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L Pennacchio

Lawrence Berkeley National Laboratory

92H-index
656Paper Count
4.4WCitation Count
Published Papers 113
Publication Date
Multiomics and deep learning dissect regulatory syntax in human development
errNature
IF48.5
err2026-04-08
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errOAAI
errBetty B. Liu; Selin Jessa; Samuel H. Kim; Yan Ting Ng; Soon Il Higashino; Georgi K. Marinov; Derek C. Chen; Benjamin E. Parks; Li Li; Tri C. Nguyen; Austin T. Wang; Sean K. Wang; Meng How Tan; Serena Y. Tan; Michael Kosicki; Len A. Pennacchio; Eyal Ben-David; Anca M. Pasca; Anshul Kundaje; Kyle K. H. Farh; William J. Greenleaf
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Enhancers that direct gene expression to central nervous system vascular endothelial cells in vivo
errNeuron
IF15
err2026-03-30
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errOAAI
errZhongming Li; Amir Rattner; Yanshu Wang; Philip M. Smallwood; Mark Sabbagh; Brandon J. Mannion; Len A. Pennacchio; Jeremy Nathans
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An expanded registry of candidate cis-regulatory elements
errNature
IF48.5
err2026-01-07
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errOAAI
errJill E. Moore; Henry E. Pratt; Kaili Fan; Nishigandha Phalke; Jonathan Fisher; Shaimae I. Elhajjajy; Gregory Andrews; Mingshi Gao; Nicole Shedd; Yu Fu; Matthew C. Lacadie; Jair Meza; Mansi Khandpekar; Mohit Ganna; Eva Choudhury; Ross Swofford; Huong Phan; Christian C. Ramirez; Maxwell Campbell; Mary Likhite; Nina P. Farrell; Annika K. Weimer; Anusri Pampari; Vivekanandan Ramalingam; Fairlie Reese; Beatrice Borsari; Xuezhu Yu; Eve Wattenberg; Marina Ruiz-Romero; Milad Razavi-Mohseni; Jinrui Xu; Timur Galeev; Andres Colubri; Michael A. Beer; Roderic Guigó; Mark B. Gerstein; Jesse M. Engreitz; Mats Ljungman; Timothy E. Reddy; Michael P. Snyder; Charles B. Epstein; Elizabeth Gaskell; Bradley E. Bernstein; Diane E. Dickel; Axel Visel; Len A. Pennacchio; Ali Mortazavi; Anshul Kundaje; Zhiping Weng
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SOX2-driven enhancer landscape defines the transcriptional architecture of retinogenesis
err2025-12-01
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errBian, Fuyun; Golestaneh, Kimiasadat; Davis, Emily; Khan, Abdullah; Nicholson, Brendan; Daghsni, Marwa; Flohr, Keevon; Liu, Silvia; da Silva, Susana; Pennacchio, Len; Aldiri, Issam
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Uncovering hidden enhancers through unbiased in vivo testing
err2025-08-08
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errOAAI
errBrandon J. Mannion; Stella Tran; Ingrid Plajzer-Frick; Catherine S. Novak; Veena Afzal; Jennifer A. Akiyama; Ismael Sospedra-Arrufat; Sarah Barton; Erik Beckman; Tyler H. Garvin; Patrick Godfrey; Janeth Godoy; Riana D. Hunter; Momoe Kato; Michael Kosicki; Anne N. Kronshage; Elizabeth A. Lee; Eman M. Meky; Quan T. Pham; Kianna von Maydell; Yiwen Zhu; Javier Lopez-Rios; Diane E. Dickel; Marco Osterwalder; Axel Visel; Len A. Pennacchio
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Range extender mediates long-distance enhancer activity
errNature
IF48.5
err2025-07-02
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errOAAI
errGrace Bower; Ethan W. Hollingsworth; Sandra H. Jacinto; Joshua A. Alcantara; Benjamin Clock; Kaitlyn Cao; Mandy Liu; Adam Dziulko; Ana Alcaina-Caro; Qianlan Xu; Dorota Skowronska-Krawczyk; Javier Lopez-Rios; Diane E. Dickel; Anaïs F. Bardet; Len A. Pennacchio; Axel Visel; Evgeny Z. Kvon
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Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity
err2025-05-23
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errOAAI
errKosicki, Michael; Cintron, Dianne Laboy; Keukeleire, Pia; Schubach, Max; Page, Nicholas F.; Georgakopoulos-Soares, Ilias; Akiyama, Jennifer A.; Plajzer-Frick, Ingrid; Novak, Catherine S.; Kato, Momoe; Hunter, Riana D.; von Maydell, Kianna; Barton, Sarah; Godfrey, Patrick; Beckman, Erik; Sanders, Stephan J.; Kircher, Martin; Pennacchio, Len A.; Ahituv, Nadav
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Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues
err2024-12-16
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errYu, Miao; Zemke, Nathan R.; Chen, Ziyin; Juric, Ivan; Hu, Rong; Raviram, Ramya; Abnousi, Armen; Fang, Rongxin; Zhang, Yanxiao; Gorkin, David U.; Li, Yang E.; Zhao, Yuan; Lee, Lindsay; Mishra, Shreya; Schmitt, Anthony D.; Qiu, Yunjiang; Dickel, Diane E.; Visel, Axel; Pennacchio, Len A.; Hu, Ming; Ren, Bing
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VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers
err2024-10-29
err1
errOAAI
errKosicki, Michael; Baltoumas, Fotis A.; Kelman, Guy; Boverhof, Joshua; Ong, Yeongshnn; Cook, Laura E.; Dickel, Diane E.; Pavlopoulos, Georgios A.; Pennacchio, Len A.; Visel, Axel
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A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival
err2024-10-10
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errAbassah-Oppong, Samuel; Zoia, Matteo; Mannion, Brandon J.; Rouco, Raquel; Tissieres, Virginie; Spurrell, Cailyn H.; Roland, Virginia; Darbellay, Fabrice; Itum, Anja; Gamart, Julie; Festa-Daroux, Tabitha A.; Sullivan, Carly S.; Kosicki, Michael; Rodriguez-Carballo, Eddie; Fukuda-Yuzawa, Yoko; Hunter, Riana D.; Novak, Catherine S.; Plajzer-Frick, Ingrid; Tran, Stella; Akiyama, Jennifer A.; Dickel, Diane E.; Lopez-Rios, Javier; Barozzi, Iros; Andrey, Guillaume; Visel, Axel; Pennacchio, Len A.; Cobb, John; Osterwalder, Marco
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A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders
err2024-09-27
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errOAAI
errLee, Arthur S.; Ayers, Lauren J.; Kosicki, Michael; Chan, Wai-Man; Fozo, Lydia N.; Pratt, Brandon M.; Collins, Thomas E.; Zhao, Boxun; Rose, Matthew F.; Sanchis-Juan, Alba; Fu, Jack M.; Wong, Isaac; Zhao, Xuefang; Tenney, Alan P.; Lee, Cassia; Laricchia, Kristen M.; Barry, Brenda J.; Bradford, Victoria R.; Jurgens, Julie A.; England, Eleina M.; Lek, Monkol; Macarthur, Daniel G.; Lee, Eunjung Alice; Talkowski, Michael E.; Brand, Harrison; Pennacchio, Len A.; Engle, Elizabeth C.
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Nr2f1 enhancers have distinct functions in controlling Nr2f1 expression during cortical development
err2024-09-23
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errOAAI
errLiu, Zhidong; Ypsilanti, Athena R.; Papadimitriou, Eirene Markenscoff-; Dickel, Diane E.; Sanders, Stephan J.; Dong, Shan; Pennacchio, Len A.; Visel, Axel; Rubenstein, John L.
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Rare variation in non-coding regions with evolutionary signatures contributes to autism spectrum disorder risk
err2024-08-01
err4
errOAAI
errShin, Taehwan; Song, Janet H. T.; Kosicki, Michael; Kenny, Connor; Beck, Samantha G.; Kelley, Lily; Antony, Irene; Qian, Xuyu; Bonacina, Julieta; Papandile, Frances; Gonzalez, Dilenny; Scotellaro, Julia; Bushinsky, Evan M.; Andersen, Rebecca E.; Maury, Eduardo; Pennacchio, Len A.; Doan, Ryan N.; Walsh, Christopher A.
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Increased enhancer-promoter interactions during developmental enhancer activation in mammals
err2024-03-20
err9
errOAAI
errChen, Zhuoxin; Snetkova, Valentina; Bower, Grace; Jacinto, Sandra; Clock, Benjamin; Dizehchi, Atrin; Barozzi, Iros; Mannion, Brandon J.; Alcaina-Caro, Ana; Lopez-Rios, Javier; Dickel, Diane E.; Visel, Axel; Pennacchio, Len A.; Kvon, Evgeny Z.
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Dynamic enhancer landscapes in human craniofacial development
err2024-03-06
err2
errOAAI
errRajderkar, Sudha Sunil; Paraiso, Kitt; Amaral, Maria Luisa; Kosicki, Michael; Cook, Laura E.; Darbellay, Fabrice; Spurrell, Cailyn H.; Osterwalder, Marco; Zhu, Yiwen; Wu, Han; Afzal, Sarah Yasmeen; Blow, Matthew J.; Kelman, Guy; Barozzi, Iros; Fukuda-Yuzawa, Yoko; Akiyama, Jennifer A.; Afzal, Veena; Tran, Stella; Plajzer-Frick, Ingrid; Novak, Catherine S.; Kato, Momoe; Hunter, Riana D.; von Maydell, Kianna; Wang, Allen; Lin, Lin; Preissl, Sebastian; Lisgo, Steven; Ren, Bing; Dickel, Diane E.; Pennacchio, Len A.; Visel, Axel
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Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis
err2023-06-29
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errTenney, Alan P.; Di Gioia, Silvio Alessandro; Webb, Bryn D.; Chan, Wai-Man; de Boer, Elke; Garnai, Sarah J.; Barry, Brenda J.; Ray, Tammy; Kosicki, Michael; Robson, Caroline D.; Zhang, Zhongyang; Collins, Thomas E.; Gelber, Alon; Pratt, Brandon M.; Fujiwara, Yuko; Varshney, Arushi; Lek, Monkol; Warburton, Peter E.; Van Ryzin, Carol; Lehky, Tanya J.; Zalewski, Christopher; King, Kelly A.; Brewer, Carmen C.; Thurm, Audrey; Snow, Joseph; Facio, Flavia M.; Narisu, Narisu; Bonnycastle, Lori L.; Swift, Amy; Chines, Peter S.; Bell, Jessica L.; Mohan, Suresh; Whitman, Mary C.; Staffieri, Sandra E.; Elder, James E.; Demer, Joseph L.; Torres, Alcy; Rachid, Elza; Al-Haddad, Christiane; Boustany, Rose-Mary; Mackey, David A.; Brady, Angela F.; Fenollar-Cortes, Maria; Fradin, Melanie; Kleefstra, Tjitske; Padberg, George W.; Raskin, Salmo; Sato, Mario Teruo; Orkin, Stuart H.; Parker, Stephen C. J.; Hadlock, Tessa A.; Vissers, Lisenka E. L. M.; van Bokhoven, Hans; Jabs, Ethylin Wang; Collins, Francis S.; Pennacchio, Len A.; Manoli, Irini; Engle, Elizabeth C.
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Genetic determinants of switchgrass- root-associated microbiota in field sites spanning its natural range
err2023-05-01
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errOAAI
errEdwards, Joseph A.; Saran, Usha Bishnoi; Bonnette, Jason; MacQueen, Alice; Yin, Jun; Nguyen, Tu Uyen; Schmutz, Jeremy; Grimwood, Jane; Pennacchio, Len A.; Daum, Chris; del Rio, Tijana Glavina; Fritschi, Felix B.; Lowry, David B.; Juenger, Thomas E.
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Topologically associating domain boundaries are required for normal genome function
err2023-04-20
err31
errOAAI
errRajderkar, Sudha; Barozzi, Iros; Zhu, Yiwen; Hu, Rong; Zhang, Yanxiao; Li, Bin; Caro, Ana Alcaina; Fukuda-Yuzawa, Yoko; Kelman, Guy; Akeza, Adyam; Blow, Matthew J.; Pham, Quan; Harrington, Anne N.; Godoy, Janeth; Meky, Eman M.; von Maydell, Kianna; Hunter, Riana D.; Akiyama, Jennifer A.; Novak, Catherine S.; Plajzer-Frick, Ingrid; Afzal, Veena; Tran, Stella; Lopez-Rios, Javier; Talkowski, Michael E.; Lloyd, K. C. Kent; Ren, Bing; Dickel, Diane E.; Visel, Axel; Pennacchio, Len A.
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Insulin-mediated down-regulation of apolipoprotein A5 gene expression through the phosphatidylinositol 3-kinase pathway: Role of upstream stimulatory factor
err2023-03-27
err114
errOAAI
errNowak, M; Helleboid-Chapman, A; Jakel, H; Martin, G; Duran-Sandoval, D; Staels, B; Rubin, EM; Pennacchio, LA; Taskinen, MR; Fruchart-Najib, J; Fruchart, JC
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Single cell evaluation of endocardial Hand2 gene regulatory networks reveals HAND2-dependent pathways that impact cardiac morphogenesis
err2023-02-06
err5
errOAAI
errGeorge, Rajani M.; Firulli, Beth A.; Podicheti, Ram; Rusch, Douglas B.; Mannion, Brandon J.; Pennacchio, Len A.; Osterwalder, Marco; Firulli, Anthony B.
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