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Manolis Kellis

Associate professor of Computer Science at MIT, in the area of Computational Biology.
Broad Broad Institute of MIT and Harvard, 03-04, Cambridge, MA
Postdoctoral Fellow.
CSHL Cold Spring Harbor Laboratory, 2003, CSHL, NY
Yeast genetics.
MIT Massachusetts Institute of Technology, 99-03, Cambridge, MA
Ph.D. in Computer Science, EECS Area II.
Sprowls Award for Best Thesis in Computer Science at MIT.
Thesis title: Computational Comparative Genomics: Genes, Regulation, Evolution.
GPA: 5.0/5.0
MIT Massachusetts Institute of Technology, 95-99, Cambridge, MA
Master of Engineering in Electrical Engineering and Computer Science, June 1999.
Thesis title: Imagina: A cognitive abstract approach to sketch-based image retrieval.
Bachelor of Science in Computer Science and Engineering, June 1999.
GPA: 5.0/5.0 Courses Taken
LFNY Lycée Français de New York, 93-95, New York, NY
Received French Baccalaureate, with emphasis on Math and Sciences, with `Mention Très-Bien,' and the Congratulations of the Jury.
France Lycée Paul Cézanne, Collège Saint Eutrope, 89-93, Aix en Provence, FRANCE
Graduated first in a class of two thousand. First prize in my city and prefecture on a country-wide math competition for high school students in France. First place in high-school's chess tournament for two consecutive years.
Greece Maraslio Pilot High School, 87-89, Athens, GREECE
Prizes of excellence in all the courses.
Faculty Alfred P. Sloan Foundation Award, 2008.
National Science Foundation NSF Career Award, 2007.
Selected as one of Top Young Principal Investigators by Genome Technology magazine, 2006.
Selected as one of the world's top young innovators under the age of 35 by Technology Review magazine (TR35), 2006.
Karl Van Tassel Career Development Professorship, 2007-2010.
Distinguished Alumnus (1964) Career Development Professorship, 2005-2007.
One of three young scientists honored as the next generation in biotechnology, Museum of Science, Boston 2004.
Grad School Sprowls award for the Best Ph.D. Thesis in Computer Science at MIT, 2004
Recipient of the NTT Fellowship, 1999-2000.
Recipient of the first Paris Kanellakis Fellowship, 1999.
Recipient of the Chorafas Foundation Award, 1999.
Undergrad Recipient of the MassGrant Award for academic excellence, 1998-99.
Inducted member of Sigma Xi, The Scientific Research Society of North America, Spring 1999
Inducted member of Tau Beta Pi, the National Engineering Honor Society, Spring 1998.
Inducted member of Eta Kappa Nu, the National Honor Society for Electrical Engineering and Computer Science, Spring 1998.
Elected President of ISA, the International Students' Asociation of MIT, 1997-1998
First prize in the TBP Intercollegiate Design Competition, representing MIT, Spring 1997.
High-School Earned French Baccalauréat with the Congratulations of the Jury, the highest distinction in France, June 1995.
Valedictorian Prize, Prix du President, Prix d'Honneur (Honor Roll), Professor Edgar Lorch's Prize of Mathematics, Special Prize of Physics.
First prizes in mathematics, physics, chemistry, biology, computer programming, English, philosophy.
Represented my school in a country-wide math competition in France (Concours Général).
First prize in South France in a country-wide math competition for high school students, 1993.
First prize in high school's chess tournament for two consecutive years, 1991-92.

Genomics and Computational Biology

(see also publications grouped by themes)
  1. Reliable prediction of regulator targets using 12 Drosophila genomes
      Kherapdour, Stark, Roy, Kellis
      Genome Research, Nov 7, 2007, Early online access, (pdf)

  2. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands
      Stark, Bushati, Jan, Kheradpour, Hodges, Brennecke, Bartel, Cohen, Kellis
      Genes and Development 22:8-13, Jan 1, 2008 (pdf)

  3. Distinguishing protein-coding and noncoding genes in the human genome
      Clamp, Fry, Kamal, Xie, Cuff, Lin, Kellis, Lindblad-Toh, Lander
      PNAS 49:19428-19433, Dec 4, 2007 (pdf)

  4. RNA Polymerase Stalling at Developmental Control Genes in the Drosophila Embryo
      Zeitlinger, Zinzen, Stark, Kellis, Young, Levine
      Nature Genetics, November 11, 2007, early online publication (Nature Genetics)

  5. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
      Stark, Lin, Kheradpour, Pedersen, Parts, Carlson, Crosby, Rasmussen, Roy, Deoras, Ruby, Brennecke, FlyBase curators, Berkeley Drosophila Genome Project, Hodges, Hinrichs, Caspi, Paten, Park, Han, Maeder, Polansky, Robson, Aerts, vanHelden, Hassan, Gilbert, Eastman, Rice, Weir, Hahn, Park, Dewey, Pachter, Kent, Haussler, Lai, Bartel, Hannon, Kaufman, Eisen, Clark, Smith, Celniker, Gelbart, Kellis
      Nature, 2007 Nov 8; 450:203-218, 14 pages (pdf) (Nature focus page) (Supplementary Information)

  6. Evolution of genes and genomes in the Drosophila Phylogeny
  7. Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
      Rasmussen, Kellis
      Genome Research, Nov 7, 2007, Early online access (pdf)

  8. Evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network following duplication
      Presser, Elowitz, Kellis, Kishony
      PNAS Jan 16, 2008, (PNAS) (pdf)

  9. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
      Ruby, Stark, Johnston, Kellis, Bartel, Lai
      Genome Research, Nov 7, 2007, Early online access (pdf)

  10. Revisiting the protein-coding gene catalog of Drosophila melanogaster using twelve fly genomes
      Lin, Carlson, Crosby, Matthews, Yu, Park, Wan, Schroeder, Gramates, Pierre, Roark, Wiley, Kulathinal, Zhang, Myrick, Antone, Celniker, Gelbart, Kellis
      Genome Research, Nov 7, 2007, Early Online Access (pdf)

  11. Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
      Zeitlinger, Zinzen, Stark, Kellis, Zhang, Young, Levine
      Genes and Development, 21:385-390, March 2, 2007 (pdf) (paper)

  12. Gene content of the human genome
      Clamp, Fry, Kamal, Xie, Cuff, Lin, Kellis, Lindblad-Toh, Lander
      PNAS, 8 pages, in press

  13. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
      Stark, Kheradpour, Brennecke, Hodges, Hannon, Kellis
      Genome Research, Nov 7, 2007, Early online access (pdf)

  14. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
      Xie, Mikkelsen, Gnirke, Lindblad-Toh, Kellis, Lander
      PNAS 104, 7145-7150, April 24, 2007 (pdf)

  15. Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila
      Brennecke, Aravin, Stark, Dus, Kellis, Sachidanandam, Hannon
      Cell 128, 1-15, March 23, 2007 (pdf)

  16. Genome sequence, comparative analysis and haplotype structure of the domestic dog
      Lindblad-Toh, Wade, Mikkelsen, Karlsson, Jaffe, Kamal, Clamp, Chang, Kulbokas, Zody, Mauceli, Xie, Breen, Wayne, Ostrander, Ponting, Galibert, Smith, deJong, Kirkness, Alvarez, Biagi, Brockman, Butler, Chin, Cook, Cuff, Daly, DeCaprio, Gnerre, Grabherr, Kellis, Kleber, Bardeleben, Goodstadt, Heger, Hitte, Kim, Koepfli, Parker, Pollinger, Searle, Sutter, Thomas, Webber, Broad Sequencing Platform, Eric Lander
      Nature 2005 Dec 8; 438 pp. 711-888 (pdf) (Nature website) (Supplementary Information)

  17. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
  18. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
  19. Sequencing and comparison of yeast species to identify genes and regulatory motifs
  20. Transcriptional regulatory code of a eukaryotic genome
      Chris Harbison et al., Ben Gordon, Tony Lee, Nicola Rinaldi, Macisaac, Danford, Hannett, Tagne, Reynolds, Yoo, Jennings, Zeitlinger, Pokholok, Kellis, Rolfe, Takusagawa, Lander, Gifford, Fraenkel, Young.
      Nature 2004 Sep 2; 431 pp. 99-104 (pdf) (Nature website)
      (Supplementary Information)

  21. Genome duplication in the teleost fish Tetraodon nigrovidridis reveals the early vertebrate proto-karyotype
      Olivier Jaillon et al., Aury, Brunet, Petit, Stange-Thomann, Mauceli, Bouneau, Fischer, Ozouf-Costaz, Bernot, Nicaud, Jaffe, Fisher, Lutfalla, Dossat, Segurens, Dasilva, Salanoubat, Levy, Boudet, Castellano, Anthouard, Jubin, Castelli, Katinka, Vacherie, Biemont, Skalli, Cattolico, Poulain, Berardinis, Cruaud, Duprat, Brottier, Coutanceau, Gouzy, Parra, Lardier, Chapple, McKernan, McEwan, Bosak, Kellis, Volff, Guigo, Zody, Mesirov, Lindblad-Toh, Birren, Nusbaum, Kahn, Robinson-Rechavi, Laudet, Schachter, Quetier, Saurin, Scarpelli, Wincker, Lander, Weissenbach, Hugues Roest Crollius.
      Nature 2004 Oct 21; 431 pp. 946-957 (pdf) (Nature website)
      (Supplementary Information)

  22. Methods in comparative genomics: genome correspondence, gene identification, regulatory motif discovery
      Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric Lander
      Journal of Computational Biology 2004; 11 pp. 319-55. (pdf).

  23. Whole-genome comparative annotation and motif discovery in yeast
      Manolis Kellis (Kamvysselis), Nick Patterson, Bruce Birren, Bonnie Berger, Eric Lander
      ACM Recomb '03 Proceedings (pdf)

  24. Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
      Derek Chiang, Alan Moses, Manolis Kellis, Eric Lander, Mike Eisen
      ACM Recomb '03 Proceedings. (pdf)

  25. Gene finding using multiple related species: a classification approach.
      Manolis Kellis
      Encyclopedia of Genetics, Genomics, Proteomics, John Wiley & Sons, special review, 2005 (in press) (pdf).

  26. What's in the human genome? Large-scale discovery and validation of functional elements
      Bradley E Bernstein and Manolis Kellis
      Genome Biology 2005 Mar 1; 6:312 (pdf)

  27. The changing face of genomics
      Manolis Kellis
      Genome Biology 2004 Apr 30; 5(5): p. 324 (pdf)

  28. Computational Comparative Genomics: Genes, Regulation, Evolution
      Manolis Kellis (Kamvysselis)
      MIT Ph.D. Thesis '03 (pdf)

  29. Position specific variation in the rate of evolution in transcription factor binding sites
      Alan Moses, Derek Chiang, Manolis Kellis, Eric Lander, Mike Eisen
      BMC Evolutionary Biology 2003, 3:19, Aug 28, 2003 (pdf)

  30. The Genome Sequence of the filamentous fungus Neurospora crassa
      James Galagan, Sarah Calvo, Borkovich, Selker, Read, Jaffe, FitzHugh, Ma, Smirnov, Purcell, Rehman, Elkins, Engels, Wang, Nielsen, Butler, Endrizzi, Qui, Ianakiev, Bell-Pedersen, Nelson, Werner-Washburne, Selitrennikoff, Kinsey, Braun, Zelter, Schulte, Kothe, Jedd, Mewes, Staben, Marcotte, Greenberg, Roy, Foley, Naylor, Stange-Thomann, Barrett, Gnerre, Kamal, Kamvysselis, Mauceli, Bielke, Rudd,, Frishman, Krystofova, Rasmussen, Metzenberg, Perkins, Kroken, Cogoni, Macino, Catcheside, Li, Pratt,, Osmani, DeSouza, Glass, Orbach, Berglund, Voelker, Yarden, Plamann, Seiler, Dunlap, Radford, Aramayo, Natvig, Alex, Mannhaupt, Ebbole, Freitag, Paulsen, Sachs, Lander, Nusbaum, Birren
      Nature, 2003 Apr 24; 422 pp 859-868. (pdf) (Nature website)
      (Supplementary Information)

  31. Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
      Derek Chiang, Alan Moses, Manolis Kellis, Eric Lander, Mike Eisen
      Genome Biology, 4(7):R43, Jun 26, 2003. (pdf)

  32. Biological Signal Discovery: The Power of Multiple Genomes
      Manolis Kellis
      Fungal comparative genomics, Springer Verlag, invited book chapter, 2004 (in preparation).

Computational Geometry

  1. Crust: A new Voronoi-Based Surface Reconstruction Algorithm
      Nina Amenta, Marshall Bern, Manolis Kamvysselis
      ACM Siggraph '98 Proceedings (pdf)

  2. ECImorph: 2D polygon morphing using the Extended Gaussian Image
      Manolis Kamvysselis
      MIT Computer Vision (6.866, Berthold Horn) Final Project (pdf)

  3. 3Dmorph: polygon-based geometry morphing
      Manolis Kamvysselis, Matt Blum, Hooman Vassef, Krzysztof Gajos
      MIT Computer Graphics (6.837, Seth Teller) Final Project (pdf)

Other manuscripts (Robotics / AI)

  1. Imagina: Sketch-based Image Retrieval using Cognitive Abstraction
      Manolis Kamvysselis, Ovidiu Marina
      MIT Masters Thesis '99 (pdf)

  2. Wavelet-based character recognition in curvature space
      Manolis Kamvysselis
      MIT Machine Learning (6.891, Paul Viola) Final Project (pdf)

  3. Robologo: Interactive programming environment for wheeled robot
      Manolis Kamvysselis, Jeremy Lueck, Christopher Rohrs
      MIT Microprocessor Design Lab (6.115, Marvin Minsky) Final Project (pdf)

  4. Meta-evolution: Computational requirements for evolutionary bursts
      Manolis Kamvysselis
      MIT Society of Mind (6.868, Marvin Minsky) Final Project (pdf)

  5. Mood: Auditory recognition and classification based on changes in attentional state
      Manolis Kamvysselis, Ovidiu Marina, Hooman Vassef, Dedric Carter, Patrick Winston
      MIT Human Intelligence Enterprise (6.892, Patrick Winston) Final Project (pdf)

  6. Webbot: A constraint model for automated web traversal
      Manolis Kamvysselis, Henryk Frystyk Nielsen
      Wold Wide Web Consortium (W3C) Online Publications (pdf)

  7. Invest: Three algorithms for predicting stock market changes
      Manolis Kamvysselis, Shishir Mehrotra, Nimrod Washawsky
      MIT Artificial Intelligence (6.038, Tomas Lozano-Perez) Final Project (pdf)

Citizenship Double citizenship: American Citizen. Greek citizen with the right to work in the European Union.
Born in Athens, Greece. Lived in Greece until 1989 and followed the normal Greek curriculum. Lived in France from 1989 to 1993 and followed the normal French curriculum. Lived in New York from 1993 to 1995 and attended the French High-School of New York in order to take the French Baccalaureate examination. Currently attending the Massachusetts Institute of Technology.
Hobbies Traveling, sailing, skiing, skating, traditional greek dancing, ballroom dancing, bicycling, volleyball, swimming, karate, photography and digital image editing, drawing and painting, chess, reading, writing poetry, Greek mythology.
Activities President of the International Students Association, Organizer of International Fair, an annual event with presentations of 50 international Clubs of MIT. Member of Sigma Xi, the Scientific Research Society. Member of the TBP and HKN Engineering Honor Societies. Member at large of the IEEE Student Group at MIT, Community Service (City Days Festival in Boston, Guide for a group of French tourists in New York, New York City Marathon Interpreter in French, Greek, German), participant in ADF literary competition, prospective of the Student Information Processing Board (SIPB) in MIT. Contributor in highschool's yearbook. Member of soccer, volleyball, and swimming teams. Represented my class in the Shakespeare Competition. Performed one of the main roles in my school's end-of-year musical.
Computational Biology
Interspecies DNA control structures by interspecies comparison, Spring 00, Whitehead Institute, MIT
The goal is to discover new regulatory motifs and other DNA meta-information by comparing multiple species. Preserved structures accross multiple species will allow short control sequences to stand out from random similarities due to noise. Code in C and Python. Supervised by Eric Lander, director of the Whitehead Institute Center for Genome Research, and Bonnie Berger, head of the Computational Biology group of LCS.
HOX Genomic Analysis of the Hox Developmental Genes, Fall 00, Whitehead Institute, MIT
Analysis of the conservation of both sequence and spacing in the Hox developmental gene clusters accross mammalian genomes (Human, Baboon, Mouse, Rat). Analysis leads to candidate elements involved in timing and regulation of body plan determination during embryonic development. Code in C and Python. Working with Ken Dewar and Eric Lander.
AI: Machine Learning
Chars New representation for character recognition, Fall 99, MIT AI Lab
Presented a compact angle representation for online characters that filters noise and facilitates recognition. Wavelet decopmosition of the character signal in derivative angle space is invariant to scaling or rotation and remains preserved within samples of the same character. Code in Matlab. Supervised by Paul Viola from the Learning and Vision group of the AI Lab at MIT.
Imagina Sketch-Based Image Retrieval, Spring 99, MIT, MA
Developped a new system for content-base image retrieval. User input is in form of a sketch. Images are segmented into regions based on color and spatial relations. Region shapes are then compared at different levels of details of different shape representations. The sketch is then matched to images based on region shape, color and configuration. Code in Java. Supervised by Professor Patrick Winston.
DiVA Learning Probabilistic Models of Human Motion, Summer 99, Xerox PARC, CA
Working on learning a probabilistic model for combinations of primitives in human motion. Code in Matlab. Supervised by Michael Black from the Digital Video Analysis Area of the Science and Pracices Lab at Xerox PARC.
Computational Geometry
Crust 3D Surface Reconstruction, Summer 97, CSL, Xerox PARC, Palo Alto, CA
Worked on developing, implementing, and testing the first provably correct algorithm for 3D surface reconstruction from scattered points. Code written in C, 3D models constructed for Geomview. Worked in the Theory Group of the Computer Science Laboratory with PARC researchers Marshall Bern and Nina Amenta. Project part of the VI-A internship program at Xerox PARC.
3DMorph 3D Model Morphing, Fall 97, Computer Graphics, MIT, MA
Invented, designed, and implemented a 3D morphing algorithm for Inventor models, that constructs a heuristically optimal match between two triangulated models, minimizing distance traveled among matched triangles. The system handles M-to-M polygon matching using the Edge Ordering Algorithm and extends this to M-to-N matching using the Incremental Edge Ordering Algorithm for polygon births. Both algorithms are generic and can be used beyond morphing for optimal matches. Presented as the final project for Seth Teller's Computer Graphics (6.837).
EciMorph Gaussian Polygon Morphing, Fall 97, Robot Vision, MIT, MA
Invented and implemented a new approach to polygon morphing using the Extended Gaussian Image representation of objects, invented by Berthold K. P. Horn, for object recognition in Robot Vision. The program maps initial and final polygon to their respective Extended Circular Images (ECI), and gradually transforms one ECI into the other and then reverses the mapping at each step to recreate intermediate polygons. The program is now limited to 2d convex polygons, but possible extensions have been presented. Code written in Java and running as an applet. Presented as the final project for Berthold K. P. Horn's Robot Vision class (6.866).
AI: Pattern Recognition
Mood Music Understanding using Patterns of Attentional State, Spring 98, MIT, MA
Invented, designed, and implemented an architecture for understanding, recognition and classification of music. With no prior knowledge, the system learns periodicity, voices and mood, based on patterns in music, abstracted in patterns of attentional state. The concept is based on Sajit Rao's and Shimon Ullman's work on constructing visual routines by combining primitives. Presented as a final project for a team of four people in Patrick Winston's The Human Intelligence Enterprise (6.892).
Invest Intelligent Investment Assistant, Spring 98, Artificial Intelligence in Practice, MIT, MA
Applied Artificial Intelligence methods to the study of the Stock Market. Implemented a Neural Net stock market predictor along with a Nearest Neighbor predictor, and a salient patterns predictor. Presented as a final project in a team of three for Tomás Lozano Perez's Artificial Intelligence in Practice, (6.038).
Webbot Constraint Model for a Web Robot, Summer 96, W3C, LCS, MIT, Cambridge, MA
The constraint model allows the user to specify how the robot navigates the web. It receives commands via a simple language for recursive definition of arbitrarily complicated rules and constraints for the robot to follow. The research project and the constraint model can be used for traversing the web, validating links, comparing pages, searching for keywords, verifying syntax, printing multiple pages. The pattern matching code was written in Tcl. The robot accesses the web via calls to the W3C library of common code for internet functionality. The research project was supervised by Henrik Frystyk Nielsen of the World Wide Web Consortium and funded by the Lab for Computer Science at MIT.
RoboLogo Programming Environment for Interactive Robots, Fall 98, MIT, MA
Developed an environment that enables children to program interactive robots. iLogo programming language modeled after Berkeley Logo. Compiler written in Java using javacc. Low-level routines written in A51 assembly. Printed circuit board designed on Protel. 6.115 project.
PolyBot Local Control of Modular Reconfigurable Robots, Summer 98, Xerox PARC, CA
Proposed a new local control architecture for modular robots. The architecture allows many identical modules to locomote, coordinate actions, share information, and arbitrate decisions based on a combination of local rules, message passing and a global bus. Code written in Java 1.2beta4 and simulation ran in Java3D from within Netscape Navigator using the Java plugin. The project is funded by the Xerox Corporation and a research grant from DARPA. Internship part of the MIT 6A program at the Xerox Palo Alto Research Center.
RoboAnt Autonomous Robot, Spring 96, MIT, Cambridge, MA
Designed, built, and programmed an autonomous robot. The Robot was built out of Lego pieces, an electronic board, and components such as touch sensors, light sensors, and infrared. Presented in the context of the annual IAP Robot Design Contest (6.270).
MBone Communications Technologies, Fall 95, CWIS, MIT, Cambridge, MA
Set up and broadcast of the Bush research symposium with the Multicast system MBone, which allows real time video and audio communication via the internet, as well as feedback in form of text or sketches. Also responsible of the slides projection companion in real time on the World Wide Web. Redesigned the Information Systems Newsletter site in a UROP funded by Campus Wide Information Systems.
Turing Universal Turing Machine, MIT, Fall 96, Cambridge, MA
Wrote a Turing Machine Implementation in Scheme.
Chess Teaching Chess Lessons, 93-95, New York, NY
Developed and taught chess courses for beginners and intermediate players. President and founder of my highschool's chess club.
Astronomy Training in an Astronomy Observatory, Summer 93, CNRS, Marseille, FRANCE
Sky mapping, photo developing, planet studying as an assistant for the Observatory of Provence, Marseille, France's National Center of Scientific Research (CNRS).