Manolis Kellis

According to our database, Manolis Kellis authored at least 45 papers between 2004 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

TrustLLM: Trustworthiness in Large Language Models.

Lichao Sun, Yue Huang, Haoran Wang, Siyuan Wu, Qihui Zhang, Chujie Gao, Yixin Huang, Wenhan Lyu, Yixuan Zhang, Xiner Li, Zhengliang Liu, Yixin Liu, Yijue Wang, Zhikun Zhang, Bhavya Kailkhura, Caiming Xiong, Chaowei Xiao, Chunyuan Li, Eric P. Xing, Furong Huang, Hao Liu, Heng Ji, Hongyi Wang, Huan Zhang, Huaxiu Yao, Manolis Kellis, Marinka Zitnik, Meng Jiang, Mohit Bansal, James Zou, Jian Pei, Jian Liu, Jianfeng Gao, Jiawei Han, Jieyu Zhao, Jiliang Tang, Jindong Wang, John Mitchell, Kai Shu, Kaidi Xu, Kai-Wei Chang, Lifang He, Lifu Huang, Michael Backes, Neil Zhenqiang Gong, Philip S. Yu, Pin-Yu Chen, Quanquan Gu, Ran Xu, Rex Ying, Shuiwang Ji, Suman Jana, Tianlong Chen, Tianming Liu, Tianyi Zhou, William Wang, Xiang Li, Xiangliang Zhang, Xiao Wang, Xing Xie, Xun Chen, Xuyu Wang, Yan Liu, Yanfang Ye, Yinzhi Cao, Yue Zhao

CoRR, 2024

2023

GENCODE: reference annotation for the human and mouse genomes in 2023.

Adam Frankish, Silvia Carbonell Sala, Mark Diekhans, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew E. Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet Riera, Daniel Cerdán-Vélez, Fiona Cunningham, Claire Davidson, Sarah M. Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos García-Girón, Jose M. Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike P. Kay, Julien Lagarde, Fergal J. Martin, Laura Martínez Gómez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew D. Yates, Zahoor Zafrulla, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek

Nucleic Acids Res., January, 2023

Contextualized Machine Learning.

Benjamin J. Lengerich, Caleb N. Ellington, Andrea Rubbi, Manolis Kellis, Eric P. Xing

CoRR, 2023

LLMs Understand Glass-Box Models, Discover Surprises, and Suggest Repairs.

Benjamin J. Lengerich, Sebastian Bordt, Harsha Nori, Mark E. Nunnally, Yin Aphinyanaphongs, Manolis Kellis, Rich Caruana

CoRR, 2023

Combinatorial Optimization for Predicting Optimal Cell-state Conversion Paths.

Shaurya Agrawal, Manolis Kellis, Martin Wohlwend

Proceedings of the 16th International Congress on Image and Signal Processing, 2023

2021

GENCODE 2021.

Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew E. Berry, Alexandra Bignell, Carles Boix, Silvia Carbonell Sala, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Kevin L. Howe, Toby Hunt, Osagie G. Izuogu, Rory Johnson, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Ferriol Calvet Riera, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Maxim Y. Wolf, Jinrui Xu, Yucheng T. Yang, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Michael L. Tress, Paul Flicek

Nucleic Acids Res., 2021

NOTMAD: Estimating Bayesian Networks with Sample-Specific Structures and Parameters.

Benjamin J. Lengerich, Caleb Ellington, Bryon Aragam, Eric P. Xing, Manolis Kellis

CoRR, 2021

2020

Spectral Alignment of Graphs.

Soheil Feizi, Gerald T. Quon, Mariana Recamonde Mendoza, Muriel Médard, Manolis Kellis, Ali Jadbabaie

IEEE Trans. Netw. Sci. Eng., 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora

Nat., 2020

2019

Network Infusion to Infer Information Sources in Networks.

Soheil Feizi, Muriel Médard, Gerald T. Quon, Manolis Kellis, Ken Duffy

IEEE Trans. Netw. Sci. Eng., 2019

GENCODE reference annotation for the human and mouse genomes.

Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew E. Berry, Alexandra Bignell, Silvia Carbonell Sala, Jacqueline Chrast, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Toby Hunt, Osagie G. Izuogu, Julien Lagarde, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Jinrui Xu, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Bronwen L. Aken, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Alexandre Reymond, Michael L. Tress, Paul Flicek

Nucleic Acids Res., 2019

Causal Mediation Analysis Leveraging Multiple Types of Summary Statistics Data.

Yongjin Park, Abhishek Sarkar, Khoi Nguyen, Manolis Kellis

CoRR, 2019

ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation.

Malene Juul, Tobias Madsen, Qianyun Guo, Johanna Bertl, Asger Hobolth, Manolis Kellis, Jakob Skou Pedersen

Bioinform., 2019

2018

Genie: A Secure, Transparent Sharing and Services Platform for Genetic and Health Data.

Shifa Zhang, Anne Kim, Dianbo Liu, Sandeep C. Nuckchadyy, Lauren Huang, Aditya Masurkar, Jingwei Zhang, Lawrence Tseng, Pratheek Karnati, Laura Martínez, Thomas Hardjono, Manolis Kellis, ZhiZhuo Zhang

CoRR, 2018

A latent topic model for mining heterogenous non-randomly missing electronic health records data.

Yue Li, Manolis Kellis

CoRR, 2018

RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss.

Mukul S. Bansal, Manolis Kellis, Misagh Kordi, Soumya Kundu

Bioinform., 2018

2017

Network Maximal Correlation.

Soheil Feizi, Ali Makhdoumi, Ken Duffy, Manolis Kellis, Muriel Médard

IEEE Trans. Netw. Sci. Eng., 2017

2016

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease.

Lucas D. Ward, Manolis Kellis

Nucleic Acids Res., 2016

Spectral Alignment of Networks.

Soheil Feizi, Gerald T. Quon, Mariana Recamonde Mendoza, Muriel Médard, Manolis Kellis, Ali Jadbabaie

CoRR, 2016

SwiSpot: modeling riboswitches by spotting out switching sequences.

Marco Barsacchi, Eva Maria Novoa, Manolis Kellis, Alessio Bechini

Bioinform., 2016

2015

Integrative analysis of 111 reference human epigenomes Open.

Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi Moussavi, Pouya Kheradpour, ZhiZhuo Zhang, Jianrong Wang, Michael J. Ziller, Viren Amin, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald T. Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kyle Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca F. Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil R. Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis

Nat., 2015

Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue.

Andrea Califano, Manolis Kellis, Gustavo Stolovitzky

J. Comput. Biol., 2015

A Perspective on Future Research Directions in Information Theory.

Jeffrey G. Andrews, Alexandros G. Dimakis, Lara Dolecek, Michelle Effros, Muriel Médard, Olgica Milenkovic, Andrea Montanari, Sriram Vishwanath, Edmund M. Yeh, Randall Berry, Ken R. Duffy, Soheil Feizi, Saul Kato, Manolis Kellis, Stuart Licht, Jon Sorenson, Lav R. Varshney, Haris Vikalo

CoRR, 2015

Improved gene tree error correction in the presence of horizontal gene transfer.

Mukul S. Bansal, Yi-Chieh Wu, Eric J. Alm, Manolis Kellis

Bioinform., 2015

2014

Comparative analysis of metazoan chromatin organization Open.

Joshua Wing Kei Ho, Youngsook L. Jung, Tao Liu, Burak Han Alver, Soohyun Lee, Kohta Ikegami, Kyung-Ah Sohn, Aki Minoda, Michael Y. Tolstorukov, Alex Appert, Stephen C. J. Parker, Tingting Gu, Anshul Kundaje, Nicole C. Riddle, Eric Bishop, Thea A. Egelhofer, Sheng'en Shawn Hu, Artyom A. Alekseyenko, Andreas Rechtsteiner, Dalal Asker, Jason A. Belsky, Sarah K. Bowman, Q. Brent Chen, Ron A.-J. Chen, Daniel S. Day, Yan Dong, Andrea C. Dose, Xikun Duan, Charles B. Epstein, Sevinc Ercan, Elise A. Feingold, Francesco Ferrari, Jacob M. Garrigues, Nils Gehlenborg, Peter J. Good, Psalm Haseley, Daniel He, Moritz Herrmann, Michael M. Hoffman, Tess E. Jeffers, Peter V. Kharchenko, Paulina Kolasinska-Zwierz, Chitra V. Kotwaliwale, Nischay Kumar, Sasha A. Langley, Erica Larschan, Isabel Latorre, Maxwell W. Libbrecht, Xueqiu Lin, Richard Park, Michael J. Pazin, Hoang N. Pham, Annette Plachetka, Bo Qin, Yuri B. Schwartz, Noam Shoresh, Przemyslaw Stempor, Anne Vielle, Chengyang Wang, Christina M. Whittle, Huiling Xue, Robert E. Kingston, Ju Han Kim, Bradley E. Bernstein, Abby F. Dernburg, Vincenzo Pirrotta, Mitzi I. Kuroda, William S. Noble, Thomas D. Tullius, Manolis Kellis, David M. MacAlpine, Susan Strome, Sarah C. R. Elgin, Xiaole Shirley Liu, Jason D. Lieb, Julie Ahringer, Gary H. Karpen, Peter J. Park

Nat., 2014

Comparative analysis of regulatory information and circuits across distant species Open.

Alan P. Boyle, Carlos L. Araya, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng, Kathryn Gardner, LaDeana W. Hillier, Judith Janette, Lixia Jiang, Dionna Kasper, Trupti Kawli, Pouya Kheradpour, Anshul Kundaje, Jingyi Jessica Li, Lijia Ma, Wei Niu, E. Jay Rehm, Joel S. Rozowsky, Matthew Slattery, Rebecca Spokony, Robert Terrell, Dionne Vafeados, Daifeng Wang, Peter Weisdepp, Yi-Chieh Wu, Dan Xie, Koon-Kiu Yan, Elise A. Feingold, Peter J. Good, Michael J. Pazin, Haiyan Huang, Peter J. Bickel, Steven E. Brenner, Valerie Reinke, Robert H. Waterston, Mark Gerstein, Kevin P. White, Manolis Kellis, Michael Snyder

Nat., 2014

RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue.

Andrea Califano, Manolis Kellis, Gustavo Stolovitzky

J. Comput. Biol., 2014

Diversifying Sparsity Using Variational Determinantal Point Processes.

Nematollah Kayhan Batmanghelich, Gerald T. Quon, Alex Kulesza, Manolis Kellis, Polina Golland, Luke Bornn

CoRR, 2014

Pareto-optimal phylogenetic tree reconciliation.

Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal, Manolis Kellis

Bioinform., 2014

2013

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State.

Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, John A. Stamatoyannopoulos, Jason Ernst, Manolis Kellis, Bing Ren

PLoS Comput. Biol., 2013

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue.

Andrea Califano, Manolis Kellis, Gustavo Stolovitzky

J. Comput. Biol., 2013

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss.

Mukul S. Bansal, Eric J. Alm, Manolis Kellis

J. Comput. Biol., 2013

Session Introduction.

Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

2012

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants.

Lucas D. Ward, Manolis Kellis

Nucleic Acids Res., 2012

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 Special Issue.

Andrea Califano, Manolis Kellis, Gustavo Stolovitzky

J. Comput. Biol., 2012

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.

Mukul S. Bansal, Eric J. Alm, Manolis Kellis

Bioinform., 2012

2011

Preface.

Manolis Kellis, Andrea Califano, Ziv Bar-Joseph

J. Comput. Biol., 2011

SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings.

Ferhat Ay, Manolis Kellis, Tamer Kahveci

J. Comput. Biol., 2011

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.

Michael F. Lin, Irwin Jungreis, Manolis Kellis

Bioinform., 2011

Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome.

Jason Ernst, Manolis Kellis

Proceedings of the Research in Computational Molecular Biology, 2011

2010

Motif discovery in physiological datasets: A methodology for inferring predictive elements.

Zeeshan Syed, Collin M. Stultz, Manolis Kellis, Piotr Indyk, John V. Guttag

ACM Trans. Knowl. Discov. Data, 2010

Information-Theoretic Inference of Gene Networks Using Backward Elimination.

Patrick Meyer, Daniel Marbach, Sushmita Roy, Manolis Kellis

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2010

2008

Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 <i>Drosophila</i> Genomes.

Michael F. Lin, Ameya N. Deoras, Matthew D. Rasmussen, Manolis Kellis

PLoS Comput. Biol., 2008

2007

Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking.

Joshua A. Grochow, Manolis Kellis

Proceedings of the Research in Computational Molecular Biology, 2007

2004

Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery.

Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander

J. Comput. Biol., 2004