robfsouza's sequence [62 articles] Export

Recent papers added to robfsouza's library classified by the tag sequence. You can also see everyone's sequence.

	Low conservation of gene content in the Drosophila Y chromosome [My Copy] Nature, Vol. 456, No. 7224. (Dec 2008), pp. 949-51. by Leonardo B. Koerich, Xiaoyun Wang, Andrew G. Clark, Antonio B. Carvalho posted to synteny sequence phylogeny molecular melanogaster linkage insect genetics genes evolution drosophila conserved chromosome animals by robfsouza on 2009-11-24 15:17:16 as
	Neutral and adaptive variation in gene expression [My Copy] Proc Natl Acad Sci USA, Vol. 103, No. 14. (Apr 2006), pp. 5425-30. by Andrew Whitehead, Douglas L. Crawford posted to variation states sequence population oligonucleotide humans genetics genetic gene fishes expression evolution array animals analysis by robfsouza on 2009-11-24 15:17:15 as
	Structure-guided recombination creates an artificial family of cytochromes P450 [My Copy] PLoS Biol, Vol. 4, No. 5. (May 2006) by Christopher R. Otey, Marco Landwehr, Jeffrey B. Endelman, Kaori Hiraga, Jesse D. Bloom, Frances H. Arnold posted to temperature system stability sequence recombination recombinant proteins protein p-450 molecular models laurates hot genetic folding enzyme engineering cytochrome conformation amino alignment acid by robfsouza on 2009-11-24 15:17:15 as
	Massive horizontal gene transfer in bdelloid rotifers [My Copy] Science, Vol. 320, No. 5880. (May 2008), pp. 1210-3. by Eugene A. Gladyshev, Matthew Meselson, Irina R. Arkhipova posted to transposable transfer telomere sequence rotifera repetitive nucleic molecular horizontal helminth genes gene fungal elements dna data bacterial animals acid by robfsouza on 2009-11-24 15:17:15 as
	Alignment uncertainty and genomic analysis [My Copy] Science, Vol. 319, No. 5862. (Jan 2008), pp. 473-6. by Karen M. Wong, Marc A. Suchard, John P. Huelsenbeck posted to uncertainty statistical software sequence selection saccharomyces reading phylogeny open monte molecular models method genomics genome genetics fungal frames evolution computational biology amino alignment algorithms acid by robfsouza on 2009-11-24 15:17:15 as
	Accuracy and quality of massively parallel DNA pyrosequencing [My Copy] Genome Biol, Vol. 8, No. 7. (Jan 2007) by Susan M. Huse, Julie A. Huber, Hilary G. Morrison, Mitchell L. Sogin, David M. Welch posted to variation sequence rrna ribosomal results reproducibility microbial genome genetics genetic genes dna analysis by robfsouza on 2009-11-24 15:17:15 as
	Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information [My Copy] PLoS Comput Biol, Vol. 4, No. 9. (Jan 2008) by Kai Wang, Jeremy A. Horst, Gong Cheng, David C. Nickle, Ram Samudrala posted to thermodynamics tertiary structure site-directed simulation sequence regression proteins protein ornithine mutagenesis motifs molecular models interaction genetic evolution domains decarboxylase databases conserved computer computational cellulose biology binding bacterial analysis amino alignment acid 14-beta-cellobiosidase by robfsouza on 2009-11-24 15:17:12 as
	Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity [My Copy] Proc Natl Acad Sci USA, Vol. 105, No. 36. (Sep 2008), pp. 13474-9. by Gue S. Chang, Yoojin Hong, Kyung D. Ko, et al.Gaurav Bhardwaj, Edward C. Holmes, Randen L. Patterson, Damian B. van Rossum posted to sequence phylogeny molecular homology evolution computational biology by robfsouza on 2009-11-24 15:17:12 as
	Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins [My Copy] Current Opinion in Chemical Biology, Vol. 7, No. 1. (Feb 2003), pp. 12-20. by Vivek Anantharaman, L. Aravind, Eugene V. Koonin posted to tertiary structure structural sequence proteins protein molecular inactive homology family evolution enzymes enzyme conserved catalysis aravind by robfsouza on 2009-11-24 15:17:11 as
	A specificity map for the PDZ domain family [My Copy] PLoS Biol, Vol. 6, No. 9. (Sep 2008) by Raffi Tonikian, Yingnan Zhang, Stephen L. Sazinsky, et al.Bridget Currell, Jung-Hua Yeh, Boris Reva, Heike A. Held, Brent A. Appleton, Marie Evangelista, Yan Wu, Xiaofeng Xin, Andrew C. Chan, Somasekar Seshagiri, Laurence A. Lasky, Chris Sander, Charles Boone, Gary D. Bader, Sachdev S. Sidhu posted to viral tumor suppressor structure sequence secondary proteome proteins protein phylogeny peptides pdz mutation molecular models membrane humans elegans domains data caenorhabditis binding animals amino acid by robfsouza on 2009-11-24 15:17:10 as
	Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? [My Copy] BMC Evol Biol, Vol. 8 (Jan 2008) by Stefanie Hartmann, Todd J. Vision posted to software sequence protein phylogeny molecular models likelihood genetic expressed evolution computational biology analysis alignment by robfsouza on 2009-11-24 15:17:10 as
	The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans [My Copy] Nature, Vol. 451, No. 7180. (Feb 2008), pp. 783-8. by Nicole King, M. Jody Westbrook, Susan L. Young, et al.Alan Kuo, Monika Abedin, Jarrod Chapman, Stephen Fairclough, Uffe Hellsten, Yoh Isogai, Ivica Letunic, Michael Marr, David Pincus, Nicholas Putnam, Antonis Rokas, Kevin J. Wright, Richard Zuzow, William Dirks, Matthew Good, David Goodstein, Derek Lemons, Wanqing Li, Jessica B. Lyons, Andrea Morris, Scott Nichols, Daniel J. Richter, Asaf Salamov, J. G. I. Sequencing, Peer Bork, Wendell A. Lim, Gerard Manning, W. Todd Miller, William McGinnis, Harris Shapiro, Robert Tjian, Igor V. Grigoriev, Daniel Rokhsar posted to transduction transcription tertiary structure speciation signal sequence regulation proteins protein phylogeny phosphotyrosine notch molecular matrix introns humans hedgehog genome genetic gene factors extracellular expression evolution eukaryotic conserved cells cell animals adhesion by robfsouza on 2009-11-24 15:17:10 as
	Automated protein subfamily identification and classification [My Copy] PLoS Comput Biol, Vol. 3, No. 8. (Aug 2007) by Duncan P. Brown, Nandini Krishnamurthy, Kimmen Sjölander posted to specificity sequence results reproducibility recognition proteins protein pattern molecular markov intelligence data analysis amino alignment algorithms acid by robfsouza on 2009-11-24 15:17:09 as
	Metagenomics: genomic analysis of microbial communities [My Copy] Annu Rev Genet, Vol. 38 (Jan 2004), pp. 525-52. by Christian S. Riesenfeld, Patrick D. Schloss, Jo Handelsman posted to sequence rhodopsin phylogeny microscopy microbiology genomic genome gene environmental biodiversity bacteriophages bacterial bacteria archaeal archaea analysis by robfsouza on 2009-11-24 15:17:09 as
	Molecular signatures of ribosomal evolution [My Copy] Proc Natl Acad Sci USA, Vol. 105, No. 37. (Sep 2008), pp. 13953-8. by Elijah Roberts, Anurag Sethi, Jonathan Montoya, Carl R. Woese, Zaida Luthey-Schulten posted to tertiary structure structural sequence rna ribosomes ribosomal quaternary proteins protein phylogeny nucleic molecular models humans homology genome evolution data conformation biosynthesis animals acid by robfsouza on 2009-11-24 15:17:09 as
	Evolutionarily conserved pathways of energetic connectivity in protein families [My Copy] Science, Vol. 286, No. 5438. (Oct 1999), pp. 295-9. by S. W. Lockless, R. Ranganathan posted to thermodynamics tertiary structure statistics sequence recombinant proteins protein mutation molecular models fusion folding evolution conserved conformation binding amino alignment acid by robfsouza on 2009-11-24 15:17:09 as
	Sequence-based prediction of protein-protein interactions by means of codon usage [My Copy] Genome Biol, Vol. 9, No. 5. (Jan 2008) by Hamed S. Najafabadi, Reza Salavati posted to specificity sequence saccharomyces protein plasmodium mapping interaction falciparum escherichia coli codon cerevisiae animals analysis amino acid by robfsouza on 2009-11-24 15:17:09 as
	Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs [My Copy] Genome Research, Vol. 18, No. 3. (Mar 2008), pp. 489-99. by Julie E. Horvath, David W. Weisrock, Stephanie L. Embry, et al.Isabella Fiorentino, James P. Balhoff, Peter Kappeler, Gregory A. Wray, Huntington F. Willard, Anne D. Yoder posted to sequence reaction primers polymerase phylogeny molecular male lemur geography genomics female evolution dna data animals by robfsouza on 2009-11-24 15:17:09 as
	Sequence similarity network reveals common ancestry of multidomain proteins [My Copy] PLoS Comput Biol, Vol. 4, No. 4. (Apr 2008) by Nan Song, Jacob M. Joseph, George B. Davis, Dannie Durand posted to sequence proteins phylogeny male humans homology growth genomics female family factor conserved amino acid by robfsouza on 2009-11-24 15:17:09 as
	Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids [My Copy] Cell Cycle, Vol. 8, No. 11. (Jun 2009), pp. 1698-710. by Lakshminarayan M. Iyer, Mamta Tahiliani, Anjana Rao, L. Aravind posted to transposases transposable tertiary structure sequence repair proteins protein predictive oxidation-reduction nucleotides molecular ketoglutaric iron humans homology genetic enzymes elements dna-binding dna dioxygenases databases data amino alignment acid by robfsouza on 2009-11-24 15:17:09 as
	uDENN, DENN, and dDENN: indissociable domains in Rab and MAP kinases signaling pathways [My Copy] Biochemical and Biophysical Research Communications, Vol. 287, No. 3. (Sep 2001), pp. 688-95. by E. Levivier, B. Goud, M. Souchet, T. P. Calmels, J. P. Mornon, I. Callebaut posted to ubiquitination ubiquitin uba1 transduction tertiary system structure signaling signal sequence receptor rats rab1 proteins protein nucleotide mvb12 motifs molecular mice map kinase humans homology guanine gtp-binding factors exchange drosophila domain databases data conserved animals analysis amino algorithms adaptor acid by robfsouza on 2009-11-24 15:17:09 as
	Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution [My Copy] Mol Biol Evol, Vol. 24, No. 3. (Mar 2007), pp. 845-52. by Oliver G. Pybus, Andrew Rambaut, Robert Belshaw, Robert P. Freckleton, Alexei J. Drummond, Edward C. Holmes posted to viruses sequence selection rna polymorphism phylogeny mutation molecular models likelihood genetics genetic evolution computational biology amino acid by robfsouza on 2009-11-24 15:17:09 as
	Gene conversion and purifying selection of a placenta-specific ERV-V envelope gene during simian evolution [My Copy] BMC Evol Biol, Vol. 8 (Jan 2008) by Anders L. Kjeldbjerg, Palle Villesen, Lars Aagaard, Finn S. Pedersen posted to viral terminal sequence selection retroviruses repeat reading proteins primates placenta open molecular humans human genome genetics gene frames female evolution envelope endogenous dna chromosomes animals analysis alignment by robfsouza on 2009-11-24 15:17:09 as
	Molecular evolution of a primate-specific microRNA family [My Copy] Mol Biol Evol, Vol. 25, No. 7. (Jul 2008), pp. 1493-502. by Rui Zhang, Yin-Qiu Wang, Bing Su posted to sequence primates placenta phylogeny nucleic molecular micrornas humans female evolution data conformation animals alignment acid by robfsouza on 2009-11-24 15:17:08 as
	Computational Approaches for Protein Function Prediction [My Copy] Techreport, No. TR 06-028. (2006) by Gaurav Pandey, Vipin Kumar, Michael Steinbach posted to sequence protein bioinformatics analysis by robfsouza on 2009-11-23 03:14:42 as
	Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics [My Copy] Microbiol. Mol. Biol. Rev., Vol. 65, No. 1. (1 Mar 2001), pp. 44-79. by Kira S. Makarova, L. Aravind, Yuri I. Wolf, et al.Roman L. Tatusov, Kenneth W. Minton, Eugene V. Koonin, Michael J. Daly posted to sequence inactive genome enzyme aravind by robfsouza on 2009-09-18 23:23:24 as along with 2 people and 1 group operon beatrizfernandez Microbial-Ecology
	Complete genome sequence of the apicomplexan, Cryptosporidium parvum. [My Copy] Science, Vol. 304, No. 5669. (16 Apr 2004), pp. 441-445. by Mitchell S. Abrahamsen, Thomas J. Templeton, Shinichiro Enomoto, et al.Juan E. Abrahante, Guan Zhu, Cheryl A. Lancto, Mingqi Deng, Chang Liu, Giovanni Widmer, Saul Tzipori, Gregory A. Buck, Ping Xu, Alan T. Bankier, Paul H. Dear, Bernard A. Konfortov, Helen F. Spriggs, Lakshminarayan Iyer, Vivek Anantharaman, L. Aravind, Vivek Kapur posted to sequence inactive genome enzyme aravind by robfsouza on 2009-09-18 23:21:49 as along with 3 people kaarsinogen Cortel shung
	Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences [My Copy] Genome Biol, Vol. 2, No. 12. (2001) by Lakshminarayan Iyer, L. Aravind, Peer Bork, et al.Kay Hofmann, Arcady Mushegian, Igor Zhulin, Eugene Koonin posted to sequence science inactive enzyme bioinformatics aravind analysis by robfsouza on 2009-09-18 22:31:39 as along with 2 people bpcusack eweaver
	Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses [My Copy] Nucl. Acids Res., Vol. 36, No. 11. (1 Jun 2008), pp. 3552-3569. by Jerzy Orlowski, Janusz M. Bujnicki posted to analysis chromatin classification endonuclease enzyme evolution fold prediction recombination restriction sequence superfamily by robfsouza on 2009-08-06 23:55:35 as
	A Database of Bacterial Lipoproteins (DOLOP) with Functional Assignments to Predicted Lipoproteins [My Copy] J. Bacteriol., Vol. 188, No. 8. (15 Apr 2006), pp. 2761-2773. by Madan M. Babu, M. Leena Priya, A. Tamil Selvan, et al.Martin Madera, Julian Gough, L. Aravind, K. Sankaran posted to signal sequence protein posttranslational modification membrane lipoprotein dataset database aravind by robfsouza on 2009-08-05 17:11:36 as
	Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses [My Copy] J. Virol., Vol. 75, No. 23. (1 Dec 2001), pp. 11720-11734. by Lakshminarayan M. Iyer, L. Aravind, Eugene V. Koonin posted to virus sequence protein phylogenomics phylogenetics evolution aravind by robfsouza on 2009-07-18 02:39:07 as
	Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases [My Copy] Bioinformatics, Vol. 23, No. 11. (1 Jun 2007), pp. 1386-1393. by Alexander V. Alekseyenko, Christopher J. Lee posted to algorithm alignment annotation bioinformatics biological database method sequence by robfsouza on 2009-06-29 23:38:18 as along with 5 people and 3 groups mkiyer cisevol urgi stajich dandaman JLab BergmanLab Mycology
	Trinucleotide repeat instability: a hairpin curve at the crossroads of replication, recombination, and repair. [My Copy] Cytogenetic and genome research, Vol. 100, No. 1-4. (2003), pp. 7-24. by B. A. Lenzmeier, C. H. Freudenreich posted to indel homopeptide low polymorphism protein recombination repair repeats replication sequence complexity disease gene human instability length by robfsouza on 2009-06-18 17:15:09 as
	Intergenic and Genic Sequence Lengths Have Opposite Relationships with Respect to Gene Expression [My Copy] PLoS ONE, Vol. 3, No. 11. (7 Nov 2008), e3670. by Juliette Colinas, Scott C. Schmidler, Gil Bohrer, Borislav Iordanov, Philip N. Benfey posted to exon expression length level protein sequence transcription by robfsouza on 2009-06-18 17:00:16 as along with 3 people and 2 groups druvus cisevol bpcusack cis-regulatory-evolution BergmanLab
	Evidence that Protein Length Expansion and Contraction Is Partly Due to Mutational Events in Premeiotic Cells [My Copy] Molecular Biology and Evolution, Vol. 23, No. 7. (Jul 2006), pp. 1339-1340. by Bowen, Suzanne, Wheals, E. Alan posted to indel homopeptide evolution gene length recombination repeats sequence by robfsouza on 2009-06-18 16:54:38 as
	Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 8. (13 Apr 1999), pp. 4482-4487. by Laurent Duret, Dominique Mouchiroud posted to bias codon gene length level protein sequence transcription by robfsouza on 2009-06-18 16:48:55 as along with 4 people and 1 group saunders thegoose2 tharris bjorns C. elegans / WormBase
	Protein length in eukaryotic and prokaryotic proteomes [My Copy] Nucleic Acids Research, Vol. 33, No. 10. (2005), pp. 3390-3400. by Luciano Brocchieri, Samuel Karlin posted to indel complexity length low protein repeats sequence by robfsouza on 2009-06-18 01:01:04 as
	Protein-length distributions for the three domains of life [My Copy] Trends in Genetics, Vol. 16, No. 3. (1 Mar 2000), pp. 107-109. by J. Zhang posted to indel complexity length low protein repeats sequence by robfsouza on 2009-06-18 00:58:37 as
	A Single Determinant Dominates the Rate of Yeast Protein Evolution [My Copy] Mol Biol Evol, Vol. 23, No. 2. (1 Feb 2006), pp. 327-337. by D. Allan Drummond, Alpan Raval, Claus O. Wilke posted to indel bias codon complexity correlation evolution expression gene length low protein rate repeats sequence by robfsouza on 2009-06-17 23:18:47 as along with 2 people and 1 group daveGerrard cjeans BergmanLab
	Patterns of internal gene duplication in the course of metazoan evolution [My Copy] Gene, Vol. 396, No. 1. (01 Jul 2007), pp. 59-65. by Chun-Chang Chen, Wen-Hsiung Li, Huang-Mo Sung posted to indel complexity domain duplication elongation evolution exon gene length low ontology protein repeats sequence shuffling by robfsouza on 2009-06-17 20:34:43 as
	Average Gene Length Is Highly Conserved in Prokaryotes and Eukaryotes and Diverges Only Between the Two Kingdoms [My Copy] Mol Biol Evol, Vol. 23, No. 6. (1 Jun 2006), pp. 1107-1108. by Lin Xu, Hong Chen, Xiaohua Hu, Rongmei Zhang, Ze Zhang, Z. W. Luo posted to indel eukaryote complexity gene length low prokaryotes protein sequence by robfsouza on 2009-06-17 20:28:20 as along with 1 person jjray
	Codon distribution in vertebrate genes may be used to predict gene length [My Copy] Journal of Molecular Biology, Vol. 197, No. 3. (Oct 1987), pp. 379-388. by W. Bains posted to indel bias codon complexity gene length low protein sequence by robfsouza on 2009-06-17 20:20:38 as
	Investigating the Relationship Between Genome Structure, Composition, and Ecology in Prokaryotes [My Copy] Mol Biol Evol, Vol. 19, No. 6. (1 Jun 2002), pp. 789-800. by Pietro Lio posted to indel homopeptide bias codon complexity composition dna evolution gene length low repeats sequence substitution by robfsouza on 2009-06-17 18:14:17 as along with 1 person marenzelleria
	Simple sequence repeats in proteins and their significance for network evolution [My Copy] Gene, Vol. 345, No. 1. (17 Jan 2005), pp. 113-118. by J. Hancock, M. Simon posted to indel homopeptide network codon elements evolution gene interaction length low mobile protein repeats review sequence by robfsouza on 2009-06-17 17:45:08 as
	Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats [My Copy] Genomics, Vol. 89, No. 3. (Mar 2007), pp. 316-325. by Loris Mularoni, Reiner A. Veitia, Mar M. Albà posted to indel homopeptide codon complexity elements gene length low protein repeats sequence by robfsouza on 2009-06-17 17:40:23 as
	Distribution and evolution of short tandem repeats in closely related bacterial genomes [My Copy] Gene, Vol. 410, No. 1. (29 Feb 2008), pp. 18-25. by Edit Kassai-Jáger, Csaba Ortutay, Gábor Tóth, Tibor Vellai, Zoltán Gáspári posted to indel homopeptide complexity dna evolution gene length low protein repeats sequence by robfsouza on 2009-06-17 17:31:08 as along with 1 person druvus
	Simple sequence repeats as advantageous mutators in evolution. [My Copy] Trends in genetics : TIG, Vol. 22, No. 5. (May 2006), pp. 253-259. by Yechezkel Kashi, David G. King posted to indel homopeptide complexity composition dna elements evolution gene length low protein recombination repeats review selection sequence by robfsouza on 2009-06-17 17:19:16 as along with 6 people and 2 groups operon gbloeb cambray druvus dchughes rebeccamancy G4ID Genetics-of-Gambling
	Occurrence and structure-function relationship of pentameric short sequence repeats in microbial genomes [My Copy] Research in Microbiology, Vol. 150, No. 9-10. (Nov 1999), pp. 617-626. by A. Vanbelkum posted to indel homopeptide complexity length low prokaryotes recombination repeats sequence by robfsouza on 2009-06-17 17:11:14 as along with 1 person nikkiwithers
	Selection on the genic location of disruptive elements [My Copy] Trends in Genetics, Vol. 23, No. 12. (Dec 2007), pp. 601-604. by M. Vanpassel, H. Ochman posted to indel homopeptide complexity evolution length low prokaryotes protein repeats sequence by robfsouza on 2009-06-17 16:52:05 as
	Synonymous Codon Usage in Escherichia coli: Selection for Translational Accuracy [My Copy] Molecular Biology and Evolution, Vol. 24, No. 2. (Feb 2007), pp. 374-381. by Stoletzki, Nina, Eyre-Walker, Adam posted to bias codon correlation evolution length protein sequence by robfsouza on 2009-06-17 16:04:16 as along with 5 people operon michaelbarton smbe2008 gjuggler bpcusack

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protein	154
evolution	143
aravind	65
sequence	62
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phosphotyrosine	1
phylosophy	1
physiological	1
pipeline	1
plasmodium	1
platypus	1
polarity	1
polymerases	1
posttranslational	1
predictive	1
primase	1
primers	1
programming	1
progression	1
protease	1
proteome	1
protozoa	1
punctuated	1
pupylation	1
rab1	1
reaction	1
rearrangement	1
recognition	1
reconstruction	1
regression	1
remodeling	1
repeat	1
repetitive	1
resolvases	1
retrotransposon	1
retroviruses	1
ribosomes	1
rnase	1
robustness	1
rotifera	1
r-package	1
rrna	1
self-organization	1
single-stranded	1
sirna	1
site-directed	1
skates	1
small	1
somatic	1
speciation	1
splicing	1
stability	1
states	1
static	1
statistical	1
steroid	1
stoichiometry	1
strand	1
stress	1
suchard	1
suppressor	1
synechococcus	1
synteny	1
synthetic	1
technology	1
telomere	1
temperature	1
terminal	1
theorem	1
topology	1
transglutaminase	1
transposases	1
tree	1
tutorial	1
uncertainty	1
vertebrates	1
vesicular	1
videos	1
yeast	1
zinc-finger	1

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