Michael J, Rodriguez, Diego J, Bayyat, Zaid, Dempster, Joshua M, Kesar, Devishi, Yang, Xiaoping, Zamanighomi, Mahdi, Vakoc, Christopher R, Ito, Takahiro, Sellers, William R (May 2022) Comparative optimization of combinatorial CRISPR screens. Nature Communications, 13 (1). p. 2469. ISSN 2041-1723

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

He, Xue-Yan, Ng, David, Egeblad, Mikala (April 2022) Caught in a Web: Emerging Roles of Neutrophil Extracellular Traps in Cancer. Annual Review of Cancer Biology, 6 (1). ISSN 2472-3428

Kitagawa, Munenori, Jackson, David (March 2022) A Forward Genetic Approach to Identify Plasmodesmal Trafficking Regulators Based on Trichome Rescue. Methods in Molecular Biology, 2457. pp. 393-407. ISSN 1064-3745

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

Bast, Walter Germán, Albeanu, Dinu F (March 2022) Mapping odorant receptors to their glomeruli. Nature Neuroscience. ISSN 1097-6256

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)

Kaminow, Benjamin, Ballouz, Sara, Gillis, Jesse, Dobin, Alexander (March 2022) Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses. Genome Research. gr.275613.121-gr.275613.121. ISSN 1088-9051

Omary, Moutasem, Gil-Yarom, Naama, Yahav, Chen, Steiner, Evyatar, Hendelman, Anat, Efroni, Idan (March 2022) A conserved superlocus regulates above- and belowground root initiation. Science, 375 (6584). eabf4368. ISSN 0036-8075

Dvorkin, Roman, Shea, Stephen D (February 2022) Precise and pervasive phasic bursting in locus coeruleus during maternal behavior in mice. The Journal of Neuroscience. ISSN 0270-6474

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Giovanniello, J., Yu, K., Furlan, A., Nachtrab, G. T., Sharma, R., Chen, X., Li, B. (November 2020) A Central Amygdala-Globus Pallidus Circuit Conveys Unconditioned Stimulus-Related Information and Controls Fear Learning. J Neurosci, 40 (47). pp. 9043-9054. ISSN 0270-6474 (Print)0270-6474

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Chevy, Q., Kepecs, A. (February 2018) When Acetylcholine Unlocks Feedback Inhibition in Cortex. Neuron, 97 (3). pp. 481-484. ISSN 0896-6273

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

Xu, Y., Milazzo, J. P., Somerville, T. D. D., Tarumoto, Y., Huang, Y. H., Ostrander, E. L., Wilkinson, J. E., Challen, G. A., Vakoc, C. R. (January 2018) A TFIID-SAGA Perturbation that Targets MYB and Suppresses Acute Myeloid Leukemia. Cancer Cell, 33 (1). 13-28 e8. ISSN 1878-3686 (Electronic)1535-6108 (Linking)

Kim, S. H., Kwon, C. T., Song, G., Koh, H. J., An, G., Paek, N. C. (January 2018) The rice zebra3 (z3) mutation disrupts citrate distribution and produces transverse dark-green/green variegation in mature leaves. Rice (N Y), 11 (1). p. 1. ISSN 1939-8425 (Print)1939-8425

Tello-Ruiz, M. K., Naithani, S., Stein, J. C., Gupta, P., Campbell, M., Olson, A., Wei, S., Preece, J., Geniza, M. J., Jiao, Y., Lee, Y. K., Wang, B., Mulvaney, J., Chougule, K., Elser, J., Al-Bader, N., Kumari, S., Thomason, J., Kumar, V., Bolser, D. M., Naamati, G., Tapanari, E., Fonseca, N., Huerta, L., Iqbal, H., Keays, M., Munoz-Pomer Fuentes, A., Tang, A., Fabregat, A., D'Eustachio, P., Weiser, J., Stein, L. D., Petryszak, R., Papatheodorou, I., Kersey, P. J., Lockhart, P., Taylor, C., Jaiswal, P., Ware, D. (January 2018) Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res, 46 (D1). D1181-D1189. ISSN 0305-1048

Yu, K., Ahrens, S., Zhang, X., Schiff, H., Ramakrishnan, C., Fenno, L., Deisseroth, K., Zhao, F., Luo, M. H., Gong, L., He, M., Zhou, P., Paninski, L., Li, B. (December 2017) The central amygdala controls learning in the lateral amygdala. Nat Neurosci, 20 (12). pp. 1680-1685. ISSN 1097-6256

Qian, Y., Cao, Y., Deng, B., Yang, G., Li, J., Xu, R., Zhang, D., Huang, J., Rao, Y. (October 2017) Sleep homeostasis regulated by 5HT2b receptor in a small subset of neurons in the dorsal fan-shaped body of drosophila. Elife, 6. e26519. ISSN 2050-084x

Roe, J. S., Hwang, C. I., Somerville, T. D. D., Milazzo, J. P., Lee, E. J., Da Silva, B., Maiorino, L., Tiriac, H., Young, C. M., Miyabayashi, K., Filippini, D., Creighton, B., Burkhart, R. A., Buscaglia, J. M., Kim, E. J., Grem, J. L., Lazenby, A. J., Grunkemeyer, J. A., Hollingsworth, M. A., Grandgenett, P. M., Egeblad, M., Park, Y., Tuveson, D. A., Vakoc, C. R. (August 2017) Enhancer Reprogramming Promotes Pancreatic Cancer Metastasis. Cell, 170 (5). pp. 875-888. ISSN 0092-8674

Ballouz, S., Gillis, J. (July 2017) Strength of functional signature correlates with effect size in autism. Genome Med, 9 (1). p. 64. ISSN 1756-994x

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&nbsp;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

Jiao, Y., Peluso, P., Shi, J., Liang, T., Stitzer, M. C., Wang, B., Campbell, M. S., Stein, J. C., Wei, X., Chin, C. S., Guill, K., Regulski, M., Kumari, S., Olson, A., Gent, J., Schneider, K. L., Wolfgruber, T. K., May, M. R., Springer, N. M., Antoniou, E., McCombie, W. R., Presting, G. G., McMullen, M., Ross-Ibarra, J., Dawe, R. K., Hastie, A., Rank, D. R., Ware, D. (June 2017) Improved maize reference genome with single-molecule technologies. Nature, 546 (7659). pp. 524-527. ISSN 0028-0836 (Public Dataset)

Wenda, J. M., Homolka, D., Yang, Z., Spinelli, P., Sachidanandam, R., Pandey, R. R., Pillai, R. S. (June 2017) Distinct Roles of RNA Helicases MVH and TDRD9 in PIWI Slicing-Triggered Mammalian piRNA Biogenesis and Function. Dev Cell, 41 (6). 623-637.e9. ISSN 1534-5807

Li, Q., Ko, H., Qian, Z. M., Yan, L. Y. C., Chan, D. C. W., Arbuthnott, G., Ke, Y., Yung, W. H. (June 2017) Refinement of learned skilled movement representation in motor cortex deep output layer. Nat Commun, 8. p. 15834. ISSN 2041-1723

Giralt, A., Brito, V., Chevy, Q., Simonnet, C., Otsu, Y., Cifuentes-Diaz, C., de Pins, B., Coura, R., Alberch, J., Gines, S., Poncer, J. C., Girault, J. A. (May 2017) Pyk2 modulates hippocampal excitatory synapses and contributes to cognitive deficits in a Huntington's disease model. Nature Communications, 8. p. 15592. ISSN 2041-1723

Munoz, Adriana, Yamrom, Boris, Lee, Yoon-ha, Andrews, Peter, Marks, Steven, Lin, Kuan-Ting, Wang, Zihua, Krainer, Adrian R., Darnell, Robert B., Wigler, Michael, Iossifov, Ivan (May 2017) De novo indels within introns contribute to ASD incidence. bioRxiv. p. 137471. (Unpublished)

Bronstein, R., Kyle, J., Abraham, A. B., Tsirka, S. E. (May 2017) Neurogenic to Gliogenic Fate Transition Perturbed by Loss of HMGB2. Front Mol Neurosci, 10. p. 153. ISSN 1662-5099

Balasooriya, G., Goschorska, M., Piddini, E., Rawlins, E. L. (May 2017) FGFR2 is required for airway basal cell self-renewal and terminal differentiation. Development, 144 (9). pp. 1600-1606. ISSN 0950-1991

Narasimhan, Arun, Venkataraju, Kannan Umadevi, Mizrachi, Judith, Albeanu, Dinu F, Osten, Pavel (April 2017) Oblique light-sheet tomography: fast and high resolution volumetric imaging of mouse brains. bioRxiv. (Submitted)

Balkunde, R., Kitagawa, M., Xu, X. M., Wang, J., Jackson, D. (April 2017) SHOOT MERISTEMLESS trafficking controls axillary meristem formation, meristem size and organ boundaries in Arabidopsis. Plant J, 90 (3). pp. 435-446. ISSN 0960-7412

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)

Ohlund, D., Handly-Santana, A., Biffi, G., Elyada, E., Almeida, A. S., Ponz-Sarvise, M., Corbo, V., Oni, T. E., Hearn, S. A., Lee, E. J., Chio, II, Hwang, C. I., Tiriac, H., Baker, L. A., Engle, D. D., Feig, C., Kultti, A., Egeblad, M., Fearon, D. T., Crawford, J. M., Clevers, H., Park, Y., Tuveson, D. A. (March 2017) Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer. J Exp Med, 214 (3). pp. 579-596. ISSN 0022-1007

Kitagawa, M., Jackson, D. (March 2017) Plasmodesmata-Mediated Cell-to-Cell Communication in the Shoot Apical Meristem: How Stem Cells Talk. Plants, 6 (1). p. 12. ISSN 2223-7747

Biffi, G., Tuveson, D. A. (February 2017) Cancer: Double trouble for tumours. Nature, 542 (7639). pp. 34-35. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Ballouz, S., Weber, M., Pavlidis, P., Gillis, J. (February 2017) EGAD: ultra-fast functional analysis of gene networks. Bioinformatics, 33 (4). pp. 612-614. ISSN 1367-4803

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)

Mathew, G., Hannan, A., Hertzler-Schaefer, K., Wang, F., Feng, G. S., Zhong, J., Zhao, J. J., Downward, J., Zhang, X. (November 2016) Targeting of Ras-mediated FGF signaling suppresses Pten-deficient skin tumor. Proc Natl Acad Sci U S A, 113 (46). pp. 13156-13161. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Starosta, Sarah, Uengoer, Metin, Bartetzko, Isabelle, Lucke, Sara, Güntürkün, Onur, Stüttgen, Maik C (November 2016) Context specificity of both acquisition and extinction of a Pavlovian conditioned response. Learning & memory (Cold Spring Harbor, N.Y.), 23 (11). pp. 639-643. ISSN 1072-0502

Ballouz, S., Pavlidis, P., Gillis, J. (October 2016) Using predictive specificity to determine when gene set analysis is biologically meaningful. Nucleic Acids Res. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Wei, Y., Gokhale, R. H., Sonnenschein, A., Montgomery, K. M., Ingersoll, A., Arnosti, D. N. (October 2016) Complex cis-regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator. Development, 143 (19). pp. 3591-3603. ISSN 0950-1991

Gupta, Priyanka, Albeanu, Dinu F, Bhalla, Upinder S (September 2016) An odor delivery system for arbitrary time-varying patterns of odors, mixtures and concentrations. bioRxiv. (Submitted)

Hachiya, T., Ueda, N., Kitagawa, M., Hanke, G., Suzuki, A., Hase, T., Sakakibara, H. (September 2016) Arabidopsis Root-Type Ferredoxin:NADP(H) Oxidoreductase 2 Is Involved in Detoxification of Nitrite in Roots. Plant Cell Physiol, 57 (11). pp. 2440-2450. ISSN 1471-9053 (Electronic)0032-0781 (Linking)

Kebschull, Justus M, Garcia da Silva, Pedro, Reid, Ashlan P, Peikon, Ian D, Albeanu, Dinu F, Zador, Anthony M (September 2016) High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA. Neuron, 91 (5). pp. 975-987. ISSN 0896-6273 (Public Dataset)

Huang, L., Ung, K., Garcia, I., Quast, K. B., Cordiner, K., Saggau, P., Arenkiel, B. R. (August 2016) Task Learning Promotes Plasticity of Interneuron Connectivity Maps in the Olfactory Bulb. Journal of Neuroscience, 36 (34). pp. 8856-8871. ISSN 1529-2401

Biffi, G., Ohlund, D., Tuveson, D. (August 2016) Building up the tension between the epithelial and stromal compartment in pancreatic ductal adenocarcinoma. Cell Death Differ, 23 (8). pp. 1265-1266. ISSN 1476-5403 (Electronic)1350-9047 (Linking)

Huang, Yu-Han, Vakoc, Christopher R (July 2016) A Biomarker Harvest from One Thousand Cancer Cell Lines. Cell, 166 (3). pp. 536-537. ISSN 0092-8674

Somerville, Tim D D., Vakoc, Christopher R (July 2016) Modeling the Epigenetic Chain Reaction Downstream of DNMT3A(R882H). Cancer Cell, 30 (1). pp. 9-10. ISSN 1535-6108

Je, B. I., Gruel, J., Lee, Y. K., Bommert, P., Arevalo, E. D., Eveland, A. L., Wu, Q., Goldshmidt, A., Meeley, R., Bartlett, M., Komatsu, M., Sakai, H., Jonsson, H., Jackson, D. (July 2016) Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits. Nat Genet, 48 (7). pp. 785-791. ISSN 1546-1718 (Electronic)1061-4036 (Linking) (Public Dataset)

Jiao, Y., Burke, J. J., Chopra, R., Burow, G., Chen, J., Wang, B., Hayes, C., Emendack, Y., Ware, D., Xin, Z. (July 2016) A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses. Plant Cell, 28 (7). pp. 1551-1562. ISSN 1532-298X (Electronic)1040-4651 (Linking)

Wang, B., Tseng, E., Regulski, M., Clark, T. A., Hon, T., Jiao, Y., Lu, Z., Olson, A., Stein, J. C., Ware, D. (June 2016) Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun, 7. p. 11708. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

Gupta, P., Bhalla, U. S. (June 2016) Minority odors get equal say. Elife, 5. ISSN 2050-084X (Electronic)2050-084X (Linking)

Öhlund, Daniel, Handly-Santana, Abram, Elyada, Ela, Biffi, Giulia, Tuveson, David A. (June 2016) Pancreatic stellate cell heterogeneity in cancer. Pancreatology, 16 (3, Sup). S15. ISSN 1424-3903

Ballouz, Sara, Weber, Melanie, Pavlidis, Paul, Gillis, Jesse (May 2016) EGAD: Ultra-fast functional analysis of gene networks. BioRxiv. (Unpublished)

Crow, M., Paul, A., Ballouz, S., Huang, Z. J., Gillis, J. (May 2016) Exploiting single-cell expression to characterize co-expression replicability. Genome Biol, 17 (1). p. 101. ISSN 1474-760X (Electronic)1474-7596 (Linking) (Public Dataset)

Ballouz, S., Gillis, J. (April 2016) AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression. PLoS Comput Biol, 12 (4). e1004868. ISSN 1553-7358 (Electronic)1553-734X (Linking)

Verleyen, W., Ballouz, S., Gillis, J. (April 2016) Positive and negative forms of replicability in gene network analysis. Bioinformatics, 32 (7). pp. 1065-73. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

Tello-Ruiz, M. K., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarasinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J., Kumari, S., Chougule, K., Elser, J., Wang, B., Thomason, J., Bolser, D. M., Kerhornou, A., Walts, B., Fonseca, N. A., Huerta, L., Keays, M., Tang, Y. A., Parkinson, H., Fabregat, A., McKay, S., Weiser, J., D'Eustachio, P., Stein, L., Petryszak, R., Kersey, P. J., Jaiswal, P., Ware, D. (January 2016) Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res, 44 (D1). D1133-40. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Muñoz, A., Santos Muñoz, D., Zimin, A., Yorke, J. A. (2016) Evolution of transcriptional networks in yeast: Alternative teams of transcriptional factors for different species. BMC Genomics, 17 (Suppl ). p. 826. ISSN 1471-2164

O'Meara, M. J., Ballouz, S., Shoichet, B. K., Gillis, J. (2016) Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PLoS One, 11 (7). e0160098. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Chakrabortty, S. K., Prakash, A., Nechooshtan, G., Hearn, S., Gingeras, T. R. (November 2015) Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA. RNA, 21 (11). pp. 1966-1979. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

Wasik, K., Gurtowski, J., Zhou, X., Ramos, O. M., Delas, M. J., Battistoni, G., El Demerdash, O., Falciatori, I., Vizoso, D. B., Smith, A. D., Ladurner, P., Scharer, L., McCombie, W. R., Hannon, G. J., Schatz, M. (September 2015) Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A, 112 (40). pp. 12462-12467. ISSN 1091-6490 (Electronic)0027-8424 (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)

Otazu, Gonzalo H, Chae, Honggoo, Davis, Martin B, Albeanu, Dinu F (June 2015) Cortical Feedback Decorrelates Olfactory Bulb Output in Awake Mice. Neuron, 86 (6). pp. 1461-1477. ISSN 0896-6273

Grover, M. P., Ballouz, S., Mohanasundaram, K. A., George, R. A., Goscinski, A., Crowley, T. M., Sherman, C. D., Wouters, M. A. (May 2015) Novel therapeutics for coronary artery disease from genome-wide association study data. BMC Med Genomics, 8 (Suppl ). S1. ISSN 1755-8794 (Electronic)1755-8794 (Linking)

Penzo, M. A., Robert, V., Tucciarone, J., De Bundel, D., Wang, M., Van Aelst, L., Darvas, M., Parada, L. F., Palmiter, R. D., He, M., Huang, Z. J., Li, B. (March 2015) The paraventricular thalamus controls a central amygdala fear circuit. Nature, 519 (7544). pp. 455-459. ISSN 0028-0836

Verleyen, W., Ballouz, S., Gillis, J. (March 2015) Measuring the wisdom of the crowds in network-based gene function inference. Bioinformatics, 31 (5). pp. 745-752. ISSN 1367-4803

Ballouz, S., Verleyen, W., Gillis, J. (February 2015) Guidance for RNA-seq co-expression network construction and analysis: safety in numbers. Bioinformatics. ISSN 1367-4803

Stein, P., Rozhkov, N. V., Li, F., Cardenas, F. L., Davydenk, O., Vandivier, L. E., Gregory, B. D., Hannon, G. J., Schultz, R. M. (February 2015) Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes. PLoS Genetics, 11 (2). e1005013. ISSN 1553-7390

Gupta, P., Albeanu, D. F., Bhalla, U. S. (January 2015) Olfactory bulb coding of odors, mixtures and sniffs is a linear sum of odor time profiles. Nature Neuroscience, 18. pp. 272-281. ISSN 1097-6256

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

Fortunato, S. A. V., Adamski, M., Ramos, O. M., Leininger, S., Liu, J., Ferrier, D. E. K., Adamska, M. (October 2014) Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes. Nature, 514 (7524). pp. 620-623. ISSN 00280836

Le Thomas, A., Stuwe, E., Li, S., Du, J., Marinov, G., Rozhkov, N., Chen, Y. C., Luo, Y., Sachidanandam, R., Toth, K. F., Patel, D., Aravin, A. A. (August 2014) Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Genes & Development, 28 (15). pp. 1667-80. ISSN 0890-9369

Ohlund, D., Elyada, E., Tuveson, D. (July 2014) Fibroblast heterogeneity in the cancer wound. Journal of Experimental Medicine, 211 (8). pp. 1503-23. ISSN 0022-1007

Wang, M., Perova, Z., Arenkiel, B. R., Li, B. (May 2014) Synaptic modifications in the medial prefrontal cortex in susceptibility and resilience to stress. Journal of Neuroscience, 34 (22). pp. 7485-92. ISSN 0270-6474

Gillis, J., Ballouz, S., Pavlidis, P. (January 2014) Bias tradeoffs in the creation and analysis of protein-protein interaction networks. Journal of Proteomics, 100. pp. 44-54.

Chipman, A. D., Ferrier, D. E. K., Brena, C., Qu, J., Hughes, D. S. T., Schröder, R., Torres-Oliva, M., Znassi, N., Jiang, H., Almeida, F. C., Alonso, C. R., Apostolou, Z., Aqrawi, P., Arthur, W., Barna, J. C. J., Blankenburg, K. P., Brites, D., Capella-Gutiérrez, S., Coyle, M., Dearden, P. K., Du Pasquier, L., Duncan, E. J., Ebert, D., Eibner, C., Erikson, G., Evans, P. D., Extavour, C. G., Francisco, L., Gabaldón, T., Gillis, W. J., Goodwin-Horn, E. A., Green, J. E., Griffiths-Jones, S., Grimmelikhuijzen, C. J. P., Gubbala, S., Guigó, R., Han, Y., Hauser, F., Havlak, P., Hayden, L., Helbing, S., Holder, M., Hui, J. H. L., Hunn, J. P., Hunnekuhl, V. S., Jackson, L. R., Javaid, M., Jhangiani, S. N., Jiggins, F. M., Jones, T. E., Kaiser, T. S., Kalra, D., Kenny, N. J., Korchina, V., Kovar, C. L., Kraus, F. B., Lapraz, F., Lee, S. L., Lv, J., Mandapat, C., Manning, G., Mariotti, M., Mata, R., Mathew, T., Neumann, T., Newsham, I., Ngo, D. N., Ninova, M., Okwuonu, G., Ongeri, F., Palmer, W. J., Patil, S., Patraquim, P., Pham, C., Pu, L. L., Putman, N. H., Rabouille, C., Ramos, O. M., Rhodes, A. C., Robertson, H. E., Robertson, H. M., Ronshaugen, M., Rozas, J., Saada, N., Sánchez-Gracia, A., Scherer, S. E., Schurko, A. M., Siggens, K. W., Simmons, D. N., Stief, A., Stolle, E., Telford, M. J., Tessmar-Raible, K., Thornton, R., van der Zee, M., von Haeseler, A., Williams, J. M., Willis, J. H., Wu, Y., Zou, X. (2014) The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima. PLoS Biology, 12 (11).

Grover, M. P., Ballouz, S., Mohanasundaram, K. A., George, R. A., H Sherman, C. D., Crowley, T. M., Wouters, M. A. (2014) Identification of novel therapeutics for complex diseases from genome-wide association data. BMC Medical Genomics, 7 (SUPPL.). ISSN 17558794 (ISSN)

Ballouz, S., Liu, J. Y., George, R. A., Bains, N., Liu, A., Oti, M., Gaeta, B., Fatkin, D., Wouters, M. A. (August 2013) Gentrepid V2.0: a web server for candidate disease gene prediction. BMC Bioinformatics, 14. ISSN 1471-2105

Rozhkov, N. V., Schostak, N. G., Zelentsova, E. S., Yushenova, I. A., Zatsepina, O. G., Evgen'ev, M. B. (February 2013) Evolution and Dynamics of Small RNA Response to a Retroelement Invasion in Drosophila. Molecular Biology and Evolution, 30 (2). pp. 397-408. ISSN 0737-4038

Sokolova, Marina I, Zelentsova, Elena S, Shostak, Natalia G, Rozhkov, Nikolay V, Evgen'ev, Michael B (2013) Ontogenetic consequences of dysgenic crosses in Drosophila virilis. International Journal of Developmental Biology, 57 (9-10). pp. 731-739. ISSN 0214-6282

Muerdter, F., Olovnikov, I., Molaro, A., Rozhkov, N. V., Czech, B., Gordon, A., Hannon, G. J., Aravin, A. A. (January 2012) Production of artificial piRNAs in flies and mice. RNA, 18 (1). pp. 42-52. ISSN 1355-8382

Conference or Workshop Item

Puckett, L., Fein, M. R., He, X., Egeblad, M. (2017) Targeting Tumor-Mediated Immune Suppression in a Murine Model of Breast Cancer: Radiation and Chemokine Receptor CCR2. In: UNSPECIFIED.