Tag motifs [at least 200 articles] Export

Recent papers classified by the tag motifs.

	The small world of the cerebral cortex. [My Copy] Neuroinformatics, Vol. 2, No. 2. (2004), pp. 145-162. by Olaf Sporns, Jonathan D. Zwi posted to path_length organizational_principles organizational_features motifs graph_theory graph functional_brain cerebral_cortex brain_areas brain_anatomy by winterstream on 2009-11-09 16:36:22 as along with 8 people and 1 group pbellec mague balicea AbnerCYH xinian jmarcelino lilith ebalp 8_01
	Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling [My Copy] Vol. 139, No. 3. (30 October 2009), pp. 610-622. by Shaohui Hu, Zhi Xie, Akishi Onishi, et al.Xueping Yu, Lizhi Jiang, Jimmy Lin, Hee-sool Rho, Crystal Woodard, Hong Wang, Jun-Seop Jeong, Shunyou Long, Xiaofei He, Herschel Wade, Seth Blackshaw, Jiang Qian, Heng Zhu posted to specificity protein-dna-interactions motifs human data by pedrobeltrao on 2009-10-29 17:51:32 as along with 2 people and 1 group snow_dragon daveGerrard BergmanLab
	Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network [My Copy] Journal of Biology, Vol. 4, No. 2. (2005), 6. by Lan Zhang, Oliver King, Sharyl Wong, et al.Debra Goldberg, Amy Tong, Guillaume Lesage, Brenda Andrews, Howard Bussey, Charles Boone, Frederick Roth posted to readlater networks motifs genetic-interactions by colmryan on 2009-10-27 17:39:13 as along with 11 people and 1 group lfriedl marcora jjray ssb benny nirfriedman koller iris_2001 gwcarter carlk ksiek kdl
	Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse [My Copy] Vol. 17, No. 4. (20 October 2009), pp. 568-579. by Miriam R. Kantorovitz, Majid Kazemian, Sarah Kinston, et al.Diego Miranda-Saavedra, Qiyun Zhu, Gene E. Robinson, Berthold Göttgens, Marc S. Halfon, Saurabh Sinha posted to tools tfbs prediction motifs motif-discovery algorithm by isimpson on 2009-10-27 14:16:21 as along with 1 person and 1 group daveGerrard BergmanLab
	Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins [My Copy] PLoS Biology, Vol. 7, No. 10. (20 October 2009), e1000218. by Raffi Tonikian, Xiaofeng Xin, Christopher P. Toret, et al.David Gfeller, Christiane Landgraf, Simona Panni, Serena Paoluzi, Luisa Castagnoli, Bridget Currell, Somasekar Seshagiri, Haiyuan Yu, Barbara Winsor, Marc Vidal, Mark B. Gerstein, Gary D. Bader, Rudolf Volkmer, Gianni Cesareni, David G. Drubin, Philip M. Kim, Sachdev S. Sidhu, Charles Boone posted to specificity sh3 scerevisiae motifs data bioinformatics by pedrobeltrao on 2009-10-21 21:45:29 as along with 2 people venancio cabbagesofdoom
	How curved membranes recruit amphipathic helices and protein anchoring motifs [My Copy] Nat Chem Biol, Vol. 5, No. 11. (13 September 2009), pp. 835-841. by Nikos S. Hatzakis, Vikram K. Bhatia, Jannik Larsen, et al.Kenneth L. Madsen, Pierre-Yves Bolinger, Andreas H. Kunding, John Castillo, Ulrik Gether, Per Hedegard, Dimitrios Stamou posted to recruit motifs membrane helices hatzak09pdf curvature anchoring amphipathic by paulschlesinger on 2009-10-20 02:18:56 as along with 4 people cjryan amphibina bertelsen samjlord
	info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2715-2722. by Matthieu Defrance, Jacques van Helden posted to motifs by TRHvidsten on 2009-10-09 13:17:25 as along with 3 people maximilianh natstreet nuin
	Genomic DNA k-mer spectra: models and modalities [My Copy] Genome Biology, Vol. 10, No. 10. (2009), R108. by Benny Chor, David Horn, Yaron Levy, Nick Goldman, Tim Massingham posted to motifs by TRHvidsten on 2009-10-09 12:08:57 as along with 3 people and 1 group djkt medic0747 gjuggler iSEEM
	Network Motifs: Simple Building Blocks of Complex Networks [My Copy] Science, Vol. 298, No. 5594. (25 October 2002), pp. 824-827. by R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon posted to systems-biology networks motifs gene bioinformatics by arsyed on 2009-09-25 03:35:27 as along with 69 people and 9 groups nurban balabu ocs mjoach makrehchi schwartzjmc poirel tomhebbron vtraag sergiun fierykylin Akimasa operon dlobo daforerog chasmand wei_tang darian orahcio babakap brewbooks phoenixzxl Md_2007 mtagaya heliopais kaarsinogen galyardt cswinburne mullonc camster korakot aalibes ChaTo imouthesmp Borelli lfriedl alexg balicea tny ssb wnpx ddahlem cmm donade neveaire griota gurkanbebek jtaylor josepe iris_2001 michaelmampaey rebeccamancy karfunkel lenov Evangelia roys tfogal zibuyu maralena stefanoallesina pbull cmor renatomilani shikin carlk applesnow subhacom i-stevenson ethkim GEB Philosophy_of_Information dbk-lab Blog_and_Wiki_Research kdl FAB-lab ColDyn ADMiRes GeneGo
	A proposed syntax for Minimotif Semantics, version 1 [My Copy] BMC Genomics, Vol. 10, No. 1. (2009), 360. by Jay Vyas, Ronald Nowling, Mark Maciejewski, Sanguthevar Rajasekaran, Michael Gryk, Martin Schiller posted to semantics motifs by nuin on 2009-09-22 14:50:03 as
	Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2473-2477. by Antonio Marco, Charlotte Konikoff, Timothy L. Karr, Sudhir Kumar posted to motifs expression by nuin on 2009-09-22 14:36:56 as along with 8 people and 1 group Garamonfok TRHvidsten djkt rdiaz natstreet sebastien_vigneau maximilianh isimpson Jarman Lab
	Motif discovery and motif finding from genome-mapped DNase footprint data. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 18. (15 September 2009), pp. 2318-2325. by Ivan V. Kulakovskiy, Alexander V. Favorov, Vsevolod J. Makeev posted to motifs finding by nuin on 2009-09-11 02:37:21 as along with 3 people operon maximilianh cisevol
	The mechanism of transport by mitochondrial carriers based on analysis of symmetry [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 46. (18 November 2008), pp. 17766-17771. by Alan J. Robinson, Catherine Overy, Edmund R. S. Kunji posted to uncoupling_proteins transporters transport_mechanism symmetry substrates substrate salt_bridge pnas motifs mitochondrial_matrix mitochondrial_carriers ions interaction_energies disruption coupling central_cavity bridge_network binding_site by girayenkavi on 2009-09-09 17:18:28 as along with 3 people ec430 martainn kshundyak
	Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics [My Copy] PLoS Comput Biol, Vol. 4, No. 3. (21 March 2008), e1000021. by Stephen A. Ramsey, Sandy L. Klemm, Daniel E. Zak, et al.Kathleen A. Kennedy, Vesteinn Thorsson, Bin Li, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Vladimir Litvak, Garnet Navarro, Jared C. Roach, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, Ilya Shmulevich posted to tfbs must-read motifs motif-discovery bayesian by isimpson to the group Jarman Lab on 2009-08-26 16:53:14 as along with 3 people nicholasflann talponer ptrobajo
	A data integration framework for prediction of transcription factor targets. [My Copy] Annals of the New York Academy of Sciences, Vol. 1158 (March 2009), pp. 205-214. by Matti Nykter, Harri Lähdesmäki, Alistair Rust, Vesteinn Thorsson, Ilya Shmulevich posted to tfbs must-read motifs motif-discovery bayesian by isimpson to the group Jarman Lab on 2009-08-26 16:53:14 as
	Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources [My Copy] PLoS ONE, Vol. 3, No. 3. (26 March 2008), e1820. by Harri Lähdesmäki, Alistair G. Rust, Ilya Shmulevich posted to tfbs software must-read motifs motif-discovery bayesian by isimpson to the group Jarman Lab on 2009-08-26 16:49:30 as along with 4 people nklee dolchan druvus guhjy
	Functional classification of proteins by pattern discovery and top-down clustering of primary sequences [My Copy] IBM Syst. J., Vol. 40, No. 2. (2001), pp. 379-393. by A. H. Liu, A. Califano posted to pattern-discovery motifs clustering by Dulce to the group Gene Regulation on 2009-08-25 17:06:06 as
	Genomic characterization of a repetitive motif strongly associated with developmental genes in Drosophila. [My Copy] BMC genomics, Vol. 4, No. 1. (16 December 2003) by Javier Costas, Cristina P. Vieira, Fernando Casares, Jorge Vieira posted to transcription-regulation motifs drosophila development by isimpson on 2009-08-21 09:44:03 as along with 1 person operon
	Integrin ligands at a glance. [My Copy] Journal of cell science, Vol. 119, No. Pt 19. (1 October 2006), pp. 3901-3903. by Jonathan D. Humphries, Adam Byron, Martin J. Humphries posted to motifs molecular models ligands integrins evolution biological amino acid by adambyron on 2009-08-21 09:20:32 as
	Detecting Subdimensional Motifs: An Efficient Algorithm for Generalized Multivariate Pattern Discovery [My Copy] Data Mining, 2007. ICDM 2007. Seventh IEEE International Conference on In Data Mining, 2007. ICDM 2007. Seventh IEEE International Conference on (2007), pp. 601-606. by D. Minnen, C. Isbell, M. Essa, T. Starner posted to motifs by pimmy on 2009-08-20 23:28:36 as along with 2 people wowalz cmoewes
	Detecting time series motifs under uniform scaling [My Copy] In KDD '07: Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining (2007), pp. 844-853. by Dragomir Yankov, Eamonn Keogh, Jose Medina, Bill Chiu, Victor Zordan posted to motifs by pimmy on 2009-08-20 23:17:33 as along with 2 people seninp cmoewes
	Partial elastic matching of time series [My Copy] Data Mining, Fifth IEEE International Conference on In Data Mining, Fifth IEEE International Conference on (2005), 4 pp.. by L. J. Latecki, V. Megalooikonomou, Qiang Wang, R. Lakaemper, C. A. Ratanamahatana, E. Keogh posted to motifs by pimmy on 2009-08-20 23:16:53 as
	Finding Motifs in Time Series [My Copy] (2002), pp. 53-68. by Jessica Lin, Eamonn Keogh, Stefano Lonardi, Pranav Patel posted to motifs by pimmy on 2009-08-20 23:15:25 as
	Detecting Motifs in System Call Sequences [My Copy] Information Security Applications In Information Security Applications, No. 4867. (2008), pp. 157-172. by William Wilson, Jan Feyereisl, Uwe Aickelin posted to motifs by pimmy on 2009-08-20 23:10:19 as along with 1 person thefillm
	Mining Motifs in Massive Time Series Databases [My Copy] In In Proceedings of IEEE International Conference on Data Mining (ICDM’02 (2002), pp. 370-377. by Pranav Patel, Eamonn Keogh, Jessica Lin, Stefano Lonardi posted to motifs by pimmy on 2009-08-20 23:09:28 as
	Discovery of Time-Series Motif from Multi-Dimensional Data Based on MDL Principle [My Copy] Machine Learning, Vol. 58, No. 2. (1 February 2005), pp. 269-300. by Yoshiki Tanaka, Kazuhisa Iwamoto, Kuniaki Uehara posted to motifs by pimmy on 2009-08-20 23:01:43 as along with 3 people cmoewes jaberg balicea
	CEAS: cis-regulatory element annotation system [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2605-2606. by Hyunjin Shin, Tao Liu, Arjun K. Manrai, X. Shirley Liu posted to motifs annotation by nuin on 2009-08-20 22:05:32 as along with 5 people maximilianh druvus ewilban1 guhjy idonaldson
	A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles [My Copy] Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2006-2012. by Yanglan Gan, Jihong Guan, Shuigeng Zhou posted to motifs by TRHvidsten on 2009-08-09 13:14:49 as along with 2 people junehlee sriesenfeld
	Statistical detection of cooperative transcription factors with similarity adjustment [My Copy] Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2103-2109. by Utz J. Pape, Holger Klein, Martin Vingron posted to motifs by TRHvidsten on 2009-08-09 13:10:42 as along with 2 people idonaldson djkt
	ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs [My Copy] Bioinformatics (14 July 2009), btp424. by J. A. Encinar, G. Fernandez-Ballester, I. E. Sanchez, et al.E. Hurtado-Gomez, F. Stricher, P. Beltrao, L. Serrano posted to database domain interaction motifs prediction protein by robfsouza on 2009-08-06 01:53:27 as along with 1 person neils
	Conservation and topology of protein interaction networks under duplication-divergence evolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 29. (22 July 2008), pp. 9863-9868. by Kirill Evlampiev, Hervé Isambert posted to evolution model_based motifs time_machine by saket on 2009-08-04 21:41:32 as along with 3 people winterschlaefer Garamonfok bpcusack
	Aggregation-Prone Motifs in Human Immunoglobulin G. [My Copy] Journal of molecular biology (13 June 2009) by Naresh Chennamsetty, Bernhard Helk, Vladimir Voynov, Veysel Kayser, Bernhardt L. Trout posted to aggregation immunoglobulin motifs by marti on 2009-07-15 15:47:13 as
	NestedMICA as an ab initio protein motif discovery tool. [My Copy] BMC bioinformatics, Vol. 9 (14 January 2008), 19. by Mutlu Doğruel, Thomas A. Down, Tim Jp J. Hubbard posted to machine_learning motifs tjph by timhubbard on 2009-07-13 21:30:05 as along with 1 person idonaldson
	Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster [My Copy] PLoS Comput Biol, Vol. 3, No. 1. (19 January 2007), e7. by Thomas A. Down, Casey M. Bergman, Jing Su, Tim J. P. Hubbard posted to machine_learning motifs tjph by timhubbard on 2009-07-13 21:24:40 as along with 11 people and 1 group daveGerrard ychromosome lusk wowalz indigoviolet dpollard dquest SeungjoonOh nklee emptyhb isimpson EisenLab
	A machine learning strategy to identify candidate binding sites in human protein-coding sequence. [My Copy] BMC bioinformatics, Vol. 7 (26 September 2006), 419. by T. Down, B. Leong, T. J. Hubbard posted to machine_learning motifs tjph by timhubbard on 2009-07-13 21:21:20 as along with 1 person gpalidwor
	Conservation of Palindromic and Mirror Motifs within Inverted Terminal Repeats of mariner-like Elements [My Copy] Journal of Molecular Biology, Vol. 351, No. 1. (05 August 2005), pp. 108-116. by Yves Bigot, Benjamin Brillet, Corinne Augé-Gouillou posted to mariner-like motifs tirs by gwallau on 2009-07-13 20:39:19 as
	NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. [My Copy] Nucleic acids research, Vol. 33, No. 5. (2005), pp. 1445-1453. by T. A. Down, T. J. Hubbard posted to motifs machine_learning tjph by timhubbard on 2009-07-13 08:47:59 as along with 5 people and 1 group emptyhb lyongu dpollard dquest waszak EisenLab
	Computing paths and cycles in biological interaction graphs [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 181. by Steffen Klamt, Axel von Kamp posted to approximations attractors biological-networks biological-systems cellnetanalyzer computational-systems-biology extremal-biology interaction-graphs motifs network-analysis reconstructing by Scis0000002 on 2009-07-05 08:33:57 as along with 4 people rdiaz barriot imina shikin
	Finding sequence motifs in prokaryotic genomes--a brief practical guide for a microbiologist [My Copy] Brief Bioinform, Vol. 10, No. 5. (24 June 2009), pp. bbp032-536. by Jan Mrazek posted to identification motifs by nuin on 2009-07-03 23:06:22 as along with 4 people Vincent_Rouilly reyez nyyu druvus
	Antibody Responses Are Generated to Immunodominant ELK/KLE-Type Motifs on the Nonstructural-1 Glycoprotein during Live Dengue Virus Infections in Mice and Humans: Implications for Diagnosis, Pathogenesis, and Vaccine Design [My Copy] Clinical and Vaccine Immunology, Vol. 14, No. 5., pp. 493-504. by A. K. I. Falconar posted to antibody dengue motifs ns1 by feltesm on 2009-07-01 23:07:41 as
	Structural motifs recurring in different folds recognize the same ligand fragments [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 182. by Gabriele Ausiello, Pier Gherardini, Elena Gatti, Ottaviano Incani, Manuela H. Citterich posted to binding function ligand motifs protein structure by neils on 2009-06-16 00:30:24 as along with 5 people and 2 groups cdsouthan sillitoe VGreiff TRHvidsten reyez Orengo Group Journal Picks Journal picks
	A survey of motif discovery methods in an integrated framework [My Copy] Biology Direct, Vol. 1, No. 1. (06 April 2006), 11. by Geir K. Sandve, Finn Drabløs posted to motifs by Scis0000002 on 2009-06-13 09:50:43 as along with 11 people and 1 group tomhebbron maximilianh wowalz AbnerCYH aprasad dpollard samal yevishere csdhwang idonaldson yoonk EisenLab
	Automatic annotation of protein motif function with Gene Ontology terms. [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (2 September 2004) by X. Lu, C. Zhai, V. Gopalakrishnan, B. G. Buchanan posted to annotating motifs ontologies proteins by Scis0000002 on 2009-06-13 09:47:16 as along with 1 person ziquje
	Identifying regulatory elements in eukaryotic genomes [My Copy] Brief Funct Genomic Proteomic, Vol. 8, No. 4. (1 July 2009), pp. 215-230. by Leelavati Narlikar, Ivan Ovcharenko posted to crm motifs review by idonaldson on 2009-06-08 16:56:05 as along with 3 people and 1 group daveGerrard ppgardne natstreet Journal picks
	Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W247-252. by Federico Zambelli, Graziano Pesole, Giulio Pavesi posted to motifs search by nuin on 2009-06-05 17:59:30 as along with 5 people druvus natstreet idonaldson nklee isimpson
	Efficient exact motif discovery. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. i356-364. by T. Marschall, S. Rahmann posted to discovery motifs by nuin on 2009-06-02 18:19:20 as along with 4 people wowalz dquest idonaldson maximilianh
	Assessing phylogenetic motif models for predicting transcription factor binding sites [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i339-347. by John Hawkins, Charles Grant, William S. Noble, Timothy L. Bailey posted to motifs phylogenetics prediction by nuin on 2009-06-02 18:17:52 as along with 8 people and 3 groups dquest Stew marti Lombardo_7 megraw operon AlexBateman scjparker EisenLab Bioinformatics - CRUK Journal picks
	Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Handling Counterintuitive Results [My Copy] Journal of Molecular Evolution by James Balmer, Rune Blomhoff posted to evolution motifs by nuin on 2009-06-02 18:14:22 as along with 3 people and 1 group leemond31 cisevol maximilianh cis-regulatory-evolution
	seeMotif: exploring and visualizing sequence motifs in 3D structures [My Copy] Nucl. Acids Res. (28 May 2009), gkp439. by Darby T. Chang, Ting-Ying Chien, Chien-Yu Chen posted to motifs visualization by nuin on 2009-06-02 18:13:25 as
	Clustering protein environments for function prediction: finding PROSITE motifs in 3D [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 4. (2007), S10. by Sungroh Yoon, Jessica Ebert, Eui Y. Chung, Giovanni De Micheli, Russ Altman posted to function_prediction functional_sites machine_learning motifs protein_structure by iaolier on 2009-06-02 15:53:59 as along with 3 people and 1 group HawkinsJohnC shadowman Einat structural_bioinformatics

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networks	111
bioinformatics	28
network	27
protein	24
review	23
prediction	20
evolution	18
motif-discovery	17
linear	16
rna	16
identification	15
peptides	15
domains	14
structure	14
tfbs	14
tools	14
algorithm	13
algorithms	13
database	12
software	12
must-read	11
binding	10
mining	10
protein_structure	10
rev_ref	10
senior-project	10
transcription	10
dynamics	9
interaction	9
regulation	9
clustering	8
detection	8
discovery	8
ppi	8
promoter	8
signaling	8
transcription-regulation	7
bayesian	6
conservation	6
dna	6
domain	6
from-kell	6
interactions	6
logic	6
machine_learning	6
methods	6
neural	6
search	6
sequence	6
motif	5
position	5
protein-protein	5
specificity	5
yeast	5
bigmotifs	4
brain	4
comment	4
comparison	4
computational	4
expression-regulation	4
finding	4
function_prediction	4
htp	4
mirna	4
mouse	4
nanobiology	4
patterns	4
protein-families	4
secondary-structure	4
server	4
statistics	4
sysbio	4
tjph	4
visualization	4
alignment	3
analysis	3
binding_site	3
cyclic	3
data	3
drosophila	3
elements	3
factor	3
feedback	3
function	3
gibbs	3
language	3
mammalian	3
modular	3
modularity	3
original	3
pathway	3
pathways	3
proline-rich	3
sequence-structure	3
series	3
sh3	3
similarity	3
solved	3
time	3
transcription_factor	3

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