Manolis Kellis Publications - Chronological

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1. 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)
   
   
2. An endogenous small interfering RNA pathway in Drosophila.
   
   Czech, Malone, Zhou, Stark, Schlingeheyde, Dus, Perrimon, Kellis, Wohlschlegel, Sachidanandam, Hannon, Brennecke
   Nature, May 7, 2008
   
   
3. Conservation of small RNA pathways in platypus
   
   Murchison, Kheradpour, Sachidanandam, Smith, Hodges, Xuan, Kellis, Grutzner, Stark, Hannon
   Genome Research, May 7, 2008
   
   
4. 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)
   
   
5. Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes
   
   Lin, Deoras, Rasmussen, Kellis
   PLoS Computational Biology 4(4):e1000067, Apr 18, 2008.
   


6. Evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network following duplication
   
   Presser, Elowitz, Kellis, Kishony
   PNAS Jan 16, 2008, (PNAS) (pdf)
   
   
7. 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)
   
   
8. 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)
   
   
9. 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)
   
   
10. Evolution of genes and genomes in the Drosophila Phylogeny
    
    Drosophila 12 Genomes Consortium
    Nature 450:203-218, Nov 8, 2007 (pdf) (Nature focus page)
    
    
11. 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)
    
    
12. Reliable prediction of regulator targets using 12 Drosophila genomes
    
    Kherapdour, Stark, Roy, Kellis
    Genome Research, Nov 7, 2007, Early online access, (pdf)
    
    
13. 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)
    
    
14. 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)
    
    
15. 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)
    
    
16. 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
    
    
17. 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)
    
    
18. 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)
    
    
19. 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)
    
    
20. 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)
    
    
21. 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)
    
    
22. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
    
    Xiaohui Xie, Jun Lu, EJ. Kulbokas, Todd Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric Lander, Manolis Kellis
    Nature 2005 Feb 27, doi:10.1038/nature03441 (pdf) (Nature website)
    (Supplementary Information)
    
    
23. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
    
    Manolis Kellis, Bruce Birren, Eric Lander
    Nature 2004 Apr 8; 428 pp. 617-24 (pdf) (Nature website)
    (Supplementary Information)
    
    
24. Sequencing and comparison of yeast species to identify genes and regulatory motifs
    
    Manolis Kellis, Nick Patterson, Matt Endrizzi, Bruce Birren, Eric Lander
    Nature 2003 May 15; 423 pp. 241-254 (pdf) (Nature website)
    (Supplementary Information)
    
    
25. 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)
    
    
26. 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)
    
    
27. 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).
    
    
28. 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)
    
    
29. 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)
    
    
30. 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).
    
    
31. 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)
    
    
32. The changing face of genomics
    
    Manolis Kellis
    Genome Biology 2004 Apr 30; 5(5): p. 324 (pdf)
    
    
33. Computational Comparative Genomics: Genes, Regulation, Evolution
    
    Manolis Kellis (Kamvysselis)
    MIT Ph.D. Thesis '03 (pdf)
    
    
34. 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)
    
    
35. 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)
    
    
36. 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)
    
    
37. Biological Signal Discovery: The Power of Multiple Genomes
    
    Manolis Kellis
    Fungal comparative genomics, Springer Verlag, invited book chapter, 2004 (in preparation).
    
    
38. Crust: A new Voronoi-Based Surface Reconstruction Algorithm
    
    Nina Amenta, Marshall Bern, Manolis Kamvysselis
    ACM Siggraph '98 Proceedings (pdf)
    
    
39. ECImorph: 2D polygon morphing using the Extended Gaussian Image
    
    Manolis Kamvysselis
    MIT Computer Vision (6.866, Berthold Horn) Final Project (pdf)
    
    
40. 3Dmorph: polygon-based geometry morphing
    
    Manolis Kamvysselis, Matt Blum, Hooman Vassef, Krzysztof Gajos
    MIT Computer Graphics (6.837, Seth Teller) Final Project (pdf)
    
41. Imagina: Sketch-based Image Retrieval using Cognitive Abstraction
    
    Manolis Kamvysselis, Ovidiu Marina
    MIT Masters Thesis '99 (pdf)
    
    
42. Wavelet-based character recognition in curvature space
    
    Manolis Kamvysselis
    MIT Machine Learning (6.891, Paul Viola) Final Project (pdf)
    
    
43. Robologo: Interactive programming environment for wheeled robot
    
    Manolis Kamvysselis, Jeremy Lueck, Christopher Rohrs
    MIT Microprocessor Design Lab (6.115, Marvin Minsky) Final Project (pdf)
    
    
44. Meta-evolution: Computational requirements for evolutionary bursts
    
    Manolis Kamvysselis
    MIT Society of Mind (6.868, Marvin Minsky) Final Project (pdf)
    
    
45. 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)
    
    
46. Webbot: A constraint model for automated web traversal
    
    Manolis Kamvysselis, Henryk Frystyk Nielsen
    Wold Wide Web Consortium (W3C) Online Publications (pdf)
    
    
47. 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)