Manolis Kellis Publications - Grouped

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• 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)
  
  
• Sequencing and comparison of yeast species to identify genes and regulatory motifs
  
  Kellis, Patterson, Endrizzi, Birren, Lander
  Nature 2003 May 15; 423 pp. 241-254 (pdf) (Nature website) (Supplementary Information)
  
  
• 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, Lander
  Nature 2005 Dec 8; 438 pp. 711-888 (pdf) (Nature website) (Supplementary Information)
  
  
• 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)
  
  
• Evolution of genes and genomes in the Drosophila Phylogeny
  
  Drosophila 12 Genomes Consortium
  Nature 450:203-218, Nov 8, 2007 (pdf) (Nature focus page)
  
  
• Genome analysis of the platypus reveals unique signatures of evolution
  
  Warren, Hillier, Marshall Graves, Birney, Ponting, Gr|tzner, Belov, Miller, Clarke, Chinwalla, Yang, Heger, Locke, Miethke, Waters, Veyrunes, Fulton, Fulton, Graves, Wallis, Puente, Lopez-Otin, Ordonez, Eichler, Chen, Cheng, Deakin, Alsop, Thompson, Kirby, Papenfuss, Wakefield, Olender, Lancet, Huttley, Smit, Pask, Temple-Smith, Batzer, Walker, Konkel, Harris, Whittington, Wong, Gemmell, Buschiazzo, Vargas Jentzsch, Merkel, Schmitz, Zemann, Churakov, Ole Kriegs, Brosius, Murchison, Sachidanandam, Smith, Hannon, Tsend-Ayush, McMillan, Attenborough, Rens, Ferguson-Smith, Lefhvre, Sharp, Nicholas, Ray, Kube, Reinhardt, Pringle, Taylor, Jones, Nixon, Dacheux, Niwa, Sekita, Huang, Stark, Kheradpour, Kellis, Flicek, Chen, Webber, Hardison, Nelson, Hallsworth-Pepin, Delehaunty, Markovic, Minx, Feng, Kremitzki, Mitreva, Glasscock, Wylie, Wohldmann, Thiru, Nhan, Pohl, Smith, Hou, Renfree, Mardi, Wilson
  Nature 453:175-183, May 8, 2008 (pdf)

Small regulatory RNAs (and large regulatory RNAs)

• Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
  Guttman, Amit, Garber, French, Lin, Feldser, Huarte, Zuk, Carey, Cassady, Cabili, Jaenisch, Mikkelsen, Jacks, Hacohen, Bernstein, Kellis, Regev, Rinn, Lander
  Nature, Feb 1, 2009 (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)
  
  
• 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 human promoters and 3' UTRs by comparison of several mammals
  
  Xie, Lu, Kulbokas, Golub, Mootha, Lindblad-Toh, Lander, Kellis
  Nature 2005 Feb 27, doi:10.1038/nature03441 (pdf) (Nature website) (Supplementary Information)
  
  
• An endogenous small interfering RNA pathway in Drosophila.
  
  Czech, Malone, Zhou, Stark, Schlingeheyde, Dus, Perrimon, Kellis, Wohlschlegel, Sachidanandam, Hannon, Brennecke
  Nature, May 7, 2008
  
  
• 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)
  
  
• 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)
  
  
• Conservation of small RNA pathways in platypus
  
  Murchison, Kheradpour, Sachidanandam, Smith, Hodges, Xuan, Kellis, Grutzner, Stark, Hannon
  Genome Research, May 7, 2008
  

Protein-coding genes

• 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)
  
  
• 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)
  
  
• Sequencing and comparison of yeast species to identify genes and regulatory motifs
  
  Kellis, Patterson, Endrizzi, Birren, Lander
  Nature 2003 May 15; 423 pp. 241-254 (pdf) (Nature website)
  (Supplementary Information)
  
  
• Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes
  
  Lin, Deoras, Rasmussen, Kellis
  PLoS Computational Biology, 14 pages, in review
  

Chromatin, regulation, and developmental programs

• Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
  Guttman, Amit, Garber, French, Lin, Feldser, Huarte, Zuk, Carey, Cassady, Cabili, Jaenisch, Mikkelsen, Jacks, Hacohen, Bernstein, Kellis, Regev, Rinn, Lander
  Nature, Feb 1, 2009 (pdf)
  
  
• RNA Polymerase Stalling at Developmental Control Genes in the Drosophila Embryo
  
  Zeitlinger, Zinzen, Stark, Kellis, Young, Levine
  Nature Genetics, Nov 11, 2007, early online publication (Nature Genetics)
  
  
• 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)
  
  
• Transcriptional regulatory code of a eukaryotic genome
  
  Harbison, Gordon, Lee, 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)

Regulatory motifs

• Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
  
  Xie, Lu, Kulbokas, Golub, Mootha, Lindblad-Toh, Lander, Kellis
  Nature 2005 Feb 27, doi:10.1038/nature03441 (pdf) (Nature website)
  (Supplementary Information)
  
  
• Sequencing and comparison of yeast species to identify genes and regulatory motifs
  
  Kellis, Patterson, Endrizzi, Birren, Lander
  Nature 2003 May 15; 423 pp. 241-254 (pdf) (Nature website)
  (Supplementary Information)
  
  
• 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)
  
  
• Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
  
  Chiang, Moses, Kellis, Lander, Eisen
  Genome Biology, 4(7):R43, Jun 26, 2003. (pdf)
  
  
• Position specific variation in the rate of evolution in transcription factor binding sites
  
  Moses, Chiang, Kellis, Lander, Eisen
  BMC Evolutionary Biology 2003, 3:19, Aug 28, 2003 (pdf)

Biological Networks

• Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking
  
  Grochow, Kellis
  RECOMB 2007, April 22, 2007 (pdf)
  
  
• Evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network following duplication
  
  Presser, Elowitz, Kellis, Kishony
  PNAS Jan 16, 2008, (PNAS) (pdf)
  
  
• Reliable prediction of regulator targets using 12 Drosophila genomes
  
  Kherapdour, Stark, Roy, Kellis
  Genome Research, Nov 7, 2007, Early online access, (pdf)

Genome Evolution

• Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
  
  Kellis, Birren, Lander
  Nature 2004 Apr 8; 428 pp. 617-24 (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)
  
  
• Evolution of genes and genomes in the Drosophila Phylogeny
  
  Drosophila 12 Genomes Consortium
  Nature 450:203-218, Nov 8, 2007 (pdf)

Phylogenomics

• 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)
  
  

Algorithmic papers in Computational Biology

• Whole-genome comparative annotation and motif discovery in yeast
  
  Kellis (Kamvysselis), Patterson, Birren, Berger, Lander
  RECOMB 2003, April 10, 2003 (pdf)
  
  
• Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
  
  Chiang, Moses, Kellis (Kamvysselis), Lander, Eisen
  RECOMB 2003, April 10, 2003 (pdf)
  
  
• Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking
  
  Grochow, Kellis
  RECOMB 2007, April 22, 2007 (pdf)
  
  
• Methods in comparative genomics: genome correspondence, gene identification, regulatory motif discovery
  
  Kellis, Patterson, Birren, Berger, Lander
  Journal of Computational Biology 2004; 11 pp. 319-55. (pdf).
  
  
• Computational Comparative Genomics: Genes, Regulation, Evolution
  
  Kellis (Kamvysselis)
  MIT Ph.D. Thesis '03 (pdf)

Computational Geometry / Vision / Graphics

• Crust: A new Voronoi-Based Surface Reconstruction Algorithm
  
  Amenta, Bern, Kamvysselis (Kellis)
  ACM Siggraph '98 Proceedings (pdf)
  
  
• ECImorph: 2D polygon morphing using the Extended Gaussian Image
  
  Kamvysselis (Kellis)
  MIT Computer Vision (6.866, Berthold Horn) Final Project (pdf)
  
  
• 3Dmorph: polygon-based geometry morphing
  
  Kamvysselis (Kellis), Blum, Vassef, Gajos
  MIT Computer Graphics (6.837, Seth Teller) Final Project (pdf)
  
  
• Imagina: Sketch-based Image Retrieval using Cognitive Abstraction
  
  Kamvysselis (Kellis), Marina
  MIT Masters Thesis '99 (pdf)
  
  
• Wavelet-based character recognition in curvature space
  
  Kamvysselis (Kellis)
  MIT Machine Learning (6.891, Paul Viola) Final Project (pdf)
  
  

Other manuscripts (Robotics / AI)

• Robologo: Interactive programming environment for wheeled robot
  
  Kamvysselis (Kellis), Lueck, Rohrs
  MIT Microprocessor Design Lab (6.115, Marvin Minsky) Final Project (pdf)
  
  
• Mood: Auditory recognition and classification based on changes in attentional state
  
  Kamvysselis (Kellis), Marina, Vassef, Carter, Winston
  MIT Human Intelligence Enterprise (6.892, Patrick Winston) Final Project (pdf)
  
  
• Webbot: A constraint model for automated web traversal
  
  Kamvysselis (Kellis), Frystyk Nielsen
  Wold Wide Web Consortium (W3C) Online Publications (pdf)
  
  
• Invest: Three algorithms for predicting stock market changes
  
  Kamvysselis (Kellis), Mehrotra, Washawsky
  MIT Artificial Intelligence (6.038, Tomas Lozano-Perez) Final Project (pdf)
  
  

• What's in the human genome? Large-scale discovery and validation of functional elements
  
  Bernstein, Kellis
  Genome Biology 2005 Mar 1; 6:312 (pdf)
  
  
• The changing face of genomics
  
  Kellis
  Genome Biology 2004 Apr 30; 5(5): p. 324 (pdf)
  
  
• Gene finding using multiple related species: a classification approach.
  
  Kellis
  Encyclopedia of Genetics, Genomics, Proteomics, John Wiley & Sons, special review, 2005 (pdf).
  
  
• Biological Signal Discovery: The Power of Multiple Genomes
  
  Kellis
  Fungal comparative genomics, Springer Verlag, invited book chapter, 2004 (in preparation).
  
  
• Meta-evolution: Computational requirements for evolutionary bursts
  
  Kamvysselis (Kellis)
  MIT Society of Mind (6.868, Marvin Minsky) Final Project (pdf)