sujaikumar's library 81 articles Export

	Local DNA topography correlates with functional noncoding regions of the human genome. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5925. (17 April 2009), pp. 389-392. by Stephen C. Parker, Loren Hansen, Hatice Ozel O. Abaan, Thomas D. Tullius, Elliott H. Margulies posted to structure human_genome human functional detection cne by sujaikumar on 2009-10-21 15:48:13 as along with 38 people and 6 groups daveGerrard operon antonkratz pradiptaray roys gjuggler benjaminsb gdb hagechouchin443 tomtullius scjparker psique orzenil emptyhb ilyashl coela VGreiff APRegier myzhang pkonings akundaje athma absterga rpatward timflutre stajich bpcusack jbhiatt djkt dhlbh friendpine dpollard inesdesantiago JustinCrocker aprasad maximilianh idonaldson kshundyak BergmanLab Mycology structural_bioinformatics RockmanLab EisenLab cis-regulatory-evolution
	Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. [My Copy] Cell, Vol. 134, No. 1. (11 July 2008), pp. 25-36. by Sean B. Carroll posted to regulatory_sequences evolutionary_developmental_biology complex by sujaikumar on 2009-10-19 17:18:03 as along with 4 people icq242500260 dchughes djkt Stew
	Organization of Conserved Elements Near Key Developmental Regulators in Vertebrate Genomes [My Copy] Adv Genet In Long-Range Control of Gene Expression, Vol. 61 (2008), pp. 307-338. by A. Woolfe, G. Elgar posted to vertebrate development cne by sujaikumar on 2009-10-19 11:49:48 as along with 1 person maximilianh
	Genomic regulatory blocks underlie extensive microsynteny conservation in insects [My Copy] Genome Research, Vol. 17, No. 12. (7 December 2007), pp. 1898-1908. by PÃ¤r G. EngstrÃ¶m, Shannan J. Ho Sui, Ãyvind Drivenes, Thomas S. Becker, Boris Lenhard posted to methodology insects drosophila cne by sujaikumar on 2009-10-14 10:48:36 as along with 1 person maximilianh
	Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 40. (6 October 2009), pp. 17077-17082. by Gregory E. Sims, Se-Ran R. Jun, Guohong Albert A. Wu, Sung-Hou H. Kim posted to no-tag by sujaikumar on 2009-10-08 08:20:49 as along with 7 people djkt wendygarnica Geknitics jsatkosk mkiyer antariksh bpcusack
	Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines [My Copy] Genome Research, Vol. 19, No. 7. (13 July 2009), pp. 1195-1201. by Peter D. Keightley, Urmi Trivedi, Marian Thomson, Fiona Oliver, Sujai Kumar, Mark L. Blaxter posted to no-tag by sujaikumar on 2009-10-04 16:34:07 as along with 6 people and 1 group druvus megraw darian gjuggler ppgardne JustinCrocker Journal picks
	PLoS Biology: Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny [My Copy] posted to elegans comparative chromosome_organization celegans cbriggsae briggsae by sujaikumar on 2009-09-28 12:12:06 as
	TRADE-OFFS IN DETECTING EVOLUTIONARILY CONSTRAINED SEQUENCE BY COMPARATIVE GENOMICS [My Copy] Annual Review of Genomics and Human Genetics, Vol. 6, No. 1. (2005), pp. 143-164. by Eric A. Stone, Gregory M. Cooper, Arend Sidow posted to comparative cne by sujaikumar on 2009-09-16 15:12:27 as along with 4 people diamantis jwortman aprasad eckart_bindewald
	De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. [My Copy] Genome biology, Vol. 10, No. 9. (2009), R94. by Scott Diguistini, Nancy Y. Liao, Darren Platt, et al.Gordon Robertson, Michael Seidel, Simon K. Chan, T. Roderick Docking, Inanc Birol, Robert A. Holt, Martin Hirst, Elaine Mardis, Marco A. Marra, Richard C. Hamelin, Jörg Bohlmann, Colette Breuil, Steven Jm J. Jones posted to solexa sequencing illumina denovo assembler 454 by sujaikumar on 2009-09-14 10:07:52 as along with 9 people and 2 groups GustavoLacerda sotacam gillianturgeon natstreet druvus jamselem kiekyon ppgardne stajich Journal picks Mycology
	Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (08 September 2009), 282. by Matteo Re, Graziano Pesole, David Horner posted to cne by sujaikumar on 2009-09-14 09:04:12 as
	Structural Relationships between Highly Conserved Elements and Genes in Vertebrate Genomes [My Copy] PLoS ONE, Vol. 3, No. 11. (14 November 2008), e3727. by Hong Sun, Geir Skogerbø, Zhen Wang, Wei Liu, Yixue Li posted to cne by sujaikumar on 2009-09-10 19:21:03 as along with 4 people and 1 group hpaces bpcusack Ema sameetmehta Bioinformatics
	$My PDF mitra_06_fractal.pdf$ Fractal Replication in Time-manipulated One-dimensional Cellular Automata [My Copy] Complex Systems, Vol. 16, No. 3. (2006) by Sugata Mitra, Sujai Kumar posted to ca fractal simulation by sujaikumar on 2009-07-27 13:22:49 as
	Self-Organizing Traffic at a Malfunctioning Intersection [My Copy] Journal of Artificial Societies and Social Simulation, Vol. 9, No. 4. (31 October 2006) by Sujai Kumar, Sugata Mitra posted to self-organizing-system simulation traffic by sujaikumar on 2009-07-27 13:18:28 as
	Should genetics get an information-theoretic education? [My Copy] Engineering in Medicine and Biology Magazine, IEEE In Engineering in Medicine and Biology Magazine, IEEE, Vol. 25, No. 1. (2006), pp. 34-45. by G. Battail posted to genomics information_theory by sujaikumar on 2009-07-27 00:17:36 as
	Shannon Information Theoretic Computation of Synonymous Codon Usage Biases in Coding Regions of Human and Mouse Genomes [My Copy] Genome Research, Vol. 12, No. 6. (1 June 2002), pp. 944-955. by Barry Zeeberg posted to evolution gc genome by sujaikumar on 2009-07-27 00:01:14 as along with 1 person gpalidwor
	De novo identification of repeat families in large genomes. [My Copy] Bioinformatics (Oxford, England), Vol. 21 Suppl 1, No. suppl_1. (1 June 2005), pp. i351-358. by Alkes L. Price, Neil C. Jones, Pavel A. Pevzner posted to repeat software by sujaikumar on 2009-07-22 16:56:16 as along with 8 people isimpson natstreet treangen druvus aprasad hoangmit timflutre urgi
	Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing [My Copy] Molecular Ecology, Vol. 17, No. 7. (April 2008), pp. 1636-1647. by J. Cristobal Vera, Christopher W. Wheat, Howard W. Fescemyer, et al.Mikko J. Frilander, Douglas L. Crawford, I. Ilkka Hansk, James H. Marden posted to 454 assembler genome sequencing by sujaikumar on 2009-07-22 16:48:32 as along with 5 people n00c oneilsh semrich orzenil guhjy
	Origins of recently gained introns in Caenorhabditis [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 31. (3 August 2004), pp. 11362-11367. by Avril Coghlan, Kenneth H. Wolfe posted to evolution genome intron by sujaikumar on 2009-07-15 12:24:10 as along with 3 people and 2 groups thegoose2 tharris penka C. elegans / WormBase Nie
	Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor [My Copy] Genomics, Vol. 90, No. 1. (July 2007), pp. 44-48. by Sourav Chatterji, Lior Pachter posted to duplication evolution genome intron by sujaikumar on 2009-07-15 12:15:00 as
	Evolutionary dynamics of nematode operons: Easy come, slow go. [My Copy] Genome Res (2008) by W. Qian, J. Zhang posted to evolution nematodes operons by sujaikumar on 2009-06-11 15:19:17 as along with 2 people and 1 group thegoose2 tharris C. elegans / WormBase
	The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. [My Copy] Nature genetics, Vol. 40, No. 10. (21 October 2008), pp. 1193-1198. by Christoph Dieterich, Sandra W. Clifton, Lisa N. Schuster, et al.Asif Chinwalla, Kimberly Delehaunty, Iris Dinkelacker, Lucinda Fulton, Robert Fulton, Jennifer Godfrey, Pat Minx, Makedonka Mitreva, Waltraud Roeseler, Huiyu Tian, Hanh Witte, Shiaw-Pyng P. Yang, Richard K. Wilson, Ralf J. Sommer posted to comparative genome pristionchus sequencing by sujaikumar on 2009-05-26 10:49:20 as along with 4 people and 1 group kshameer tharris mdperry pengchy C. elegans / WormBase
	nGASP - the nematode genome annotation assessment project [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (19 December 2008), 549. by Avril Coghlan, Tristan Fiedler, Sheldon McKay, et al.Paul Flicek, Todd Harris, Darin Blasiar, the nGASP Consortium, Lincoln Stein posted to annotation genome nematodes by sujaikumar on 2009-05-17 09:57:43 as along with 3 people rshe druvus ajbattle
	Genome evolution in Caenorhabditis [My Copy] Brief Funct Genomic Proteomic, Vol. 7, No. 3. (1 May 2008), pp. 211-216. by James H. Thomas posted to caenorhabditis evolution genome by sujaikumar on 2009-05-13 13:33:26 as along with 4 people and 1 group duncan742 thegoose2 mdperry tharris C. elegans / WormBase
	Evolution of the Caenorhabditis elegans genome. [My Copy] Molecular biology and evolution, Vol. 26, No. 6. (1 June 2009), pp. 1199-1234. by Asher D. Cutter, Alivia Dey, Rosalind L. Murray posted to celegans evolution genome by sujaikumar on 2009-05-13 11:49:41 as along with 5 people and 2 groups rshe operon dpollard stajich jasontsai RockmanLab Mycology
	Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time [My Copy] BMC Genomics, Vol. 8, No. 1. (2007) by Dorota Retelska, Emmanuel Beaudoing, Cedric Notredame, Victor C. Jongeneel, Philipp Bucher posted to cne evolution insects invertebrates mammals vertebrates by sujaikumar on 2009-04-23 18:05:37 as along with 2 people and 1 group maximilianh cisevol cis-regulatory-evolution
	Adaptive Evolution of Conserved Noncoding Elements in Mammals [My Copy] PLoS Genetics, Vol. 3, No. 9. (1 September 2007), e147. by Su Y. Kim, Jonathan K. Pritchard posted to cne evolution mammals by sujaikumar on 2009-04-23 14:07:39 as along with 11 people and 5 groups sriesenfeld mattjb livingthingdan djkt stajich Garamonfok cabbagezs Stew cisevol rrhudson bpcusack EisenLab ComplexAdaptiveSystems DSTO-CAS livingthing cis-regulatory-evolution
	Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. [My Copy] Molecular biology and evolution, Vol. 25, No. 4. (1 April 2008), pp. 778-786. by Asher D. Cutter posted to caenorhabditis divergence by sujaikumar on 2009-04-20 15:39:34 as along with 4 people and 1 group rshe hrogers thegoose2 tharris C. elegans / WormBase
	USING GRAPH CONCEPTS TO UNDERSTAND THE ORGANIZATION OF COMPLEX SYSTEMS [My Copy] International Journal of Bifurcation and Chaos, Vol. 17, No. 7. (July 2007), pp. 2201-2214. by Claire Christensen, Reka Albert posted to complex network by sujaikumar on 2007-10-05 16:41:23 as
	Web Services at the European Bioinformatics Institute [My Copy] Nucl. Acids Res., Vol. 35, No. Web Server issue. (18 June 2007), gkm291. by Alberto Labarga, Franck Valentin, Mikael Anderson, Rodrigo Lopez posted to no-tag by sujaikumar on 2007-08-22 22:04:37 as along with 12 people jeargle tomjad druvus Cortel daforerog moborg dullhunk sgoetz niallhaslam sim82 alanrw tny
	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. [My Copy] Nucleic acids research, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402. by S. F. Altschul, T. L. Madden, A. A. Schäffer, et al.J. Zhang, Z. Zhang, W. Miller, D. J. Lipman posted to algorithm alignment by sujaikumar on 2007-08-22 21:47:07 as along with 68 people and 5 groups rshe niallhaslam ucbcjbm timhubbard parnell tfuji maria_hauser jbhiatt yylin mgomes BioNica idoerg pjcite swp09 kgutwin mcbla cpwardell johanviklund daforerog nlapalu sebk tjimenez shung pwais dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM References for 3DSim paper EisenLab biomedical-nlp Microbial-Ecology Plantandetc
	A greedy algorithm for aligning DNA sequences. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 7, No. 1-2. (r 2000), pp. 203-214. by Z. Zhang, S. Schwartz, L. Wagner, W. Miller posted to algorithm alignment by sujaikumar on 2007-08-22 10:40:22 as along with 5 people maria_hauser AaronDarling azazello benwei bozdagd
	Identification of common molecular subsequences. [My Copy] Journal of molecular biology, Vol. 147, No. 1. (25 March 1981), pp. 195-197. by T. F. Smith, M. S. Waterman posted to algorithm alignment by sujaikumar on 2007-08-22 10:35:10 as along with 21 people rshe jengeldk maria_hauser jmanning2k cmor parnell adamnellis timflutre heliopais mcbla alessandroparini usagi-kirin creswick vavi bicko dgront rabio cjeans incovoma newton1234 bozdagd
	Improved tools for biological sequence comparison. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 85, No. 8. (April 1988), pp. 2444-2448. by W. R. Pearson, D. J. Lipman posted to fasta by sujaikumar on 2007-08-21 01:06:24 as along with 15 people and 2 groups rshe maria_hauser pachorip parnell carlosviana cawelsh9 arcticrasta ffranca gurkanbebek bsmagic CitoJam lusk cjeans Ema bozdagd Bioinformatics bioinplant
	FASTA format description [My Copy] posted to fasta by sujaikumar on 2007-08-21 01:01:20 as
	The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. [My Copy] PLoS biology, Vol. 1, No. 2. (1 November 2003), e45. by Lincoln D. Stein, Zhirong Bao, Darin Blasiar, et al.Thomas Blumenthal, Michael R. Brent, Nansheng Chen, Asif Chinwalla, Laura Clarke, Chris Clee, Avril Coghlan, Alan Coulson, Peter D'Eustachio, David H. Fitch, Lucinda A. Fulton, Robert E. Fulton, Sam Griffiths-Jones, Todd W. Harris, LaDeana W. Hillier, Ravi Kamath, Patricia E. Kuwabara, Elaine R. Mardis, Marco A. Marra, Tracie L. Miner, Patrick Minx, James C. Mullikin, Robert W. Plumb, Jane Rogers, Jacqueline E. Schein, Marc Sohrmann, John Spieth, Jason E. Stajich, C. Wei, David Willey, Richard K. Wilson, Richard Durbin, Robert H. Waterston posted to briggsae comparative by sujaikumar on 2007-08-19 23:16:28 as along with 4 people and 2 groups rshe thegoose2 tharris stajich C. elegans / WormBase Mycology
	Molecular Genealogy of Some Nematode Taxa as Based on Cytochrome c and Globin Amino Acid Sequences [My Copy] Molecular Phylogenetics and Evolution, Vol. 3, No. 2. (June 1994), pp. 92-101. by Jacques R. Vanfleteren, Yves Van De Peer, Mark L. Blaxter, et al.Susan A. Tweedie, Clive Trotman, Liu Lu, Marie-Louise Van Hauwaert, Luc Moens posted to celegans nematodes by sujaikumar on 2007-08-19 23:08:37 as
	Evolution. An embarrassment of switches. [My Copy] Science (New York, N.Y.), Vol. 317, No. 5839. (10 August 2007), pp. 758-759. by Leonid Kruglyak, David L. Stern posted to alignment cis-regulatory cne identity by sujaikumar on 2007-08-17 09:00:42 as along with 2 people maximilianh balabu
	Divergence of Transcription Factor Binding Sites Across Related Yeast Species [My Copy] Science, Vol. 317, No. 5839. (10 August 2007), pp. 815-819. by Anthony R. Borneman, Tara A. Gianoulis, Zhengdong D. Zhang, et al.Haiyuan Yu, Joel Rozowsky, Michael R. Seringhaus, Lu Y. Wang, Mark Gerstein, Michael Snyder posted to binding-site divergence yeast by sujaikumar on 2007-08-17 08:16:06 as along with 22 people and 2 groups pradiptaray gdb fenghezi dbensasson caseybrown bryankr aalibes chad_davis dpollard djkt mikaelhuss lusk cjeans zwang GustavoLacerda Jporci maximilianh cisevol njcitulike emptyhb nklee anka EisenLab cis-regulatory-evolution
	BLASTCLUST - BLAST score-based single-linkage clustering [My Copy] posted to algorithm blast by sujaikumar on 2007-08-16 18:33:57 as
	GFF (General Feature Format) Specifications Document [My Copy] by Richard Durbin, David Haussler, Lincoln Stein, Suzanna Lewis, Anders Krogh posted to gff by sujaikumar on 2007-08-14 11:45:37 as
	RepeatMasker Open-3.0 [My Copy] (1996-2004) by A. F. A. Smit, R. Hubley, P. Green posted to repeat repeatmasker software tool by sujaikumar on 2007-08-13 18:59:48 as along with 1 person dandaman
	Having a BLAST with bioinformatics (and avoiding BLASTphemy). [My Copy] Genome Biol, Vol. 2, No. 10. (2001) by A. Pertsemlidis, J. W. Fondon posted to algorithm blast by sujaikumar on 2007-08-12 16:16:16 as along with 10 people and 2 groups sandfire orzenil karbak ziquje prtmht textoris shantanu cjeans scottstensland hpaces Bioinformatics MathBio
	Into the heart of darkness: large-scale clustering of human non-coding DNA [My Copy] by Gill Bejerano posted to clustering non-coding by sujaikumar on 2007-07-31 18:30:39 as
	Active conservation of noncoding sequences revealed by three-way species comparisons. [My Copy] Genome research, Vol. 10, No. 9. (1 September 2000), pp. 1304-1306. by I. Dubchak, M. Brudno, G. G. Loots, et al.L. Pachter, C. Mayor, E. M. Rubin, K. A. Frazer posted to genome percentage_identity by sujaikumar on 2007-07-11 10:11:39 as along with 1 person holecm
	Quantification of the variation in percentage identity for protein sequence alignments [My Copy] BMC Bioinformatics, Vol. 7 (19 September 2006), 415. by Ps G. Raghava, Geoffrey J. Barton posted to genome percentage_identity by sujaikumar on 2007-07-11 10:10:58 as along with 7 people and 1 group thegoose sgoetz pansapiens bicko dpollard rabio medic0747 EisenLab
	What is a gene, post-ENCODE? History and updated definition [My Copy] Genome Research, Vol. 17, No. 6. (June 2007), pp. 669-681. by Mark B. Gerstein, Can Bruce, Joel S. Rozowsky, et al.Deyou Zheng, Jiang Du, Jan O. Korbel, Olof Emanuelsson, Zhengdong D. Zhang, Sherman Weissman, Michael Snyder posted to encode gene genome by sujaikumar on 2007-06-22 13:34:51 as along with 35 people and 4 groups daveGerrard Yanno inesdesantiago kentz ddcttrl bertelsen tmarscha thegoose2 burak guhjy carolh12 eweaver dpollard balicea dchughes dullhunk madhadron cottrell grahamc egonw ghattem Garamonfok PunkRock jasonbobe PredictER cabbagezs Jporci kmdaily krokicki antonkratz Minty hpaces tharris altotor mjoach Bioinformatics EisenLab G4ID Genetics-of-Gambling
	Computational Maps in the Visual Cortex [My Copy] (2005) by Risto Miikkulainen, James A. Bednar, Yoonsuck Choe, Joseph Sirosh posted to cnv2 oblique by sujaikumar on 2007-04-08 15:09:06 as
	A controlled, mirror-image study of second-generation antipsychotics in the treatment of schizophrenia. [My Copy] Int Clin Psychopharmacol, Vol. 22, No. 3. (May 2007), pp. 133-136. by D. Taylor, K. Hayhurst, R. Kerwin posted to schizy by sujaikumar on 2007-04-07 20:57:49 as
	The world from a cat's perspective--statistics of natural videos. [My Copy] Biol Cybern, Vol. 90, No. 1. (January 2004), pp. 41-50. by B. Y. Betsch, W. Einhäuser, K. P. Körding, P. König posted to cnv2 oblique by sujaikumar on 2007-04-06 20:27:38 as
	A horizontal bias in human visual processing of orientation and its correspondence to the structural components of natural scenes. [My Copy] J Vis, Vol. 4, No. 12. (10 December 2004), pp. 1044-1060. by B. C. Hansen, E. A. Essock posted to cnv2 oblique by sujaikumar on 2007-04-06 19:00:10 as

Note: You may cite this page as: http://www.citeulike.org/user/sujaikumar

Result page: 1 2 Next

cne	21
evolution	14
genome	11
cnv2	9
oblique	9
algorithm	6
alignment	6
comparative	6
celegans	5
csb	5
nematodes	5
vertebrates	5
worms	4
blast	3
briggsae	3
developmental	3
insects	3
mammals	3
non-coding	3
regulatory_network	3
sequencing	3
454	2
assembler	2
caenorhabditis	2
complex	2
development	2
divergence	2
drosophila	2
fasta	2
grn	2
humans	2
intron	2
percentage_identity	2
repeat	2
simulation	2
software	2
vertebrate	2
yeast	2
annotation	1
binding-site	1
ca	1
cbriggsae	1
chromosome_organization	1
cis-regulatory	1
clustering	1
database	1
denovo	1
detection	1
duplication	1
elegans	1
encode	1
enhancer	1
evolutionary_developmental_biology	1
fractal	1
functional	1
gc	1
gene	1
genomics	1
gff	1
glocal	1
human	1
human_genome	1
identification	1
identity	1
illumina	1
information_theory	1
insect	1
interaction	1
invertebrates	1
methodology	1
network	1
operons	1
phastcons	1
pristionchus	1
promoters	1
protein-dna	1
radius	1
regulatory_sequences	1
repeatmasker	1
schizy	1
self-organizing-system	1
snorna	1
solexa	1
structure	1
tool	1
traffic	1
transcriptome	1

sujaikumar's library 81 articles Export

sujaikumar's tags