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Photo of Michael O. Duff, Ph.D.

Michael O. Duff, Ph.D.

Assistant Professor, Genetics and Genome Sciences
Computational Genomics Unit
Academic Office Location:
Genetics and Genome Sciences
UConn Health
Cell and Genome Sciences
400 Farmington Avenue
Farmington, CT 06030
Phone: 860-970-2283
Email: moduff@gmail.com
Website(s):

Department of Genetics and Genome Sciences

http://graveleylab.cam.uchc.edu/WebData/mduff

Education
DegreeInstitutionMajor
B.S.University of ArizonaSystems Theory
M.S.University of ArizonaSystems Theory
Ph.D.University of MassachusettsComputer Science

Post-Graduate Training
TrainingInstitutionSpecialty
OtherAT&T Bell Laboratories Digital Signal Processing, Quantization Theory
FellowshipGatsby Computational Neuroscience Unit, University College LondonSenior Research Fellow Developed theories and algorithms relating to probabilistic modeling, Bayesian learning, and Monte Carlo computation Investigated connections between reinforcement learning theory and the dopamine system
FellowshipInstitute for Genomics & Bioinformatics, and Department of Computer Science, University of California Irvine Visiting Research Fellow collaborated on the general problem of principled statistical inferrence of biologically-plausible genetic regulatory structures from sparse data (and collateral efforts to extend standard hidden Markov models to incorporate smooth models of regime change

Awards
Name of Award/HonorAwarding Organization
NIH/BIT Fellowship National Institutes of Health
Gatsby Fellowship The Gatsby Foundation
Name & DescriptionCategoryRoleTypeScopeStart YearEnd Year
Program Committee member, International Conference on Machine Learning Study SectionCommittee MemberExternalInternational2007
Efforts are directed toward bringing computational approaches, statistical modeling methods, and bioinformatics tools to bear upon problems posed by the analysis of Next-Generation-Sequencing (NGS) data. This includes the standard repertoire of techniques drawn from computational genomics: genome assembly, sequence alignment, gene-expression analysis, motif finding, phylogenetic analysis, and identification of regulatory sequences and networks---as well as the development of special-purpose ad-hoc computational tools for particular applications and novel techniques for data visualization.

NGS data analysis:
- DNA/RNA/ChIP/CLIP/RIP-seq data analysis
- alternative splicing in D.melanogaster (modENCODE, DSCAM)
- RNA interactions and functional intronic domains
- splicing orthology between human, fly, and worm
- lincRNA data analysis in hES differentiation
- analysis of RNAi off-target effects
- transplicing
- transcription/splicing kinetic models
- alternative-splicing changes during Human embryonic stem cell - -
- differentiation
- Archaeal CRISPR-Cas systems
- Squid (Loligo pealei) genome assembly and RNA-editing analysis
- Drosophila neurogenetics


Machine learning methods:
- model-structure induction
- probabilistic graphical models
- forcement learning theory
- quential decision-making under uncertainty

How can NGS data be used to infer causal relationships between transcribed elements?
How can ambiguity and bias be modeled and resolved?

Journal Articles

  • Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing.
    Garren, Seth B; Kondaveeti, Yuvabharath; Duff, Michael O; Carmichael, Gordon G PLoS pathogens 2015 Sep;11(9):e1005166
  • Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila.
    Stoiber, Marcus H; Olson, Sara; May, Gemma E; Duff, Michael O; Manent, Jan; Obar, Robert; Guruharsha, K G; Bickel, Peter J; Artavanis-Tsakonas, Spyros; Brown, James B; Graveley, Brenton R; Celniker, Susan E Genome research 2015 Aug;25(11):1692-702
  • Regulation of alternative splicing in Drosophila by 56 RNA binding proteins.
    Brooks, Angela N; Duff, Michael O; May, Gemma; Yang, Li; Bolisetty, Mohan; Landolin, Jane; Wan, Ken; Sandler, Jeremy; Booth, Benjamin W; Celniker, Susan E; Graveley, Brenton R; Brenner, Steven E Genome research 2015 Aug;25(11):1771-80
  • Genome-wide identification of zero nucleotide recursive splicing in Drosophila.
    Duff, Michael O; Olson, Sara; Wei, Xintao; Garrett, Sandra C; Osman, Ahmad; Bolisetty, Mohan; Plocik, Alex; Celniker, Susan E; Graveley, Brenton R Nature 2015 May;521(7552):376-9
  • Comparative analysis of the transcriptome across distant species.
    Gerstein, Mark B; Rozowsky, Joel; Yan, Koon-Kiu; Wang, Daifeng; Cheng, Chao; Brown, James B; Davis, Carrie A; Hillier, LaDeana; Sisu, Cristina; Li, Jingyi Jessica; Pei, Baikang; Harmanci, Arif O; Duff, Michael O; Djebali, Sarah; Alexander, Roger P; Alver, Burak H; Auerbach, Raymond; Bell, Kimberly; Bickel, Peter J; Boeck, Max E; Boley, Nathan P; Booth, Benjamin W; Cherbas, Lucy; Cherbas, Peter; Di, Chao; Dobin, Alex; Drenkow, Jorg; Ewing, Brent; Fang, Gang; Fastuca, Megan; Feingold, Elise A; Frankish, Adam; Gao, Guanjun; Good, Peter J; Guigó, Roderic; Hammonds, Ann; Harrow, Jen; Hoskins, Roger A; Howald, Cédric; Hu, Long; Huang, Haiyan; Hubbard, Tim J P; Huynh, Chau; Jha, Sonali; Kasper, Dionna; Kato, Masaomi; Kaufman, Thomas C; Kitchen, Robert R; Ladewig, Erik; Lagarde, Julien; Lai, Eric; Leng, Jing; Lu, Zhi; MacCoss, Michael; May, Gemma; McWhirter, Rebecca; Merrihew, Gennifer; Miller, David M; Mortazavi, Ali; Murad, Rabi; Oliver, Brian; Olson, Sara; Park, Peter J; Pazin, Michael J; Perrimon, Norbert; Pervouchine, Dmitri; Reinke, Valerie; Reymond, Alexandre; Robinson, Garrett; Samsonova, Anastasia; Saunders, Gary I; Schlesinger, Felix; Sethi, Anurag; Slack, Frank J; Spencer, William C; Stoiber, Marcus H; Strasbourger, Pnina; Tanzer, Andrea; Thompson, Owen A; Wan, Kenneth H; Wang, Guilin; Wang, Huaien; Watkins, Kathie L; Wen, Jiayu; Wen, Kejia; Xue, Chenghai; Yang, Li; Yip, Kevin; Zaleski, Chris; Zhang, Yan; Zheng, Henry; Brenner, Steven E; Graveley, Brenton R; Celniker, Susan E; Gingeras, Thomas R; Waterston, Robert Nature 2014 Aug;512(7515):445-8
  • Comparative validation of the D. melanogaster modENCODE transcriptome annotation.
    Chen, Zhen-Xia; Sturgill, David; Qu, Jiaxin; Jiang, Huaiyang; Park, Soo; Boley, Nathan; Suzuki, Ana Maria; Fletcher, Anthony R; Plachetzki, David C; FitzGerald, Peter C; Artieri, Carlo G; Atallah, Joel; Barmina, Olga; Brown, James B; Blankenburg, Kerstin P; Clough, Emily; Dasgupta, Abhijit; Gubbala, Sai; Han, Yi; Jayaseelan, Joy C; Kalra, Divya; Kim, Yoo-Ah; Kovar, Christie L; Lee, Sandra L; Li, Mingmei; Malley, James D; Malone, John H; Mathew, Tittu; Mattiuzzo, Nicolas R; Munidasa, Mala; Muzny, Donna M; Ongeri, Fiona; Perales, Lora; Przytycka, Teresa M; Pu, Ling-Ling; Robinson, Garrett; Thornton, Rebecca L; Saada, Nehad; Scherer, Steven E; Smith, Harold E; Vinson, Charles; Warner, Crystal B; Worley, Kim C; Wu, Yuan-Qing; Zou, Xiaoyan; Cherbas, Peter; Kellis, Manolis; Eisen, Michael B; Piano, Fabio; Kionte, Karin; Fitch, David H; Sternberg, Paul W; Cutter, Asher D; Duff, Michael O; Hoskins, Roger A; Graveley, Brenton R; Gibbs, Richard A; Bickel, Peter J; Kopp, Artyom; Carninci, Piero; Celniker, Susan E; Oliver, Brian; Richards, Stephen Genome research 2014 Jul;24(7):1209-23
  • Diversity and dynamics of the Drosophila transcriptome.
    Brown, James B; Boley, Nathan; Eisman, Robert; May, Gemma E; Stoiber, Marcus H; Duff, Michael O; Booth, Ben W; Wen, Jiayu; Park, Soo; Suzuki, Ana Maria; Wan, Kenneth H; Yu, Charles; Zhang, Dayu; Carlson, Joseph W; Cherbas, Lucy; Eads, Brian D; Miller, David; Mockaitis, Keithanne; Roberts, Johnny; Davis, Carrie A; Frise, Erwin; Hammonds, Ann S; Olson, Sara; Shenker, Sol; Sturgill, David; Samsonova, Anastasia A; Weiszmann, Richard; Robinson, Garret; Hernandez, Juan; Andrews, Justen; Bickel, Peter J; Carninci, Piero; Cherbas, Peter; Gingeras, Thomas R; Hoskins, Roger A; Kaufman, Thomas C; Lai, Eric C; Oliver, Brian; Perrimon, Norbert; Graveley, Brenton R; Celniker, Susan E Nature 2014 Mar;512(7515):393-9
  • Effects of cocaine and withdrawal on the mouse nucleus accumbens transcriptome.
    Eipper-Mains, J E; Kiraly, D D; Duff, M O; Horowitz, M J; McManus, C J; Eipper, B A; Graveley, B R; Mains, R E Genes, brain, and behavior 2013 Feb;12(1):21-33
  • Global patterns of tissue-specific alternative polyadenylation in Drosophila.
    Smibert, Peter; Miura, Pedro; Westholm, Jakub O; Shenker, Sol; May, Gemma; Duff, Michael O; Zhang, Dayu; Eads, Brian D; Carlson, Joe; Brown, James B; Eisman, Robert C; Andrews, Justen; Kaufman, Thomas; Cherbas, Peter; Celniker, Susan E; Graveley, Brenton R; Lai, Eric C Cell reports 2012 Mar;1(3):277-89
  • The developmental transcriptome of Drosophila melanogaster.
    Graveley, Brenton R; Brooks, Angela N; Carlson, Joseph W; Duff, Michael O; Landolin, Jane M; Yang, Li; Artieri, Carlo G; van Baren, Marijke J; Boley, Nathan; Booth, Benjamin W; Brown, James B; Cherbas, Lucy; Davis, Carrie A; Dobin, Alex; Li, Renhua; Lin, Wei; Malone, John H; Mattiuzzo, Nicolas R; Miller, David; Sturgill, David; Tuch, Brian B; Zaleski, Chris; Zhang, Dayu; Blanchette, Marco; Dudoit, Sandrine; Eads, Brian; Green, Richard E; Hammonds, Ann; Jiang, Lichun; Kapranov, Phil; Langton, Laura; Perrimon, Norbert; Sandler, Jeremy E; Wan, Kenneth H; Willingham, Aarron; Zhang, Yu; Zou, Yi; Andrews, Justen; Bickel, Peter J; Brenner, Steven E; Brent, Michael R; Cherbas, Peter; Gingeras, Thomas R; Hoskins, Roger A; Kaufman, Thomas C; Oliver, Brian; Celniker, Susan E Nature 2011 Mar;471(7339):473-9
  • Conservation of an RNA regulatory map between Drosophila and mammals.
    Brooks, Angela N; Yang, Li; Duff, Michael O; Hansen, Kasper D; Park, Jung W; Dudoit, Sandrine; Brenner, Steven E; Graveley, Brenton R Genome research 2011 Feb;21(2):193-202
  • The transcriptional diversity of 25 Drosophila cell lines.
    Cherbas, Lucy; Willingham, Aarron; Zhang, Dayu; Yang, Li; Zou, Yi; Eads, Brian D; Carlson, Joseph W; Landolin, Jane M; Kapranov, Philipp; Dumais, Jacqueline; Samsonova, Anastasia; Choi, Jeong-Hyeon; Roberts, Johnny; Davis, Carrie A; Tang, Haixu; van Baren, Marijke J; Ghosh, Srinka; Dobin, Alexander; Bell, Kim; Lin, Wei; Langton, Laura; Duff, Michael O; Tenney, Aaron E; Zaleski, Chris; Brent, Michael R; Hoskins, Roger A; Kaufman, Thomas C; Andrews, Justen; Graveley, Brenton R; Perrimon, Norbert; Celniker, Susan E; Gingeras, Thomas R; Cherbas, Peter Genome research 2011 Feb;21(2):301-14
  • Genomewide characterization of non-polyadenylated RNAs.
    Yang, Li; Duff, Michael O; Graveley, Brenton R; Carmichael, Gordon G; Chen, Ling-Ling Genome biology 2011 Jan;12(2):R16
  • Identification of functional elements and regulatory circuits by Drosophila modENCODE.
    Roy, Sushmita; Ernst, Jason; Kheradpour, Pouya; Bristow, Christopher A; Lin, Michael F; Washietl, Stefan; Ay, Ferhat; Meyer, Patrick E; Di Stefano, Luisa; Candeias, Rogerio; Jungreis, Irwin; Marbach, Daniel; Sealfon, Rachel; Kellis, Manolis; Landolin, Jane M; Carlson, Joseph W; Booth, Benjamin; Brooks, Angela N; Davis, Carrie A; Duff, Michael O; Kapranov, Philipp; Samsonova, Anastasia A; Sandler, Jeremy E; van Baren, Marijke J; Wan, Kenneth H; Yang, Li; Yu, Charles; Andrews, Justen; Brenner, Steven E; Brent, Michael R; Cherbas, Lucy; Gingeras, Thomas R; Hoskins, Roger A; Kaufman, Thomas C; Perrimon, Norbert; Cherbas, Peter; Graveley, Brenton R; Celniker, Susan E; Comstock, Charles L G; Dobin, Alex; Drenkow, Jorg; Dudoit, Sandrine; Dumais, Jacqueline; Fagegaltier, Delphine; Ghosh, Srinka; Hansen, Kasper D; Jha, Sonali; Langton, Laura; Lin, Wei; Miller, David; Tenney, Aaron E; Wang, Huaien; Willingham, Aarron T; Zaleski, Chris; Zhang, Dayu; Kharchenko, Peter V; Tolstorukov, Michael Y; Alekseyenko, Artyom A; Gorchakov, Andrey A; Gu, Tingting; Minoda, Aki; Riddle, Nicole C; Schwartz, Yuri B; Elgin, Sarah C R; Kuroda, Mitzi I; Pirrotta, Vincenzo; Park, Peter J; Karpen, Gary H; Acevedo, David; Bishop, Eric P; Gadel, Sarah E; Jung, Youngsook L; Kennedy, Cameron D; Lee, Ok-Kyung; Linder-Basso, Daniela; Marchetti, Sarah E; Shanower, Gregory; Nègre, Nicolas; Ma, Lijia; Brown, Christopher D; Spokony, Rebecca; Grossman, Robert L; Posakony, James W; Ren, Bing; Russell, Steven; White, Kevin P; Auburn, Richard; Bellen, Hugo J; Chen, Jia; Domanus, Marc H; Hanley, David; Heinz, Elizabeth; Li, Zirong; Meyer, Folker; Miller, Steven W; Morrison, Carolyn A; Scheftner, Douglas A; Senderowicz, Lionel; Shah, Parantu K; Suchy, Sarah; Tian, Feng; Venken, Koen J T; White, Robert; Wilkening, Jared; Zieba, Jennifer; Eaton, Matthew L; MacAlpine, Heather K; Nordman, Jared T; Powell, Sara K; Sher, Noa; Orr-Weaver, Terry L; MacAlpine, David M; DeNapoli, Leyna C; Ding, Queying; Eng, Thomas; Kashevsky, Helena; Li, Sharon; Prinz, Joseph A; Robine, Nicolas; Berezikov, Eugene; Dai, Qi; Okamura, Katsutomo; Lai, Eric C; Dai, Qi; Hannon, Gregory J; Hirst, Martin; Marra, Marco; Rooks, Michelle; Zhao, Yongjun; Henikoff, Jorja G; Sakai, Akiko; Ahmad, Kami; Henikoff, Steven; Bryson, Terri D; Arshinoff, Bradley I; Washington, Nicole L; Carr, Adrian; Feng, Xin; Perry, Marc D; Kent, William J; Lewis, Suzanna E; Micklem, Gos; Stein, Lincoln D; Barber, Galt; Chateigner, Aurelien; Clawson, Hiram; Contrino, Sergio; Guillier, Francois; Hinrichs, Angie S; Kephart, Ellen T; Lloyd, Paul; Lyne, Rachel; McKay, Sheldon; Moore, Richard A; Mungall, Chris; Rutherford, Kim M; Ruzanov, Peter; Smith, Richard; Stinson, E O; Zha, Zheng; Artieri, Carlo G; Li, Renhua; Malone, John H; Sturgill, David; Oliver, Brian; Jiang, Lichun; Mattiuzzo, Nicolas; Will, Sebastian; Berger, Bonnie; Feingold, Elise A; Good, Peter J; Guyer, Mark S; Lowdon, Rebecca F; Roy, Sushmita; Ernst, Jason; Kharchenko, Peter V; Kheradpour, Pouya; Negre, Nicolas; Eaton, Matthew L; Landolin, Jane M; Bristow, Christopher A; Ma, Lijia; Lin, Michael F; Washietl, Stefan; Arshinoff, Bradley I; Ay, Ferhat; Meyer, Patrick E; Robine, Nicolas; Washington, Nicole L; Di Stefano, Luisa; Berezikov, Eugene; Brown, Christopher D; Candeias, Rogerio; Carlson, Joseph W; Carr, Adrian; Jungreis, Irwin; Marbach, Daniel; Sealfon, Rachel; Tolstorukov, Michael Y; Will, Sebastian; Alekseyenko, Artyom A; Artieri, Carlo; Booth, Benjamin W; Brooks, Angela N; Dai, Qi; Davis, Carrie A; Duff, Michael O; Feng, Xin; Gorchakov, Andrey A; Gu, Tingting; Henikoff, Jorja G; Kapranov, Philipp; Li, Renhua; MacAlpine, Heather K; Malone, John; Minoda, Aki; Nordman, Jared; Okamura, Katsutomo; Perry, Marc; Powell, Sara K; Riddle, Nicole C; Sakai, Akiko; Samsonova, Anastasia; Sandler, Jeremy E; Schwartz, Yuri B; Sher, Noa; Spokony, Rebecca; Sturgill, David; van Baren, Marijke; Wan, Kenneth H; Yang, Li; Yu, Charles; Feingold, Elise; Good, Peter; Guyer, Mark; Lowdon, Rebecca; Ahmad, Kami; Andrews, Justen; Berger, Bonnie; Brenner, Steven E; Brent, Michael R; Cherbas, Lucy; Elgin, Sarah C R; Gingeras, Thomas R; Grossman, Robert; Hoskins, Roger A; Kaufman, Thomas C; Kent, William; Kuroda, Mitzi I; Orr-Weaver, Terry; Perrimon, Norbert; Pirrotta, Vincenzo; Posakony, James W; Ren, Bing; Russell, Steven; Cherbas, Peter; Graveley, Brenton R; Lewis, Suzanna; Micklem, Gos; Oliver, Brian; Park, Peter J; Celniker, Susan E; Henikoff, Steven; Karpen, Gary H; Lai, Eric C; MacAlpine, David M; Stein, Lincoln D; White, Kevin P; Kellis, Manolis Science (New York, N.Y.) 2010 Dec;330(6012):1787-97
  • Global analysis of trans-splicing in Drosophila.
    McManus, C Joel; Duff, Michael O; Eipper-Mains, Jodi; Graveley, Brenton R Proceedings of the National Academy of Sciences of the United States of America 2010 Jul;107(29):12975-9
  • Regulatory divergence in Drosophila revealed by mRNA-seq.
    McManus, C Joel; Coolon, Joseph D; Duff, Michael O; Eipper-Mains, Jodi; Graveley, Brenton R; Wittkopp, Patricia J Genome research 2010 Jun;20(6):816-25
  • RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex.
    Hale, Caryn R; Zhao, Peng; Olson, Sara; Duff, Michael O; Graveley, Brenton R; Wells, Lance; Terns, Rebecca M; Terns, Michael P Cell 2009 Nov;139(5):945-56
  • Dopamine, uncertainty and TD learning.
    Niv, Yael; Duff, Michael O; Dayan, Peter Behavioral and brain functions : BBF 2005 May;16
  • In vitro examination of surface light scattering in hydrophobic acrylic intraocular lenses.
    Minami, Keiichiro; Maruyama, Yoko; Honbo, Masato; Matsunaga, Jiro; Miyata, Kazunori Journal of cataract and refractive surgery 1984 Jan;40(4):652-6

Book Sections

  • Monte-Carlo matrix inversion and reinforcement learning
    Barto A, Duff M Advances in Neural Information Processing Systems Vol 6 1994 Jan;687-694

Conference Papers

  • Statistical inference of biologically-plausible dynamic regulatory networks with core-leaf topology
    Duff M 2005 Jan;
  • Design for an optimal probe
    Duff, M 2003 Jan;131-138
  • Diffusion approximation for Bayesian Markov chains.
    Duff, M 2003 Jan;139-146
  • Local bandit approximation for optimal learning problems
    Duff M, Barto M 1997 Jan;1019-1025
  • Cognitively inspired reinforcement learning architecture and its application to giant-swing motion control.
    Uragami, Daisuke; Takahashi, Tatsuji; Matsuo, Yoshiki Bio Systems 1995 Jan;1161-9
  • Reinforcement learning methods for continuous-time Markov decision processes
    Bradke S, Duff M 1995 Jan;393-400
  • Solving Bellman’s equation by the method of continuation
    Duff M 1994 Jan;2671-2682
  • Backpropagation and Bach’s 5th cello suite (Sarabande)
    Duff M 1989 Jan;575

Other

  • Optimal Learning: Computational procedures for Bayes-adaptive Markov decision processes
    Duff, M Ph.D. Thesis, Dept. of Computer Science, Univ. of Massachusetts, Amherst 2002 Jan;