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Genomics and Computational Biology
(see also publications grouped by themes)
- Reliable prediction of regulator targets using 12 Drosophila genomes
Kherapdour, Stark, Roy, Kellis
Genome Research, Nov 7, 2007, Early online access, (pdf)
- 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)
- 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)
- 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)
- 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)
- Evolution of genes and genomes in the Drosophila Phylogeny
- 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)
- Evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network following duplication
Presser, Elowitz, Kellis, Kishony
PNAS Jan 16, 2008, (PNAS) (pdf)
- 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)
- 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)
- 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)
- Gene content of the human genome
Clamp, Fry, Kamal, Xie, Cuff, Lin, Kellis, Lindblad-Toh, Lander
PNAS, 8 pages, in press
- 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)
- 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)
- 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)
- 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)
- Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
- Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
- Sequencing and comparison of yeast species to identify genes and regulatory motifs
- 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)
- 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)
- 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).
- 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)
- 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)
- 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).
- 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)
- The changing face of genomics
Manolis Kellis
Genome Biology 2004 Apr 30; 5(5): p. 324 (pdf)
- Computational Comparative Genomics: Genes, Regulation, Evolution
Manolis Kellis (Kamvysselis)
MIT Ph.D. Thesis '03 (pdf)
- 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)
- 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)
- 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)
- Biological Signal Discovery: The Power of Multiple Genomes
Manolis Kellis
Fungal comparative genomics, Springer Verlag, invited book chapter, 2004 (in preparation).
Computational Geometry
- Crust: A new Voronoi-Based Surface Reconstruction Algorithm
Nina Amenta, Marshall Bern, Manolis Kamvysselis
ACM Siggraph '98 Proceedings (pdf)
- ECImorph: 2D polygon morphing using the Extended Gaussian Image
Manolis Kamvysselis
MIT Computer Vision (6.866, Berthold Horn) Final Project (pdf)
- 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)
- Imagina: Sketch-based Image Retrieval using Cognitive Abstraction
Manolis Kamvysselis, Ovidiu Marina
MIT Masters Thesis '99 (pdf)
- Wavelet-based character recognition in curvature space
Manolis Kamvysselis
MIT Machine Learning (6.891, Paul Viola) Final Project (pdf)
- Robologo: Interactive programming environment for wheeled robot
Manolis Kamvysselis, Jeremy Lueck, Christopher Rohrs
MIT Microprocessor Design Lab (6.115, Marvin Minsky) Final Project (pdf)
- Meta-evolution: Computational requirements for evolutionary bursts
Manolis Kamvysselis
MIT Society of Mind (6.868, Marvin Minsky) Final Project (pdf)
- 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)
- Webbot: A constraint model for automated web traversal
Manolis Kamvysselis, Henryk Frystyk Nielsen
Wold Wide Web Consortium (W3C) Online Publications (pdf)
- 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)
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