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ORCIDManolis Kellis
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- affiliation: Massachusetts Institute of Technology, Cambridge, USA
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2020 – today
- 2024
[c7]Yue Huang, Lichao Sun, Haoran Wang, Siyuan Wu, Qihui Zhang, Yuan Li, Chujie Gao, Yixin Huang, Wenhan Lyu, Yixuan Zhang, Xiner Li, Hanchi Sun, Zhengliang Liu, Yixin Liu, Yijue Wang, Zhikun Zhang, Bertie Vidgen, 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, Joaquin Vanschoren, John C. 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, Yong Chen, Yue Zhao:
Position: TrustLLM: Trustworthiness in Large Language Models. ICML 2024- [i12]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 C. 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:
TrustLLM: Trustworthiness in Large Language Models. CoRR abs/2401.05561 (2024) - [i11]Shania Mitra, Lei Huang, Manolis Kellis:
ProteinRPN: Towards Accurate Protein Function Prediction with Graph-Based Region Proposals. CoRR abs/2409.00610 (2024) - 2023
- [j30]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:
GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51(D1): 942-949 (2023) - [c6]Shaurya Agrawal, Manolis Kellis, Martin Wohlwend:
Combinatorial Optimization for Predicting Optimal Cell-state Conversion Paths. CISP-BMEI 2023: 1-6 - [i10]Benjamin J. Lengerich, Sebastian Bordt, Harsha Nori, Mark E. Nunnally, Yin Aphinyanaphongs, Manolis Kellis, Rich Caruana:
LLMs Understand Glass-Box Models, Discover Surprises, and Suggest Repairs. CoRR abs/2308.01157 (2023) - [i9]Benjamin J. Lengerich, Caleb N. Ellington, Andrea Rubbi, Manolis Kellis, Eric P. Xing:
Contextualized Machine Learning. CoRR abs/2310.11340 (2023) - 2021
- [j29]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:
GENCODE 2021. Nucleic Acids Res. 49(Database-Issue): D916-D923 (2021) - [i8]Benjamin J. Lengerich, Caleb Ellington, Bryon Aragam, Eric P. Xing, Manolis Kellis:
NOTMAD: Estimating Bayesian Networks with Sample-Specific Structures and Parameters. CoRR abs/2111.01104 (2021) - 2020
- [j28]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:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j27]Soheil Feizi, Gerald T. Quon, Mariana Recamonde Mendoza, Muriel Médard, Manolis Kellis, Ali Jadbabaie:
Spectral Alignment of Graphs. IEEE Trans. Netw. Sci. Eng. 7(3): 1182-1197 (2020)
2010 – 2019
- 2019
- [j26]Malene Juul, Tobias Madsen, Qianyun Guo, Johanna Bertl, Asger Hobolth, Manolis Kellis, Jakob Skou Pedersen:
ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation. Bioinform. 35(2): 189-199 (2019) - [j25]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:
GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47(Database-Issue): D766-D773 (2019) - [j24]Soheil Feizi, Muriel Médard, Gerald T. Quon, Manolis Kellis, Ken Duffy:
Network Infusion to Infer Information Sources in Networks. IEEE Trans. Netw. Sci. Eng. 6(3): 402-417 (2019) - [i7]Yongjin Park, Abhishek Sarkar, Khoi Nguyen, Manolis Kellis:
Causal Mediation Analysis Leveraging Multiple Types of Summary Statistics Data. CoRR abs/1901.08540 (2019) - 2018
- [j23]Mukul S. Bansal, Manolis Kellis, Misagh Kordi, Soumya Kundu:
RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss. Bioinform. 34(18): 3214-3216 (2018) - [i6]Yue Li, Manolis Kellis:
A latent topic model for mining heterogenous non-randomly missing electronic health records data. CoRR abs/1811.00464 (2018) - [i5]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:
Genie: A Secure, Transparent Sharing and Services Platform for Genetic and Health Data. CoRR abs/1811.01431 (2018) - 2017
- [j22]Soheil Feizi, Ali Makhdoumi, Ken Duffy, Manolis Kellis, Muriel Médard:
Network Maximal Correlation. IEEE Trans. Netw. Sci. Eng. 4(4): 229-247 (2017) - 2016
- [j21]Marco Barsacchi, Eva Maria Novoa, Manolis Kellis, Alessio Bechini:
SwiSpot: modeling riboswitches by spotting out switching sequences. Bioinform. 32(21): 3252-3259 (2016) - [j20]Lucas D. Ward, Manolis Kellis:
HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. Nucleic Acids Res. 44(Database-Issue): 877-881 (2016) - [i4]Soheil Feizi, Gerald T. Quon, Mariana Recamonde Mendoza, Muriel Médard, Manolis Kellis, Ali Jadbabaie:
Spectral Alignment of Networks. CoRR abs/1602.04181 (2016) - [i3]Soheil Feizi, Muriel Médard, Gerald T. Quon, Manolis Kellis, Ken R. Duffy:
Network Infusion to Infer Information Sources in Networks. CoRR abs/1606.07383 (2016) - 2015
- [j19]Mukul S. Bansal, Yi-Chieh Wu, Eric J. Alm, Manolis Kellis:
Improved gene tree error correction in the presence of horizontal gene transfer. Bioinform. 31(8): 1211-1218 (2015) - [j18]Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue. J. Comput. Biol. 22(4): 251-252 (2015) - [j17]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:
Integrative analysis of 111 reference human epigenomes Open. Nat. 518(7539): 317-330 (2015) - [i2]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:
A Perspective on Future Research Directions in Information Theory. CoRR abs/1507.05941 (2015) - 2014
- [j16]Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal, Manolis Kellis:
Pareto-optimal phylogenetic tree reconciliation. Bioinform. 30(12): 87-95 (2014) - [j15]Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue. J. Comput. Biol. 21(5): 371-372 (2014) - [j14]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:
Comparative analysis of metazoan chromatin organization Open. Nat. 512(7515): 449-452 (2014) - [j13]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:
Comparative analysis of regulatory information and circuits across distant species Open. Nat. 512(7515): 453-456 (2014) - [i1]Nematollah Kayhan Batmanghelich, Gerald T. Quon, Alex Kulesza, Manolis Kellis, Polina Golland, Luke Bornn:
Diversifying Sparsity Using Variational Determinantal Point Processes. CoRR abs/1411.6307 (2014) - 2013
- [j12]Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue. J. Comput. Biol. 20(5): 373-374 (2013) - [j11]Mukul S. Bansal, Eric J. Alm, Manolis Kellis:
Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. J. Comput. Biol. 20(10): 738-754 (2013) - [j10]Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, John A. Stamatoyannopoulos, Jason Ernst, Manolis Kellis, Bing Ren:
RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State. PLoS Comput. Biol. 9(3) (2013) - [c5]Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng:
Session Introduction. Pacific Symposium on Biocomputing 2013: 65-68 - [c4]Mukul S. Bansal, Eric J. Alm, Manolis Kellis:
Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss. RECOMB 2013: 1-13 - 2012
- [j9]Mukul S. Bansal, Eric J. Alm, Manolis Kellis:
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinform. 28(12): 283-291 (2012) - [j8]Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 Special Issue. J. Comput. Biol. 19(2): 101 (2012) - [j7]Lucas D. Ward, Manolis Kellis:
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 40(Database-Issue): 930-934 (2012) - 2011
- [j6]Michael F. Lin, Irwin Jungreis, Manolis Kellis:
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinform. 27(13): 275-282 (2011) - [j5]Manolis Kellis, Andrea Califano, Ziv Bar-Joseph:
Preface. J. Comput. Biol. 18(2): 131 (2011) - [j4]Ferhat Ay, Manolis Kellis, Tamer Kahveci:
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. J. Comput. Biol. 18(3): 219-235 (2011) - [c3]Jason Ernst, Manolis Kellis:
Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome. RECOMB 2011: 53 - 2010
- [j3]Zeeshan Syed, Collin M. Stultz, Manolis Kellis, Piotr Indyk, John V. Guttag:
Motif discovery in physiological datasets: A methodology for inferring predictive elements. ACM Trans. Knowl. Discov. Data 4(1): 2:1-2:23 (2010) - [c2]Patrick Meyer, Daniel Marbach, Sushmita Roy, Manolis Kellis:
Information-Theoretic Inference of Gene Networks Using Backward Elimination. BIOCOMP 2010: 700-705
2000 – 2009
- 2008
- [j2]Michael F. Lin, Ameya N. Deoras, Matthew D. Rasmussen, Manolis Kellis:
Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes. PLoS Comput. Biol. 4(4) (2008) - 2007
- [c1]Joshua A. Grochow, Manolis Kellis:
Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking. RECOMB 2007: 92-106 - 2004
- [j1]Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander:
Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery. J. Comput. Biol. 11(2/3): 319-355 (2004)
Coauthor Index
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