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Manolis Kellis

broad institute of massachusetts institute of technology

139H-index
1.1KPaper Count
12.4WCitation Count
Published Papers 214
Publication Date
Author Correction: Specific oncogene activation of the cell of origin in mucosal melanoma
err2026-08-20
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errOAAI
errSwathy Babu; Jiajia Chen; Chloé S. Baron; Kaiwen Sun; Emily Robitschek; Alicia M. McConnell; Constance Wu; Aikaterini Dedeilia; Moshe Sade-Feldman; Rodsy Modhurima; Michael P. Manos; Kevin Y. Chen; Anna M. Cox; Calvin G. Ludwig; Manolis Kellis; Elizabeth I. Buchbinder; Nir Hacohen; Jiekun Yang; Genevieve M. Boland; Brian J. Abraham; David Liu; Leonard I. Zon; Megan L. Insco
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An encyclopedia of human enhancer–gene regulatory interactions
errNature
IF48.5
err2026-07-15
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errOAAI
errAndreas R. Gschwind; Kristy S. Mualim; Alireza Karbalayghareh; Maya U. Sheth; Kushal K. Dey; Evelyn Jagoda; Ramil N. Nurtdinov; Wang Xi; Anthony S. Tan; James Galante; Hank Jones; X. Rosa Ma; David Yao; Dulguun Amgalan; Judhajeet Ray; Chad J. Munger; Joseph Nasser; Žiga Avsec; Benjamin T. James; Muhammad S. Shamim; Neva C. Durand; Suhas S. P. Rao; Ragini Mahajan; Benjamin R. Doughty; Kalina Andreeva; Jacob C. Ulirsch; Kaili Fan; Elizabeth M. Perez; Tri C. Nguyen; David R. Kelley; Hilary K. Finucane; Jill E. Moore; Zhiping Weng; Manolis Kellis; Michael C. Bassik; Berk Ustun; Alkes L. Price; Michael A. Beer; Roderic Guigó; John A. Stamatoyannopoulos; Erez Lieberman Aiden; William J. Greenleaf; Christina S. Leslie; Lars M. Steinmetz; Anshul Kundaje; Jesse M. Engreitz
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Genotype epigenome phenotype integration reveals peripheral immune contributions to type I bipolar disorder
err2026-05-15
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errOAAI
errLei Hou; Yue Li; Xushen Xiong; Yosuke Tanigawa; Yongjin Park; Samuel W. Lenz; Amy Grayson; Jeong-Heon Lee; Euijung Ryu; Janet E. Olson; Joanna M. Biernacka; Mark A. Frye; Tamas Ordog; Manolis Kellis
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Expanding the human proteome with microproteins and peptideins
errNature
IF48.5
err2026-05-01
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PREAI
errDeutsch, Eric W.; Kok, Leron W.; Mudge, Jonathan M.; Valls, Cristian F.; Jungreis, Irwin; Ruiz-Orera, Jorge; Sun, Zhi; Kusebauch, Ulrike; Fierro-Monti, Ivo; Abelin, Jennifer G.; Alba, M. Mar; Aspden, Julie L.; Bandyopadhyay, Sreejan; Banerjee, Kaushik; Baranov, Pavel V.; Bazzini, Ariel A.; Bourassa, Francis; Bruford, Elspeth A.; Calviello, Lorenzo; Carr, Steven A.; Carvunis, Anne-Ruxandra; Chothani, Sonia; Clauwaert, Jim; Dean, Kellie; Faridi, Pouya; Frankish, Adam; Goodale, Amy; Green, Thomas; Hubner, Norbert; Ingolia, Nicholas T.; Kellis, Manolis; Magrane, Michele; Martin, Maria Jesus; Martinez, Thomas F.; Menschaert, Gerben; Ohler, Uwe; Orchard, Sandra; Potter, Alisa; Rackham, Owen J. L.; Rees, Matthew G.; Root, David E.; Roth, Jennifer A.; Roucou, Xavier; Sialana, Fernando J.; Slavoff, Sarah A.; Swirski, Michal I.; Tierney, Jack A. S.; Trifiro, Felix-Antoine; Valen, Eivind; Vasylieva, Valeriia; Wacholder, Aaron; Wang, Shengbo; Wang, Li; Weissman, Jonathan S.; Wu, Wei; Choudhary, Jyoti S.; Bassani-Sternberg, Michal; Vizcaino, Juan Antonio; Ternette, Nicola; Brunet, Marie A.; Moritz, Robert L.; Prensner, John R.; van Heesch, Sebastiaan
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Interpretable deep generative ensemble learning for single-cell omics with Hydra
err2026-04-11
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errOAAI
errManoj M Wagle; Chunlei Liu; Zunpeng Liu; Yongheng Wang; Manolis Kellis; Ellis Patrick; Pengyi Yang
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Proteogenomics in cerebrospinal fluid and plasma reveals new biological fingerprint of cerebral small vessel disease
err2025-11-20
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errOAAI
errIlana Caro; Daniel Western; Shinichi Namba; Na Sun; Shuji Kawaguchi; Yunye He; Masashi Fujita; Gennady Roshchupkin; Tim D’Aoust; Marie-Gabrielle Duperron; Muralidharan Sargurupremraj; Ami Tsuchida; Masaru Koido; Marziehsadat Ahmadi; Chengran Yang; Jigyasha Timsina; Laura Ibanez; Koichi Matsuda; Yutaka Suzuki; Yoshiya Oda; Akinori Kanai; Pouria Jandaghi; Markus Munter; Daniel Auld; Iana Astafeva; Raquel Puerta; Jerome I. Rotter; Bruce M. Psaty; Joshua C. Bis; WT Longstreth; Thierry Couffinhal; Pablo García-González; Vanesa Pytel; Marta Marquié; Amanda Cano; Mercè Boada; Marc Joliot; Mark Lathrop; Quentin Le Grand; Lenore J. Launer; Joanna M. Wardlaw; Myriam Heiman; Agustin Ruiz; Paul M. Matthews; Sudha Seshadri; Myriam Fornage; Hieab Adams; Aniket Mishra; David-Alexandre Trégouët; Yukinori Okada; Manolis Kellis; Philip L. De Jager; Christophe Tzourio; Yoichiro Kamatani; Fumihiko Matsuda; Carlos Cruchaga; Stéphanie Debette
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Multi-omics analysis of a pig-to-human decedent kidney xenotransplant
errNature
IF48.5
err2025-11-13
err0
PREAI
errEloi Schmauch; Brian D. Piening; Alexa K. Dowdell; Maedeh Mohebnasab; Simon H. Williams; Alexey Stukalov; Fred L. Robinson; Robin Bombardi; Ian Jaffe; Karen Khalil; Jacqueline Kim; Imad Aljabban; Tal Eitan; Darragh P. O’Brien; Mercy Rophina; Chan Wang; Alexandra Q. Bartlett; Francesca Zanoni; Jon Albay; David Andrijevic; Berk Maden; Vincent Mauduit; Susanna Vikman; Diana Argibay; Zasha Zayas; Leah Wu; Kiana Moi; Billy Lau; Weimin Zhang; Loren Gragert; Elaina Weldon; Hui Gao; Lauren Hamilton; Larisa Kagermazova; Brendan R. Camellato; Divya Gandla; Riyana Bhatt; Sarah Gao; Rudaynah A. Al-Ali; Alawi H. Habara; Andrew Chang; Shadi Ferdosi; Han M. Chen; Jennifer D. Motter; Fiorella A. Chacon; Scott C. Thomas; Deepak Saxena; Robert L. Fairchild; Alexandre Loupy; Adriana Heguy; Ali Crawford; Serafim Batzoglou; Michael P. Snyder; Asim Siddiqui; Michael V. Holmes; Anita S. Chong; Minna U. Kaikkonen; Suvi Linna-Kuosmanen; David Ayares; Marc Lorber; Anoma Nellore; Edward Y. Skolnik; Aprajita Mattoo; Vasishta S. Tatapudi; Ryan Taft; Massimo Mangiola; Qian Guo; Ramin S. Herati; Jeffrey Stern; Adam Griesemer; Manolis Kellis; Jef D. Boeke; Robert A. Montgomery; Brendan J. Keating
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Integrating single-cell RNA-seq datasets with substantial batch effects
err2025-10-31
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errOAAI
errKarin Hrovatin; Amir Ali Moinfar; Luke Zappia; Shrey Parikh; Alejandro Tejada Lapuerta; Ben Lengerich; Manolis Kellis; Fabian J. Theis
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Programmed ribosomal frameshifting during PLEKHM2 mRNA decoding generates a constitutively active proteoform that supports myocardial function
err2025-10-24
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PREAI
errGary Loughran; Raffaella De Pace; Ningyu Ding; Jianchao Zhang; Irwin Jungreis; Gionmattia Carancini; Jonathan M. Mudge; Ji Wang; Manolis Kellis; John F. Atkins; Pavel V. Baranov; Andrew E. Firth; Xiaowei Li; Juan S. Bonifacino; Yousuf A. Khan
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Molecular hallmarks of excitatory and inhibitory neuronal resilience to Alzheimer’s disease
err2025-10-03
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errOAAI
errIsabel Castanho; Pourya Naderi Yeganeh; Carles A. Boix; Sarah L. Morgan; Hansruedi Mathys; Dmitry Prokopenko; Bartholomew White; Larisa M. Soto; Giulia Pegoraro; Saloni Shah; Athanasios Ploumakis; Nikolas Kalavros; David A. Bennett; Christoph Lange; Doo Yeon Kim; Lars Bertram; Li-Huei Tsai; Manolis Kellis; Rudolph E. Tanzi; Winston Hide
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ABCA7 variants impact phosphatidylcholine and mitochondria in neurons
errNature
IF48.5
err2025-09-10
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errOAAI
errDjuna von Maydell; Shannon E. Wright; Ping-Chieh Pao; Colin Staab; Oisín King; Andrea Spitaleri; Julia Maeve Bonner; Liwang Liu; Chung Jong Yu; Ching-Chi Chiu; Daniel Leible; Aine Ni Scannail; Mingpei Li; Carles A. Boix; Hansruedi Mathys; Guillaume Leclerc; Gloria Suella Menchaca; Gwyneth Welch; Agnese Graziosi; Noelle Leary; George Samaan; Manolis Kellis; Li-Huei Tsai
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Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma
err2025-09-01
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errOAAI
errJiekun Yang; Cassia Wang; Doris Fu; Li-Lun Ho; Kyriakitsa Galani; Lee Chen; Jose Gonzalez; Jolene Fu; Amy Y. Huang; Dennie T. Frederick; Liang He; Mukta Asnani; Rahul Tacke; Emily J. Robitschek; Sandeep K. Yadav; Wentao Deng; Kelly P. Burke; Tatyana Sharova; Ryan J. Sullivan; Sarah Weiss; Kunal Rai; David Liu; Genevieve M. Boland; Manolis Kellis
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Single-cell multiregion epigenomic rewiring in Alzheimer’s disease progression and cognitive resilience
errCell
IF42.5
err2025-08-01
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errOAAI
errZunpeng Liu; Shanshan Zhang; Benjamin T. James; Kyriaki Galani; Riley J. Mangan; Stuart Benjamin Fass; Chuqian Liang; Manoj M. Wagle; Carles A. Boix; Yosuke Tanigawa; Sukwon Yun; Yena Sung; Xushen Xiong; Na Sun; Lei Hou; Martin Wohlwend; Mufan Qiu; Xikun Han; Lei Xiong; Efthalia Preka; Lei Huang; William F. Li; Li-Lun Ho; Amy Grayson; Julio Mantero; Alexey Kozlenkov; Hansruedi Mathys; Tianlong Chen; Stella Dracheva; David A. Bennett; Li-Huei Tsai; Manolis Kellis
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Overcoming resistance to immunotherapy by targeting CD38 in human tumor explants
err2025-06-27
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errOAAI
errOr-Yam Revach; Angelina M. Cicerchia; Ofir Shorer; Claire A. Palin; Boryana Petrova; Seth Anderson; Baolin Liu; Joshua Park; Lee Chen; Arnav Mehta; Samuel J. Wright; Niamh McNamee; Aya Tal-Mason; Giulia Cattaneo; Payal Tiwari; Hongyan Xie; Johanna M. Sweere; Li-Chun Cheng; Natalia Sigal; Elizabeth Enrico; Marisa Miljkovic; Shane A. Evans; Ngan Nguyen; Mark E. Whidden; Ramji Srinivasan; Matthew H. Spitzer; Yi Sun; Tatyana Sharova; Aleigha R. Lawless; William A. Michaud; Martin Q. Rasmussen; Jacy Fang; Jeannette R. Brook; Feng Chen; Xinhui Wang; Cristina R. Ferrone; Donald P. Lawrence; Ryan J. Sullivan; David Liu; Uma M. Sachdeva; Debattama R. Sen; Keith T. Flaherty; Robert T. Manguso; Lloyd Bod; Manolis Kellis; Genevieve M. Boland; Keren Yizhak; Jiekun Yang; Naama Kanarek; Moshe Sade-Feldman; Nir Hacohen; Russell W. Jenkins
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Multisensory gamma stimulation enhances adult neurogenesis and improves cognitive function in male mice with Down Syndrome
err2025-04-24
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errOAAI
errIslam, Md Rezaul; Jackson, Brennan; Naomi, Maeesha Tasnim; Schatz, Brooke; Tan, Noah; Murdock, Mitchell; Park, Dong Shin; Amorim, Daniela Rodrigues; Jiang, Xueqiao; Pineda, S. Sebastian; Adaikkan, Chinnakkaruppan; Fernandez Avalos, Vanesa; Geigenmuller, Ute; Firenze, Rosalind Mott; Kellis, Manolis; Boyden, Edward S.; Tsai, Li-Huei
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The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles ( vol 24 , 79 , 2023)
err2025-02-13
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errOAAI
errSchreiber, Jacob Matthew; Boix, Carles A.; Lee, Jin Wook; Li, Hongyang; Guan, Yuanfang; Chang, Chun-Chieh; Chang, Jen-Chien; Hawkins-Hooker, Alex; Schoelkopf, Bernhard; Schweikert, Gabriele; Carulla, Mateo Rojas; Canakoglu, Arif; Guzzo, Francesco; Nanni, Luca; Masseroli, Marco; Carman, Mark James; Pinoli, Pietro; Hong, Chenyang; Yip, Kevin Y.; Spence, Jefrey P.; Batra, Sanjit Singh; Song, Yun S.; Mahony, Shaun; Zhang, Zheng; Tan, Wuwei; Shen, Yang; Sun, Yuanfei; Shi, Minyi; Adrian, Jessika; Sandstrom, Richard S.; Farrell, Nina P.; Halow, Jessica M.; Lee, Kristen; Jiang, Lixia; Yang, Xinqiong; Epstein, Charles B.; Strattan, J. Seth; Bernstein, Bradley E.; Snyder, Michael P.; Kellis, Manolis; Noble, William S.; Kundaje, Anshul Bharat; ENCODE Imputat Challenge Participants
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QClus: a droplet filtering algorithm for enhanced snRNA-seq data quality in challenging samples
err2024-12-05
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errOAAI
errSchmauch, Eloi; Ojanen, Johannes; Galani, Kyriakitsa; Jalkanen, Juho; Harju, Kristiina; Hollmen, Maija; Kokki, Hannu; Gunn, Jarmo; Halonen, Jari; Hartikainen, Juha; Kiviniemi, Tuomas; Tavi, Pasi; Kaikkonen, Minna U.; Kellis, Manolis; Linna-Kuosmanen, Suvi
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Deep learning prediction of ribosome profiling with Translatomer reveals translational regulation and interprets disease variants
err2024-10-23
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PREAI
errHe, Jialin; Xiong, Lei; Shi, Shaohui; Li, Chengyu; Chen, Kexuan; Fang, Qianchen; Nan, Jiuhong; Ding, Ke; Mao, Yuanhui; Boix, Carles A.; Hu, Xinyang; Kellis, Manolis; Li, Jingyun; Xiong, Xushen
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SINGLE-CELL MULTI-COHORT TRANSCRIPTOMIC DISSECTION OF BIPOLAR DISORDER
err2024-10-01
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PREAI
errHan, Xikun; Mohammadi, Shahin; Fullard, John F.; Subburaju, Sivan; Tso, Daniel R.; Hourihan, Makayla; Sun, Na; Hou, Lei; Hoffman, Gabriel E.; Bendl, Jaroslav; Lee, Donghoon; Roussos, Panos; Kellis, Manolis; Ruzicka, W. Brad
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