Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer
Becker, Winston R., Nevins, Stephanie A., Chen, Derek C., Chiu, Roxanne, Horning, Aaron M., Guha, Tuhin K., Laquindanum, Rozelle, Mills, Meredith, Chaib, Hassan, Ladabaum, Uri, Longacre, Teri, Shen, Jeanne, Esplin, Edward D., Kundaje, Anshul, Ford, James M., Curtis, Christina, Snyder, Michael P., Greenleaf, William J.
Published in Nature genetics (01.07.2022)
Published in Nature genetics (01.07.2022)
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The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
Rood, Jennifer E., Coffey, Robert J., Demir, Emek, Ghosh, Sharmistha, Iacobuzio-Donahue, Christine A., Jané-Valbuena, Judit, Mazzilli, Sarah A., Pe’er, Dana, Tan, Kai, Aguilar, Ruben A., Babur, Ozgun, Boland, Genevieve, Bosse, Kristopher, Bott, Matthew, Boyden, Ed, Brooks, James, Cerami, Ethan, Chang, Young Hwan, Chaudhary, Ojasvi, Chen, Alyce A., Chen, Feng, Chun, Jaeyoung, Cisneros, Luis, Contrepois, Kevin, Creason, Allison L., Demir, Emek, Diskin, Sharon, Drewes, Julia, Eng, Jennifer, Erwin, Graham, Flaherty, Keith, Gao, Jianjiong, Gao, Vianne R., Giannakis, Marios, Gowers, Kate, Gray, Joe W., Greenleaf, William, Gresham, Jeremy, Hacohen, Nir, Harris, Kathleen A., Hayashi, Akimasa, Herndon, John M., Huh, Won Jae, Ijaz, Heba, Izar, Benjamin, Johnson, Brett E., Kaestner, Klaus, Kim, Albert H., Kopytra, Mateusz, Kundaje, Anshul, Lau, Ken S., Lee, Hayan, Lenburg, Marc, Lim, Kian-Huat, Lin, Yiyun, Lively, Tracy, Longabaugh, William J.R., Ma, Cynthia X., Marks, Jeffrey, Masilionais, Ignas, McKinley, Eliot T., McMichael, Joshua F., Mosse, Yael, Ness, Reid, Nikolov, Milen, Oberdoerffer, Philipp, Offin, Michael, Olson, Anastasiya, Ossandon, Miguel, Polyak, Kornelia, Reid, Mary, Roy, Sudipta, Ryser, Marc D., Schrag, Deborah, Sears, Rosalie C., Shalek, Alex, Sheng, Jeff, Shoghi, Kooresh I., Sibley, Alexander B., Sorger, Peter K., Southard-Smith, Austin, Srivastava, Sudhir, Storm, Phillip, Sullivan, Ryan, Suvà, Mario, Thorsson, Vésteinn, Tran, Linh, Veis, Deborah J., Vossough, Arastoo, Wagle, Nikhil, Wang, Liang-Bo, West, Robert, Wu, Chi-yun, Wyczalkowski, Matthew A., Xie, Yubin, Yang, Xiaolu, Zhang, Mianlei, Zhang, Yantian, Zhou, Daniel Cui, Zhuang, Xiaowei
Published in Cell (16.04.2020)
Published in Cell (16.04.2020)
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Organization of the human intestine at single-cell resolution
Hickey, John W., Becker, Winston R., Nevins, Stephanie A., Horning, Aaron, Perez, Almudena Espin, Zhu, Chenchen, Zhu, Bokai, Wei, Bei, Chiu, Roxanne, Chen, Derek C., Cotter, Daniel L., Esplin, Edward D., Weimer, Annika K., Caraccio, Chiara, Venkataraaman, Vishal, Schürch, Christian M., Black, Sarah, Brbić, Maria, Cao, Kaidi, Chen, Shuxiao, Zhang, Weiruo, Monte, Emma, Zhang, Nancy R., Ma, Zongming, Leskovec, Jure, Zhang, Zhengyan, Lin, Shin, Longacre, Teri, Plevritis, Sylvia K., Lin, Yiing, Nolan, Garry P., Greenleaf, William J., Snyder, Michael
Published in Nature (London) (20.07.2023)
Published in Nature (London) (20.07.2023)
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Temporal dynamics of the multi-omic response to endurance exercise training
Amar, David, Gay, Nicole R., Jean-Beltran, Pierre M., Bae, Dam, Dasari, Surendra, Dennis, Courtney, Evans, Charles R., Gaul, David A., Ilkayeva, Olga, Ivanova, Anna A., Kachman, Maureen T., Keshishian, Hasmik, Lanza, Ian R., Lira, Ana C., Muehlbauer, Michael J., Nair, Venugopalan D., Piehowski, Paul D., Rooney, Jessica L., Smith, Kevin S., Stowe, Cynthia L., Zhao, Bingqing, Clark, Natalie M., Jimenez-Morales, David, Lindholm, Malene E., Many, Gina M., Sanford, James A., Smith, Gregory R., Vetr, Nikolai G., Zhang, Tiantian, Almagro Armenteros, Jose J., Avila-Pacheco, Julian, Bararpour, Nasim, Ge, Yongchao, Hou, Zhenxin, Marwaha, Shruti, Presby, David M., Natarajan Raja, Archana, Savage, Evan M., Steep, Alec, Sun, Yifei, Wu, Si, Zhen, Jimmy, Bodine, Sue C., Esser, Karyn A., Goodyear, Laurie J., Schenk, Simon, Montgomery, Stephen B., Fernández, Facundo M., Sealfon, Stuart C., Snyder, Michael P., Adkins, Joshua N., Ashley, Euan, Burant, Charles F., Carr, Steven A., Clish, Clary B., Cutter, Gary, Gerszten, Robert E., Kraus, William E., Li, Jun Z., Miller, Michael E., Nair, K. Sreekumaran, Newgard, Christopher, Ortlund, Eric A., Qian, Wei-Jun, Tracy, Russell, Walsh, Martin J., Wheeler, Matthew T., Dalton, Karen P., Hastie, Trevor, Hershman, Steven G., Samdarshi, Mihir, Teng, Christopher, Tibshirani, Rob, Cornell, Elaine, Gagne, Nicole, May, Sandy, Bouverat, Brian, Leeuwenburgh, Christiaan, Lu, Ching-ju, Pahor, Marco, Hsu, Fang-Chi, Rushing, Scott, Walkup, Michael P., Nicklas, Barbara, Rejeski, W. Jack, Williams, John P., Xia, Ashley, Albertson, Brent G., Barton, Elisabeth R., Booth, Frank W., Caputo, Tiziana, Cicha, Michael, De Sousa, Luis Gustavo Oliveira, Farrar, Roger, Hevener, Andrea L., Hirshman, Michael F., Jackson, Bailey E., Ke, Benjamin G., Kramer, Kyle S., Lessard, Sarah J.
Published in Nature (London) (02.05.2024)
Published in Nature (London) (02.05.2024)
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The mitochondrial multi-omic response to exercise training across rat tissues
Amar, David, Jimenez-Morales, David, Ramaker, Megan E., Raja, Archana Natarajan, Zhao, Bingqing, Marwaha, Shruti, Gaul, David A., Hershman, Steven G., Ferrasse, Alexis, Xia, Ashley, Lanza, Ian, Fernández, Facundo M., Montgomery, Stephen B., Hevener, Andrea L., Ashley, Euan A., Walsh, Martin J., Sparks, Lauren M., Rector, R. Scott, Thyfault, John, Goodpaster, Bret H., Coen, Paul M., Schenk, Simon, Lindholm, Malene E., Adkins, Joshua N., Armenteros, Jose Juan Almagro, Amper, Mary Anne S., Bae, Dam, Bamman, Marcas, Bararpour, Nasim, Barnes, Jerry, Bergman, Bryan C., Bessesen, Daniel H., Broskey, Nicholas T., Carr, Steven, Chambers, Toby L., Chavez, Clarisa, Chiu, Roxanne, Clark, Natalie, Evans, Charles R., Franczak, Edziu, Gagne, Nicole, Ge, Yongchao, Houmard, Joseph A., Huffman, Kim M., Hung, Chia-Jui, Hutchinson-Bunch, Chelsea, Ilkayeva, Olga, Jackson, Bailey E., Jankowski, Catherine M., Jin, Christopher A., Johannsen, Neil M., Keshishian, Hasmik, Kohrt, Wendy M., Kramer, Kyle S., Kraus, William E., Lester, Bridget, Li, Jun Z., Lira, Ana K., Lowe, Adam, Mani, D.R., Many, Gina M., May, Sandy, Melanson, Edward L., Moore, Samuel G., Moreau, Kerrie L., Musi, Nicolas, Nachun, Daniel, Nair, Venugopalan D., Newgard, Christopher, Nudelman, German, Piehowski, Paul D., Pincas, Hanna, Qian, Wei-Jun, Rankinen, Tuomo, Rasmussen, Blake B., Ravussin, Eric, Rooney, Jessica L., Rushing, Scott, Samdarshi, Mihir, Sanford, James A., Schauer, Irene E., Sealfon, Stuart C., Smith, Kevin S., Smith, Gregory R., Snyder, Michael, Stowe, Cynthia L., Talton, Jennifer W., Thalacker-Mercer, Anna, Trappe, Scott, Trappe, Todd A., Vasoya, Mital, Vetr, Nikolai G., Volpi, Elena, Walkup, Michael P., Wiel, Laurens, Wu, Si, Yan, Zhen, Yu, Jiye, Zaslavsky, Elena, Zhen, Jimmy
Published in Cell metabolism (04.06.2024)
Published in Cell metabolism (04.06.2024)
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The impact of exercise on gene regulation in association with complex trait genetics
Vetr, Nikolai G., Gay, Nicole R., Montgomery, Stephen B.
Published in Nature communications (01.05.2024)
Published in Nature communications (01.05.2024)
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Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis
Zhu, Yizhou, Lee, Hayan, White, Shannon, Weimer, Annika K, Monte, Emma, Horning, Aaron, Nevins, Stephanie A, Esplin, Edward D, Paul, Kristina, Krieger, Gat, Shipony, Zohar, Chiu, Roxanne, Laquindanum, Rozelle, Karathanos, Thomas V, Chua, Melissa W Y, Mills, Meredith, Ladabaum, Uri, Longacre, Teri, Shen, Jeanne, Jaimovich, Ariel, Lipson, Doron, Kundaje, Anshul, Greenleaf, William J, Curtis, Christina, Ford, James M, Snyder, Michael P
Published in Nature cancer (30.10.2024)
Published in Nature cancer (30.10.2024)
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Abstract 4742: Familial adenomatous polyposis epigenetic landscape as a precancer model of colorectal cancer
Lee, Hayan, Krieger, Gat, Clark, Tyson, Zhu, Yizhou, Khan, Aziz, Hanson, Casey R., Horning, Aaron, Esplin, Edward D., Badu, Mohan, Paul, Kristina, Chiu, Roxanne, Bahmani, Bahareh, Nevins, Stephanie, Weimer, Annika K., Jaimovich, Ariel, Curtis, Christina, Greenleaf, William, Ford, James M., Lipson, Doron, Shipony, Zohar, Snyder, Michael P.
Published in Cancer research (Chicago, Ill.) (04.04.2023)
Published in Cancer research (Chicago, Ill.) (04.04.2023)
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Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue
Many, Gina M., Sanford, James A., Sagendorf, Tyler J., Hou, Zhenxin, Nigro, Pasquale, Whytock, Katie L., Amar, David, Caputo, Tiziana, Gay, Nicole R., Gaul, David A., Hirshman, Michael F., Jimenez-Morales, David, Lindholm, Malene E., Muehlbauer, Michael J., Vamvini, Maria, Bergman, Bryan C., Fernández, Facundo M., Goodyear, Laurie J., Hevener, Andrea L., Ortlund, Eric A., Sparks, Lauren M., Xia, Ashley, Adkins, Joshua N., Bodine, Sue C., Newgard, Christopher B., Schenk, Simon
Published in Nature metabolism (01.05.2024)
Published in Nature metabolism (01.05.2024)
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Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis
Esplin, Edward D, Hanson, Casey, Wu, Si, Horning, Aaron M, Barapour, Nasim, Nevins, Stephanie A, Jiang, Lihua, Contrepois, Kévin, Lee, Hayan, Guha, Tuhin K, Hu, Zheng, Laquindanum, Rozelle, Mills, Meredith A, Chaib, Hassan, Chiu, Roxanne, Jian, Ruiqi, Chan, Joanne, Ellenberger, Mathew, Becker, Winston R, Bahmani, Bahareh, Khan, Aziz, Michael, Basil, Weimer, Annika K, Esplin, D Glen, Shen, Jeanne, Lancaster, Samuel, Monte, Emma, Karathanos, Thomas V, Ladabaum, Uri, Longacre, Teri A, Kundaje, Anshul, Curtis, Christina, Greenleaf, William J, Ford, James M, Snyder, Michael P
Published in Nature cancer (30.10.2024)
Published in Nature cancer (30.10.2024)
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Abstract 3497: The polyclonal path to malignant transformation in familial adenomatous polyposis
Schenck, Ryan O., Khan, Aziz, Horning, Aaron, Esplin, Edward D., Monte, Emma, Wu, Si, Hanson, Casey, Bararpour, Nasim, Neves, Stephanie, Jiang, Lihua, Contrepois, Kévin, Lee, Hayan, Guha, Tuhin K., Hu, Zheng, Laquindanum, Rozelle, Mills, Meredith A., Chaib, Hassan, Chiu, Roxanne, Jian, Ruiqi, Chan, Jeannie, Ellenberger, Mathew, Becker, Winston R., Bahmani, Bahareh, Michael, Basil, Shen, Jeanne, Lancaster, Samuel, Ladabaum, Uri, Kundaje, Anshul, Longacre, Teri A., Greenleaf, William J., Ford, James M., Snyder, Michael P., Curtis, Christina
Published in Cancer research (Chicago, Ill.) (04.04.2023)
Published in Cancer research (Chicago, Ill.) (04.04.2023)
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Journal Article
Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer
Becker, Winston R, Nevins, Stephanie A, Chen, Derek C, Chiu, Roxanne, Horning, Aaron, Rozelle Laquindanum, Mills, Meredith, Chaib, Hassan, Ladabaum, Uri, Longacre, Teri, Shen, Jeanne, Esplin, Edward D, Kundaje, Anshul, d, James M, Curtis, Christina, Snyder, Michael P, Greenleaf, William J
Published in bioRxiv (25.03.2021)
Published in bioRxiv (25.03.2021)
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High Resolution Single Cell Maps Reveals Distinct Cell Organization and Function Across Different Regions of the Human Intestine
Hickey, John W, Becker, Winston R, Nevins, Stephanie A, Horning, Aaron M, Almudena Espin Perez, Chiu, Roxanne, Chen, Derek C, Cotter, Daniel, Esplin, Edward D, Weimer, Annika, Caraccio, Chiara, Venkataraaman, Vishal, Schurch, Christian M, Black, Sarah, Brbic, Maria, Cao, Kaidi, Leskovec, Jure, Zhang, Zhengyan, Lin, Shin, Longacre, Teri, Plevitis, Sylvia K, Lin, Yiing, Nolan, Garry P, Greenleaf, William, Snyder, Michael P
Published in bioRxiv (25.11.2021)
Published in bioRxiv (25.11.2021)
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Temporal dynamics of the multi-omic response to endurance exercise training across tissues
Motrpac Study Group, Gay, Nicole R, Ashley, Euan, Avila-Pacheco, Julian, Bararpour, Nasim, Burant, Charles, Hou, Zhenxin, Ilkayeva, Olga, Ivanova, Anna A, Kachman, Maureen T, Kraus, William E, Lanza, Ian R, Li, Jun, Lindholm, Malene E, Many, Gina M, Marwaha, Shruti, Miller, Michael E, Muehlbauer, Michael J, Nair, K Sreekumaran, Nair, Venugopalan D, Ortlund, Eric A, Presby, David M, Wei-Jun, Qian, Rooney, Jessica L, Sanford, James A, Savage, Evan, Smith, Gregory R, Stowe, Cynthia L, Sun, Yifei, Vetr, Nikolai G, Walsh, Martin J, Zhao, Bingqing, Albertson, Brent G, Amper, Mary Anne S, Bamman, Marcas, Barton, Elisabeth R, Bergman, Bryan, Booth, Frank, Bouverat, Brian, Buford, Thomas W, Chambers, Toby L, Chavez, Clarisa, Chiu, Roxanne, Coen, Paul M, Cooper, Dan, Cornell, Elaine, Dalton, Karen P, Farrar, Roger, Gadde, Kishore, Gagne, Nicole, Goodpaster, Bret H, Haddad, Fadia, Hansen, Joshua R, Harris, Melissa, Hastie, Trevor, Hershman, Steven G, Hirshman, Michael F, Fang-Chi, Hsu, Huffman, Kim M, Jackson, Bailey E, Kohrt, Wendy M, Kramer, Kyle S, Leeuwenburgh, Christiaan, Ching-Ju, Lu, Dr Mani, Marjanovic, Nada, Marshall, Andrea, Melanson, Edward, Monroe, Matthew E, Moore, Ronald J, Moreau, Kerrie L, Mundorff, Charles C, Nachun, Daniel, Nestor, Michael D, Nigro, Pasquale, Nudelman, German, Pahor, Marco, Pincas, Hanna, Radom-Aizik, Shlomit, Ramachandran, Krithika, Rankinen, Tuomo, Alexander (Sasha) Raskind, Rasmussen, Blake B, Rejeski, W Jack, Rirak, Stas, Sagendorf, Tyler J, Samdarshi, Mihir, Schauer, Irene E, Seenarine, Nitish, Soni, Tanu, Thalacker-Mercer, Anna, Tibshirani, Rob, Vangeti, Sindhu, Volpi, Elena, Williams, John, Yu, Xuechen, Zaslavsky, Elena, Zebarjadi, Navid, Carr, Steven, Montgomery, Stephen B
Published in bioRxiv (05.10.2022)
Published in bioRxiv (05.10.2022)
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