Tag motif [at least 200 articles] Export

Recent papers classified by the tag motif.

	Combinatorial binding predicts spatio-temporal cis-regulatory activity [My Copy] Nature, Vol. 462, No. 7269. (05 November 2009), pp. 65-70. by Robert P. Zinzen, Charles Girardot, Julien Gagneur, Martina Braun, Eileen E. M. Furlong posted to network motif integration by fenghezi on 2009-11-06 19:58:32 as along with 7 people inesdesantiago balabu iskathy djkt megraw TRHvidsten pedrobeltrao
	Identification of a target RNA motif for RNA-binding protein HuR [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 9. (2 March 2004), pp. 2987-2992. by Isabel L. de Silanes, Ming Zhan, Ashish Lal, Xiaoling Yang, Myriam Gorospe posted to rna_binding_protein posttranscriptional_regulator motif hur by tonamswish on 2009-11-06 14:55:14 as along with 1 person hcoller
	Noise-induced dynamics in the mixed-feedback-loop network motif [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 77, No. 1. (2008), 011903. by Difei Li, Chunguang Li posted to stochastic-resonance stochastic nonlinear noise network motif genetic feedback dynamics biology by nurban on 2009-11-02 22:05:28 as
	Network motifs in integrated cellular networks of transcriptionâregulation and proteinâprotein interaction [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 16. (20 April 2004), pp. 5934-5939. by Esti Yeger-Lotem, Shmuel Sattath, Nadav Kashtan, et al.Shalev Itzkovitz, Ron Milo, Ron Y. Pinter, Uri Alon, Hanah Margalit posted to network motif genetic feedback dynamics biology by nurban on 2009-11-02 22:04:35 as along with 12 people and 4 groups sergiun cswinburne camster snuppepuppan dbk korakot LeightonP hununu jtextori koller maralena carlk streptomyces Philosophy_of_Information dbk-lab Blog_and_Wiki_Research
	Network motifs: theory and experimental approaches [My Copy] Nature Reviews Genetics, Vol. 8, No. 6. (01 June 2007), pp. 450-461. by Uri Alon posted to review neural network motif genetic biology by nurban on 2009-11-02 22:03:18 as along with 31 people and 4 groups mjoach vtraag mlee1 myzhang hkuhn mtagaya cambray dswan renatomilani heliopais snow_dragon druvus pengchy cswinburne dlobo kentz icases aalibes cmmorel jtaylor dbikard margaritis shigepong zwang grinfish Pascalichouchou xingxu karfunkel vietanh0 haarcuba Borelli GEB TNT Centre de Recherches Interdisciplinaires SynBioSys
	Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking [My Copy] Research in Computational Molecular Biology (2007), pp. 92-106. by Joshua Grochow, Manolis Kellis posted to symmetry network motif detection by nurban on 2009-11-02 22:02:51 as along with 4 people saket mjoach tmmurali carlk
	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 network motif by nurban on 2009-11-02 21:59:34 as along with 69 people and 9 groups balabu ocs mjoach makrehchi schwartzjmc poirel tomhebbron arsyed 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
	Conserved network motifs allow protein-protein interaction prediction [My Copy] Bioinformatics, Vol. 20, No. 18. (12 December 2004), pp. 3346-3352. by Istvan Albert, Reka Albert posted to prediction network motif microbiology genetic dynamics biology by nurban on 2009-11-02 21:55:18 as along with 4 people jperkins cjeans Evangelia iris_2001
	Structure and function of the feed-forward loop network motif [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 21. (14 October 2003), pp. 11980-11985. by S. Mangan, U. Alon posted to network motif microbiology genetic feedback dynamics by nurban on 2009-11-02 21:46:49 as along with 14 people and 3 groups kaarsinogen camster rklancer korakot zqshen jstajic jjray alexg balicea ddahlem jtaylor gcalda marck hannahrajasingh Philosophy_of_Information dbk-lab Blog_and_Wiki_Research
	Distinguishing direct versus indirect transcription factorâDNA interactions [My Copy] Genome Research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca GordÃ¢n, Alexander J. Hartemink, Martha L. Bulyk posted to tf motif chip-chip by djkt on 2009-11-02 18:17:10 as along with 9 people vingron venancio owhitney tmmurali emptyhb idonaldson maximilianh jbhiatt frohike
	An ensemble model of competitive multi-factor binding of the genome [My Copy] Genome Research, Vol. 19, No. 11. (31 November 2009), pp. 2101-2112. by Todd Wasson, Alexander J. Hartemink posted to tf proteins motif by djkt on 2009-11-02 18:15:45 as along with 6 people megraw vingron xianjun owhitney bpcusack natstreet
	Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets. [My Copy] Genome research (14 April 2008) by Chaim Linhart, Yonit Halperin, Ron Shamir posted to transcription platform motif microrna metazoan factor discovery amadeus by dolchan on 2009-10-29 17:18:03 as along with 12 people and 1 group akshayk wowalz natstreet valeriehilgers jfr ealloza idonaldson maralena fpattyn isimpson tmmurali maximilianh BergmanLab
	Exhaustive search for over-represented DNA sequence motifs with CisFinder. [My Copy] DNA research : an international journal for rapid publication of reports on genes and genomes, Vol. 16, No. 5. (9 October 2009), pp. 261-273. by Alexei A. Sharov, Minoru S. Ko posted to word transcription-factor tf motif k-word ctcf consensus binding-site binding-motif binding by sebastien_vigneau to the group CTCF on 2009-10-28 22:59:36 as along with 2 people and 1 group operon polivares BergmanLab
	The value of prior knowledge in discovering motifs with MEME. [My Copy] Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, Vol. 3 (1995), pp. 21-29. by T. L. Bailey, C. Elkan posted to motif meme em by Mehlhorn on 2009-10-28 16:32:14 as along with 3 people wowalz AaronDarling noano
	Performance Evaluation for Motif-Based Patterned Texture Defect Detection [My Copy] Automation Science and Engineering, IEEE Transactions on, Vol. PP, No. 99. (09 December 2008), 1. by H. Y. T. Ngan, G. K. H. Pang, N. H. C. Yung posted to texture motif fabric_inspection defect_detection by corgan on 2009-10-28 13:53:42 as
	Patterned Fabric Defect Detection using a Motif-Based Approach [My Copy] Image Processing, 2007. ICIP 2007. IEEE International Conference on, Vol. 2 (12 November 2007), pp. II - 33-II - 36. by H. Y. T. Ngan, G. K. H. Pang, N. H. C. Yung posted to wallpaper motif fabric_inspection defect_detection by corgan on 2009-10-28 13:43:45 as
	Motif-based defect detection for patterned fabric [My Copy] Pattern Recognition, Vol. 41, No. 6. (June 2008), pp. 1878-1894. by H. Ngan, G. Pang, N. Yung posted to wallpaper texture motif fabric_inspection defect_detection by corgan on 2009-10-28 13:40:32 as
	MEME SUITE: tools for motif discovery and searching [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W202-208. by Timothy L. Bailey, Mikael Boden, Fabian A. Buske, et al.Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble posted to tfbs motif bioinformatics 2009 by suizifish on 2009-10-28 05:55:27 as along with 6 people jlike maximilianh natstreet idonaldson nuin cassj
	Associating transcription factor-binding site motifs with target GO terms and target genes [My Copy] Nucl. Acids Res. (10 June 2008), gkn374. by Mikael Boden, Timothy L. Bailey posted to tfbs tf motif bioinformatics 2008 by suizifish on 2009-10-28 05:49:05 as along with 5 people aramesh2 mikaelboden maximilianh guhjy dgroth
	Diabetes mellitus due to misfolding of a beta-cell transcription factor: stereospecific frustration of a Schellman motif in HNF-1alpha. [My Copy] Journal of molecular biology, Vol. 362, No. 3. (22 September 2006), pp. 414-429. by Narendra Narayana, Nelson B. Phillips, Qing-xin X. Hua, Wenhua Jia, Michael A. Weiss posted to transcription schellman naraya06pdf motif hnf-1a frustration factor by paulschlesinger on 2009-10-27 23:08:48 as
	Exploiting structural and topological information to improve prediction of RNA-protein binding sites. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (18 October 2009), 341. by Stefan R. Maetschke, Zheng Yuan posted to sites rna protein prediction motif binding by jlike on 2009-10-23 14:05:03 as along with 3 people and 1 group sillitoe reyez heliopais Orengo Group Journal Picks
	Different gene regulation strategies revealed by analysis of binding motifs [My Copy] Trends in Genetics, Vol. 25, No. 10. (06 October 2009), pp. 434-440. by Zeba Wunderlich, Leonid A. Mirny posted to tf motif expression by djkt to the group iSEEM on 2009-10-21 18:50:54 as along with 2 people francemirko behindtherabbit
	Assortative Mixing in Networks [My Copy] Physical Review Letters, Vol. 89, No. 20. (28 Oct 2002), 208701. by M. E. J. Newman posted to topology technological_network social_network network motif data biological_network assortativity by tomhebbron on 2009-10-21 11:29:55 as along with 11 people andreacapocci ganden s25060331s kubyaddi Kovanen muraken jmenche ChaTo nolodie chibatching ddahlem
	Finding community structure in networks using the eigenvectors of matrices [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 74, No. 3. (2006), 036104. by M. E. J. Newman posted to topology network motif modularity algorithm by tomhebbron on 2009-10-21 11:28:20 as along with 9 people and 1 group AaronMcDaid lawraga studentx vtraag muraken cgaugain bigbossman hannu Diego_Prada ThinkTank
	Gene networks and liar paradoxes [My Copy] BioEssays, Vol. 31, No. 10. (31 August 2009), pp. 1110-1115. by Mark Isalan posted to topology motif logic liar_paradox genome gene_regulatory_networks feedback by tomhebbron on 2009-10-20 09:51:39 as along with 1 person VGreiff
	Quantifying similarity between motifs [My Copy] Genome Biology, Vol. 8, No. 2. (26 February 2007), R24. by Shobhit Gupta, John Stamatoyannopoulos, Timothy Bailey, William Noble posted to similarity motif by jlike on 2009-10-19 15:13:42 as along with 6 people and 1 group Dulce maximilianh cwbrown grahamc nklee gracio EisenLab
	Detailing regulatory networks through large scale data integration [My Copy] Bioinformatics (13 October 2009), btp588. by Curtis Huttenhower, K. Tsheko Mutungu, Natasha Indik, et al.Woongcheol Yang, Mark Schroeder, Joshua J. Forman, Olga G. Troyanskaya, Hilary A. Coller posted to motif module e-coli data_integration biclustering bayesian_integration by frohike on 2009-10-14 11:08:07 as along with 4 people aaron_webber zufar ptrobajo rdiaz
	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 motif discovery by maximilianh on 2009-10-13 11:41:24 as along with 3 people TRHvidsten natstreet nuin
	Metabolic pathfinding using RPAIR annotation. [My Copy] Journal of molecular biology, Vol. 388, No. 2. (1 May 2009), pp. 390-414. by Karoline Faust, Didier Croes, Jacques van Helden posted to pathway motif metabolomics by druvus on 2009-10-12 17:12:22 as along with 1 person ptrobajo
	Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules [My Copy] Nature Protocols, Vol. 3, No. 10. (18 September 2008), pp. 1578-1588. by Jean-Valery Turatsinze, Morgane Thomas-Chollier, Matthieu Defrance, Jacques van Helden posted to tf motif genome cis by druvus on 2009-10-12 17:01:52 as along with 5 people and 1 group heliopais fhsantanna polivares idonaldson natstreet BergmanLab
	Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences [My Copy] Nature Protocols, Vol. 3, No. 10. (18 September 2008), pp. 1589-1603. by Matthieu Defrance, Rekin's Janky, Olivier Sand, Jacques van Helden posted to sequence oligo motif by druvus on 2009-10-12 17:01:27 as along with 2 people and 1 group polivares natstreet BergmanLab
	Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services\|[mdash]\|an example with ChIP-chip data [My Copy] Nature Protocols, Vol. 3, No. 10. (18 September 2008), pp. 1604-1615. by Olivier Sand, Morgane Thomas-Chollier, Eric Vervisch, Jacques van Helden posted to web_services soap motif by druvus on 2009-10-12 17:00:58 as along with 1 person and 1 group polivares BergmanLab
	Word-based characterization of promoters involved in human DNA repair pathways [My Copy] BMC Genomics, Vol. 10, No. Suppl 1. (2009), S18. by Jens Lichtenberg, Edwin Jacox, Joshua Welch, et al.Kyle Kurz, Xiaoyu Liang, Mary Yang, Frank Drews, Klaus Ecker, Stephen Lee, Laura Elnitski, Lonnie Welch posted to word_clusters transfac signature regulatory_networks regulatory_factors regulatory_aspects regulatory promoters promoter_sequences promoter_regions pattern motif jaspar human_dna_repair genomic functional_elements dna_sequences dna_repair_pathways dna_repair_genes dna_damage discovery bidirectional by lichtenj on 2009-10-12 13:24:11 as
	The word landscape of the non-coding segments of the Arabidopsis thaliana genome [My Copy] BMC Genomics, Vol. 10, No. 1. (08 October 2009), 463. by Jens Lichtenberg, Alper Yilmaz, Joshua Welch, et al.Kyle Kurz, Xiaoyu Liang, Frank Drews, Klaus Ecker, Stephen Lee, Matt Geisler, Erich Grotewold, Lonnie Welch posted to signature regulatory pattern motif genomic discovery arabidopsis by lichtenj on 2009-10-12 13:22:12 as along with 2 people druvus natstreet
	HMM-based databases in InterPro [My Copy] Brief Bioinform, Vol. 3, No. 3. (1 January 2002), pp. 236-245. by Alex Bateman, Daniel H. Haft posted to signature protein pattern motif interproscan hmm domain database databank bank annotation by nlapalu on 2009-10-09 16:46:40 as
	Applications of InterPro in protein annotation and genome analysis [My Copy] Brief Bioinform, Vol. 3, No. 3. (1 January 2002), pp. 285-295. by Margaret Biswas, John F. O'Rourke, Evelyn Camon, et al.Gill Fraser, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia Kriventseva, Virginie Mittard, Nicola Mulder, Isabelle Phan, Florence Servant, Rolf Apweiler posted to signature prosite prediction pattern motif interproscan functional domain database databank annotation by nlapalu on 2009-10-09 16:43:47 as
	ProRule: a new database containing functional and structural information on PROSITE profiles [My Copy] Bioinformatics, Vol. 21, No. 21. (1 November 2005), pp. 4060-4066. by Christian J. A. Sigrist, Edouard De Castro, Petra S. Langendijk-Genevaux, Virginie Le Saux, Amos Bairoch, Nicolas Hulo posted to signature protein prosite pattern motif functional domain database databank bank by nlapalu on 2009-10-09 16:41:31 as
	ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins [My Copy] Nucl. Acids Res., Vol. 34, No. suppl_2. (1 July 2006), pp. W362-365. by Edouard de Castro, Christian J. A. Sigrist, Alexandre Gattiker, et al.Virginie Bulliard, Petra S. Langendijk-Genevaux, Elisabeth Gasteiger, Amos Bairoch, Nicolas Hulo posted to signature protein prosite pattern motif functional database databank bank by nlapalu on 2009-10-09 16:39:14 as along with 3 people Copper_Calcio niallhaslam fbristow
	PROSITE: A documented database using patterns and profiles as motif descriptors [My Copy] Brief Bioinform, Vol. 3, No. 3. (1 January 2002), pp. 265-274. by Christian J. A. Sigrist, Lorenzo Cerutti, Nicolas Hulo, et al.Alexandre Gattiker, Laurent Falquet, Marco Pagni, Amos Bairoch, Philipp Bucher posted to protein prosite pattern motif functional domain database databank bank by nlapalu on 2009-10-09 16:37:11 as along with 4 people jwm siebertm shung jteyra
	TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2625-2631. by Sanghamitra Bandyopadhyay, Ramkrishna Mitra posted to rna motif by djkt on 2009-10-09 16:36:18 as along with 8 people and 2 groups jforment heliopais dswan reyez morrislab TRHvidsten guhjy frohike Bioinformatics Core Service microRNA
	A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation [My Copy] Nucl. Acids Res. (28 September 2009), gkp668. by Thomas Geissmann, Clement Chevalier, Marie-Josee Cros, et al.Sandrine Boisset, Pierre Fechter, Celine Noirot, Jacques Schrenzel, Patrice Francois, Francois Vandenesch, Christine Gaspin, Pascale Romby posted to staphylococcus small sequence rnas noncoding motif conserved bioinformatics aureus by Winzer on 2009-10-09 14:56:19 as along with 1 person and 1 group ppgardne Journal picks
	Discovering multiple realistic TFBS motifs based on a generalized model. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (7 October 2009), 321. by Tak-Ming M. Chan, Gang Li, Kwong-Sak S. Leung, Kin-Hong H. Lee posted to motif discovery by maximilianh on 2009-10-09 11:30:08 as along with 2 people idonaldson ashishanand
	Efficient computation of absent words in genomic sequences [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (26 March 2008), 167. by Julia Herold, Stefan Kurtz, Robert Giegerich posted to suffix_trees repeats regulatory motif metrics genomics genome computational bioinformatics algorithms by kmdaily on 2009-10-08 22:51:06 as along with 3 people operon xili03 langmead
	W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high throughput data [My Copy] Bioinformatics (1 October 2009), btp570. by Victor X. Jin, Jeff Apostolos, Naga S. Nagisetty, Peggy J. Farnham posted to motif chip by nklee on 2009-10-08 10:06:32 as along with 1 person maximilianh
	The 20 years of PROSITE [My Copy] Nucl. Acids Res., Vol. 36, No. Database issue. (14 November 2007), gkm977. by Nicolas Hulo, Amos Bairoch, Virginie Bulliard, et al.Lorenzo Cerutti, Beatrice A. Cuche, Edouard Castro, Corinne Lachaize, Petra S. Langendijk-Genevaux, Christian J. A. Sigrist posted to signature prosite motif domain database databank bank by nlapalu on 2009-10-07 17:47:20 as along with 7 people Zoltan_Barczikay fbristow ojabado reyez dullhunk hplatero Evangelia
	Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (21 August 2009), e1000475. by Joost Van Durme, Sebastian Maurer-Stroh, Rodrigo Gallardo, Hannah Wilkinson, Frederic Rousseau, Joost Schymkowitz posted to substrate_recognition sep09 protein plos motif homology dnak binding by klexa on 2009-10-07 14:07:50 as along with 2 people pansapiens biomcgary
	Residues of 14-3-3 zeta required for activation of exoenzyme S of Pseudomonas aeruginosa. [My Copy] Biochemistry, Vol. 38, No. 37. (14 September 1999), pp. 12159-12164. by L. Zhang, H. Wang, S. C. Masters, B. Wang, J. T. Barbieri, H. Fu posted to motif exos binding 14-3-3zeta by nns1987 on 2009-10-06 10:36:59 as
	D-MATRIX: A web tool for constructing weight matrix of conserved DNA motifs. [My Copy] Bioinformation, Vol. 3, No. 10. (2009), pp. 415-418. by Naresh Sen, Manoj Mishra, Feroz Khan, Abha Meena, Ashok Sharma posted to websites tools motif by maximilianh on 2009-10-05 19:09:34 as
	A common sequence motif associated with recombination hot spots and genome instability in humans. [My Copy] Nature genetics, Vol. 40, No. 9. (September 2008), pp. 1124-1129. by Simon Myers, Colin Freeman, Adam Auton, Peter Donnelly, Gil McVean posted to recombination pwm prdm6 motif insability human hot_spot genome by Stew to the group Bioinformatics - CRUK on 2009-10-02 10:53:55 as along with 1 person bpcusack
	Understanding hydrogen-bond patterns in proteins using network motifs [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 2921-2928. by Ofer Rahat, Uri Alon, Yaakov Levy, Gideon Schreiber posted to protein network motif chemistry by tomhebbron on 2009-10-01 13:08:47 as along with 4 people VGreiff zwang scmelton phoenixzxl

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discovery	133
network	115
rna	62
bioinformatics	60
prediction	59
transcription	55
protein	52
regulation	51
sequence	50
structure	47
promoter	46
evolution	45
tfbs	45
tf	44
binding	42
genome	40
algorithm	39
review	38
conserved	30
regulatory	30
expression	29
yeast	26
targeting	25
genomics	24
pattern	22
search	22
structural_biology	20
clustering	19
combination	19
database	19
detection	19
dna	19
interaction	19
microarray	19
software	19
alignment	17
finding	16
conservation	15
human	15
scanning	15
somatodendritic	15
axon	14
biology	14
domain	14
gene	14
pwm	14
function	13
methods	13
ribosome	13
arabidopsis	12
complex	12
method	12
microrna	12
analysis	11
chromatin	11
de-novo	11
factor	11
module	11
computational	10
dendrites	10
development	10
drosophila	10
eisen_journal_club	10
enhancers	10
ion-channels	10
ppi	10
round_robin	10
splicing	10
algorithms	9
ctcf	9
ncrna	9
peptide	9
tool	9
tools	9
bayesian	8
chip	8
chip-chip	8
crm	8
functional	8
geneexp	8
mirna	8
signature	8
site	8
2004	7
_edc	7
ais	7
comparative	7
dynamics	7
elm	7
enhancerprediction	7
integration	7
mining	7
mrna	7
pathway	7
phylogeny	7
projects	7
promotor	7
prosite	7
statistics	7
cis-regulatory	6

Tag motif [at least 200 articles] Export

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