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	A study of the relationship between student communication interaction and sense of community [My Copy] The Internet and Higher Education, Vol. 9, No. 3. (MarchMarch 2006), pp. 153-162. by S. Dawson posted to tool social_networks measurement by hansaagard on 2009-11-07 17:57:23 as along with 2 people and 1 group smogit alisonruth SITCRC
	SimBoolNet - A Cytoscape Plugin for Dynamic Simulation of Signaling Networks [My Copy] Bioinformatics (3 November 2009), btp617. by Jie Zheng, David Zhang, Pawel F. Przytycki, Rafal Zielinski, Jacek Capala, Teresa M. Przytycka posted to tool signaling networks cytoscape bioinformatics by renatomilani on 2009-11-06 02:02:43 as
	Proof and Disproof in Formal Logic: An Introduction for Programmers (Oxford Texts in Logic) [My Copy] (29 September 2005) by Richard Bornat posted to tool textbook proof logic jape formal book 2005 by michaelbanks on 2009-11-04 12:12:06 as
	multiplierz: an extensible API based desktop environment for proteomics data analysis. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (29 October 2009), 364. by Jignesh R. Parikh, Manor Askenazi, Scott B. Ficarro, et al.Tanya Cashorali, James T. Webber, Nathaniel C. Blank, Yi Zhang, Jarrod A. Marto posted to tool proteomics data by renatomilani on 2009-11-03 02:01:33 as along with 1 person neilswainston
	Energy Bucket: A Tool for Power Profiling and Debugging of Sensor Nodes [My Copy] Sensor Technologies and Applications, International Conference on, Vol. 0 (2009), pp. 132-138. by Jacob Andersen, Morten T. Hansen posted to tool profiling energy debugging analysis by bedieber on 2009-11-02 17:42:20 as along with 1 person mortenthansen
	Value chain analysis: a tool for enhancing export supply policies [My Copy] International Journal of Technological Learning, Innovation and Development, Vol. 1, No. 3. (1 January 2008), pp. 283-308. by Raphael Kaplinsky, Mike Morris posted to value tool supply policies export enhancing chain analysis by derchao on 2009-10-30 17:23:38 as
	RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (12 November 2008), 478. by James Hane, Richard Oliver posted to tool rip genome fungal_genomes alignment by nlapalu on 2009-10-30 17:07:17 as along with 2 people operon jamselem
	Tissue and Process Specific microRNA–mRNA Co-Expression in Mammalian Development and Malignancy [My Copy] PLoS ONE, Vol. 4, No. 5. (5 May 2009), e5436. by Hongye Liu, Issac S. Kohane posted to tool microrna-mrna microrna bioinfo by tonamswish to the group microRNA on 2009-10-30 15:31:37 as along with 4 people gdb giovenko roys ealloza
	CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 33. (17 August 2004), pp. 12114-12119. by Qing Zhou, Wing H. Wong posted to tool tf hmm crm bioinfo by tonamswish on 2009-10-30 14:00:29 as along with 4 people and 1 group isimpson indigoviolet dpollard ep161302 EisenLab
	SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W600-605. by Zongli Xu, Jack A. Taylor posted to tool tagsnp snp gwas by songpku on 2009-10-29 19:58:17 as along with 6 people daed misonneh guhjy psique jdbowes daforerog
	Fine-Grained Analysis of Web Tasks through Data Visualization [My Copy] Web Engineering (2009), pp. 1-15. by Gennaro Costagliola, Vittorio Fuccella posted to visualisation user usability tracking tool of interactions information evaluation behaviour by zanzibarsperlary on 2009-10-29 11:45:36 as
	SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (4 January 2009), gkn756. by Alexander R. Pico, Ivan V. Smirnov, Jeffrey S. Chang, et al.Ru-Fang F. Yeh, Joseph L. Wiemels, John K. Wiencke, Tarik Tihan, Bruce R. Conklin, Margaret Wrensch posted to tool snp functional by daed on 2009-10-29 11:40:25 as along with 2 people and 1 group guhjy AlexanderPico ConklinLab
	Sofia: a framework for the development of group storytelling tools [My Copy] In SRMC '08: Proceeding of the 2nd ACM international workshop on Story representation, mechanism and context (2008), pp. 41-48. by Cláudio M. Luz, Marcos R. S. Borges, Maria Luiza posted to tool storytelling framework by locatellimp on 2009-10-29 10:03:32 as
	NGSView: an extensible open source editor for next-generation sequencing data. [My Copy] Bioinformatics (Oxford, England) (24 October 2009), btp611. by Erik Arner, Yoshihide Hayashizaki, Carsten O. Daub posted to viewer tool software sequencing open-source ngsview by n00c on 2009-10-28 12:44:41 as along with 3 people operon heliopais druvus
	OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. [My Copy] BMC proceedings, Vol. 3 Suppl 4 (2009) by Pieter Bt B. Neerincx, Han Rauwerda, Haisheng Nie, Martien Am A. Groenen, Timo M. Breit, Jack Am A. Leunissen posted to webservices tool target specificity pipelines oligonucleotide microarray high-throughput annotation by bertelsen on 2009-10-28 12:07:39 as
	ChIP-seq accurately predicts tissue-specific activity of enhancers [My Copy] Nature, Vol. 457, No. 7231. (12 February 2009), pp. 854-858. by Axel Visel, Matthew J. Blow, Zirong Li, et al.Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, Bing Ren, Edward M. Rubin, Len A. Pennacchio posted to tool enhancer chip-seq bioinfo by tonamswish on 2009-10-27 19:20:00 as along with 22 people and 2 groups ewilban1 samanthacooper ashkelon13 isimpson gdb dnewburger jochenG bertelsen oelemento rpatward cajunsushi WanderingAengus absterga provero cassj anphony dpollard caseybrown biomcgary xingxu idonaldson djkt RockmanLab cis-regulatory-evolution
	The multisensory attentional consequences of tool use: a functional magnetic resonance imaging study. [My Copy] PLoS ONE, Vol. 3, No. 10. (2008) by N. P. Holmes, C. Spence, P. C. Hansen, C. E. Mackay, G. A. Calvert posted to tool multisensory by wnbair on 2009-10-27 17:36:33 as along with 1 person jeclark
	The neural basis of tool use [My Copy] Brain, Vol. 132, No. 6. (1 June 2009), pp. 1645-1655. by G. Goldenberg, J. Spatt posted to tool by wnbair on 2009-10-27 17:36:03 as along with 4 people amorgan77 ybysk nishiokov jeclark
	BayesPeak: Bayesian analysis of ChIP-seq data [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 299. by Christiana Spyrou, Rory Stark, Andy Lynch, Simon Tavare posted to tool hmm chip-seq bioinfo bayesian by tonamswish to the group Bioinformatics on 2009-10-27 13:08:34 as along with 10 people and 3 groups dswan fenghezi inesdesantiago idonaldson polivares mkiyer druvus stajich humburg rschulz JLab BergmanLab Mycology
	Metabolic network analysis. A powerful tool in metabolic engineering. [My Copy] Advances in biochemical engineering/biotechnology, Vol. 66 (2000), pp. 209-231. by B. Christensen, J. Nielsen posted to topology tool network metabolic engineering analysis by Winzer on 2009-10-27 11:49:09 as
	An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome [My Copy] PLoS ONE, Vol. 4, No. 5. (12 May 2009), e5501. by Kyoung-Jae Won, Saurabh Agarwal, Li Shen, Robert Shoemaker, Bing Ren, Wei Wang posted to tool tf hmm chip-seq bioinfo by tonamswish on 2009-10-27 03:01:09 as along with 3 people and 1 group guhjy idonaldson cisevol BergmanLab
	Profile Comparer: a program for scoring and aligning profile hidden Markov models [My Copy] Bioinformatics, Vol. 24, No. 22. (15 November 2008), pp. 2630-2631. by Martin Madera posted to tool profile_hmm hmm bioinfo by tonamswish on 2009-10-27 02:31:05 as along with 3 people and 1 group j3xucite djkt nuin iSEEM
	A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2787-2794. by Andreas Keller, Christina Backes, Andreas Gerasch, et al.Michael Kaufmann, Oliver Kohlbacher, Eckart Meese, Hans-Peter Lenhof posted to tool gsea bioinfo bayesian by tonamswish on 2009-10-24 18:30:00 as along with 7 people heliopais dolchan greg zufar rdiaz ptrobajo brianb
	3D-SURFER: software for high-throughput protein surface comparison and analysis [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2843-2844. by David La, Juan Esquivel-Rodriguez, Vishwesh Venkatraman, et al.Bin Li, Lee Sael, Stephen Ueng, Steven Ahrendt, Daisuke Kihara posted to tool structure bioinformatics by renatomilani on 2009-10-24 01:58:46 as along with 3 people and 1 group operon kshameer nickolay structural_bioinformatics
	CloudBurst: highly sensitive read mapping with MapReduce [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1363-1369. by Michael C. Schatz posted to tool short-read ngs mapping by idonaldson on 2009-10-22 09:32:17 as along with 29 people and 2 groups walshtp orzenil heliopais dakelley bozdagd agbiotec jandot guhjy n00c cymacs semrich nuin operon AlexBateman fgibson rschulz dswan mitko djkt humburg jmeppley coela vagoskar svenrahmann natstreet brianb Neeperando druvus neils KCL & UCL Bioinformatics Bioinformatics
	Predicting tissue-specific enhancers in the human genome [My Copy] Genome Research, Vol. 17, No. 2. (8 February 2007), pp. 201-211. by Len A. Pennacchio, Gabriela G. Loots, Marcelo A. Nobrega, Ivan Ovcharenko posted to tool enhancer bioinfo by tonamswish on 2009-10-19 23:00:14 as along with 7 people and 1 group cisstem indigoviolet cwbrown maximilianh heliopais roys barwil EisenLab
	Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (02 November 2007), 427. by Jeff Chou, Tong Zhou, William Kaufmann, Richard Paules, Pierre Bushel posted to tool epig clustering_tool clustering bioinfo by tonamswish on 2009-10-19 18:52:45 as along with 6 people and 1 group thegoose2 tharris shigepong hpaces dps renatomilani C. elegans / WormBase
	ncRNAppi - A tool for identifying disease-related miRNA and siR-NA targeting pathways. [My Copy] Bioinformatics (Oxford, England) (6 October 2009), btp574. by Ka-Lok L. Ng, Hsueh-Chuan C. Liu, Shan-Chih C. Lee posted to tool tissue_specific software pathway mirna microrna by frohike on 2009-10-14 11:11:48 as along with 1 person daforerog
	Computation of recurrent minimal genomic alterations from array-CGH data [My Copy] Bioinformatics, Vol. 22, No. 7. (1 April 2006), pp. 849-856. by C. Rouveirol, N. Stransky, Ph Hupe, et al.Ph Rosa, E. Viara, E. Barillot, F. Radvanyi posted to tool pattern mining dna_copy data cgh bioinformatics analysis by dolchan on 2009-10-13 18:58:14 as along with 1 person stharward
	Model-based clustering of array CGH data [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i30-38. by Sohrab P. Shah, K-John Cheung, Nathalie A. Johnson, et al.Guillaume Alain, Randy D. Gascoyne, Douglas E. Horsman, Raymond T. Ng, Kevin P. Murphy posted to tool number hidden_markov_model dna_copy copy clustering change cgh bioinformatics by dolchan on 2009-10-13 18:48:12 as along with 4 people jonilaserson rdiaz kdpreter nuin
	Product Line Tools are Product Lines Too: Lessons Learned from Developing a Tool Suite [My Copy] Automated Software Engineering, 2008. ASE 2008. 23rd IEEE/ACM International Conference on In Automated Software Engineering, 2008. ASE 2008. 23rd IEEE/ACM International Conference on (07 October 2008), pp. 351-354. by P. Grunbacher, R. Rabiser, D. Dhungana posted to tool spl by benavides on 2009-10-13 10:04:00 as along with 1 person architect
	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 tool motif-discovery by idonaldson on 2009-10-12 12:05:29 as along with 2 people maximilianh ashishanand
	Tsigas P.: CiteWiz: A Tool for the Visualization of Scientific Citation Networks [My Copy] (2004) by Niklas Elmqvist posted to visualization tool polygons growing citewiz citation by mrFijol on 2009-10-12 11:31:55 as
	Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2739-2740. by Olivier Sand, Morgane Thomas-Chollier, Jacques van Helden posted to tool sequence retrieve ensembl by idonaldson on 2009-10-09 08:53:57 as along with 4 people druvus inesdesantiago natstreet sebastien_vigneau
	Qupe - a Rich Internet Application to take a Step Forward in the Analysis of Mass Spectrometry-Based Quantitative Proteomics Experiments [My Copy] Bioinformatics (6 October 2009), btp568. by Stefan P. Albaum, Heiko Neuweger, Benjamin Franzel, et al.Sita Lange, Dominik Mertens, Christian Trotschel, Dirk Wolters, Jorn Kalinowski, Tim W. Nattkemper, Alexander Goesmann posted to tool phosphoproteome mass-spec bioinformatics by renatomilani on 2009-10-08 15:00:26 as
	An editor for pathway drawing and data visualization in the Biopathways Workbench [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 99. by Robert Byrnes, Dawn Cotter, Andreia Maer, Joshua Li, David Nadeau, Shankar Subramaniam posted to tool systems pathway bioinformatics by renatomilani on 2009-10-07 06:02:46 as along with 1 person perkeo
	DIANA-mirPath: Integrating human and mouse microRNAs in pathways. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 15. (1 August 2009), pp. 1991-1993. by G. L. Papadopoulos, P. Alexiou, M. Maragkakis, M. Reczko, A. G. Hatzigeorgiou posted to tool pathway mouse microrna kegg integration human by ealloza on 2009-10-01 18:47:20 as along with 7 people and 2 groups megraw Stew dswan daforerog tmmurali guhjy pengchy Bioinformatics - CRUK Bioinformatics
	CAP3: A DNA Sequence Assembly Program [My Copy] Genome Research, Vol. 9, No. 9. (1 September 1999), pp. 868-877. by Xiaoqiu Huang, Anup Madan posted to tool software dna cap3 assembly by n00c on 2009-10-01 16:09:21 as along with 5 people nwpuzebra Neeperando dakelley gpappas dmp
	TransmiR: a transcription factor-microRNA regulation database. [My Copy] Nucleic acids research (28 September 2009), gkp803. by Juan Wang, Ming Lu, Chengxiang Qiu, Qinghua Cui posted to transcription_factor tool regulatory_relationships regulation microrna database by ealloza on 2009-09-30 18:41:32 as along with 6 people and 2 groups frohike daforerog epinatel heliopais samgj tonamswish cube_and_beyond microRNA
	A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions [My Copy] Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2658-2666. by A. Callegaro, D. Basso, S. Bicciato posted to gastric-cancer-group tumour transcription tool statistical sequence-analysis ontologies integration gene-expression expression chromosomal-localization chromosomal-expression cancer annotations by bertelsen on 2009-09-30 17:32:49 as
	EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (06 February 2009), 50. by Michael Dondrup, Stefan P. Albaum, Thasso Griebel, et al.Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K. Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J. Runte, Andreas Tauch, Felix Tille, Alfred Pühler, Alexander Goesmann posted to tool standard software microarray miame mage integration data analysis by bertelsen on 2009-09-30 17:22:13 as along with 4 people and 1 group barriot guhjy cassj dswan Bioinformatics
	Genome Expression Pathway Analysis Tool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context. [My Copy] BMC bioinformatics, Vol. 8 (02 June 2007), 179. by Markus Weniger, Julia C. Engelmann, Jörg Schultz posted to webservices visualization tool software proteomics pathways metabolic integration genomics gene-expression functional-genomics analysis by bertelsen on 2009-09-28 15:54:07 as along with 10 people and 1 group barriot daforerog udivi GeeSharpMinor guhjy jfr rdiaz ealloza frohike fmenolascina BioinfoCIPF
	RePS: a sequence assembler that masks exact repeats identified from the shotgun data. [My Copy] Genome research, Vol. 12, No. 5. (1 May 2002), pp. 824-831. by Jun Wang, Gane Ka-Shu K. Wong, Peixiang Ni, et al.Yujun Han, Xiangang Huang, Jianguo Zhang, Chen Ye, Yong Zhang, Jianfei Hu, Kunlin Zhang, Xin Xu, Lijuan Cong, Hong Lu, Xide Ren, Xiaoyu Ren, Jun He, Lin Tao, Douglas A. Passey, Jian Wang, Huanming Yang, Jun Yu, Songgang Li posted to tool tandem-repeats software reps repeats mask assembly assembler by n00c on 2009-09-28 15:42:47 as along with 3 people natstreet seb1 orzenil
	galign: A Tool for Rapid Genome Polymorphism Discovery [My Copy] PLoS ONE, Vol. 4, No. 9. (25 September 2009), e7188. by Shai Shaham posted to tool software snp-discovert snp polymorphism galign alignment by n00c on 2009-09-28 15:36:27 as along with 7 people and 1 group maren scmelton natstreet Benedikt_Zimmermann torfinnnome druvus stajich Mycology
	Short read fragment assembly of bacterial genomes [My Copy] Genome Research, Vol. 18, No. 2. (1 February 2008), pp. 324-330. by Mark J. Chaisson, Pavel A. Pevzner posted to tool software short-read genome eulerian assembly assembler by n00c on 2009-09-28 15:23:30 as along with 17 people pachorip APRegier thegoose2 dakelley Neeperando hpaces idoerg druvus jasontsai acn orzenil azazello GustavoLacerda dandaman caseybrown iris42 tharris
	ALLPATHS: De novo assembly of whole-genome shotgun microreads [My Copy] Genome Research, Vol. 18, No. 5. (13 May 2008), pp. 810-820. by Jonathan Butler, Iain MacCallum, Michael Kleber, et al.Ilya A. Shlyakhter, Matthew K. Belmonte, Eric S. Lander, Chad Nusbaum, David B. Jaffe posted to tool software de-novo assembly allpaths algorithm by n00c on 2009-09-28 15:17:37 as along with 22 people and 1 group carlk jmanning2k APRegier pachorip jonilaserson operon thegoose2 natstreet AaronDarling mhz dakelley druvus stajich azazello hpaces tharris jwhitney iris42 Neeperando sharpton GustavoLacerda GeeSharpMinor Mycology
	The Sequence Alignment/Map format and SAMtools [My Copy] Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2078-2079. by Heng Li, Bob Handsaker, Alec Wysoker, et al.Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup posted to tool ngs by idonaldson on 2009-09-28 10:04:43 as along with 25 people and 2 groups seb1 heliopais urgi GustavoLacerda stubrown cassj kshameer ciax polivares carlosjavierna jandot katholt jmcq guhjy orzenil jasontsai operon farhat AlexBateman chrisamiller nuin n00c natstreet sandfire druvus BergmanLab Journal picks
	Ontological analysis of gene expression data: current tools, limitations, and open problems [My Copy] Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3587-3595. by Purvesh Khatri, Sorin Draghici posted to tool review ontologies microarray gene-expression enrichment-analysis comparison analysis by bertelsen on 2009-09-27 20:19:00 as along with 17 people and 1 group jperkins ipark-kaist gjuggler isakemal Stew shikin diamantis Cortel dragonrez macavity1g Garamonfok sgoetz heliopais kristen yggdrasil ellakat marck Bioinformatics - CRUK
	Pathways to the analysis of microarray data. [My Copy] Trends in biotechnology, Vol. 23, No. 8. (August 2005), pp. 429-435. by R. Keira Curtis, Matej Oresic, Antonio Vidal-Puig posted to tool review pathways pathway-analysis microarray integration gene-expression enrichment-analysis analysis by bertelsen on 2009-09-27 20:16:12 as along with 11 people and 2 groups thomaskelder udivi AlexanderPico jfr saman_vp snuppepuppan textoris Ayest tardigrade ealloza heliopais ConklinLab BioinfoCIPF
	ssahaSNP A Polymorphism Detection Tool on a Whole Genome Scale [My Copy] 2005 IEEE Computational Systems Bioinformatics Conference - Workshops, Vol. 0 (2005), pp. 251-254. by Zemin Ning, Mario Caccamo, James C. Mullikin posted to tool ssahasnp software snp polymorphism genome by n00c on 2009-09-26 02:39:24 as

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software	152
network	100
bioinformatics	91
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analysis	64
microarray	44
bib	42
gene	41
nlp	40
review	39
pathway	38
bio	34
user_interface_design	32
visualization	32
microrna	31
protein	31
alignment	29
data	29
softnet	29
database	28
interaction	28
prediction	28
prototyping	28
tfbs	28
motif-discovery	25
chip-seq	24
ontology	24
annotation	23
expression	23
cognition	21
sequence	20
txtmining	20
design	19
gene-expression	18
measurement	17
models	17
integration	16
statistics	16
testing	16
go	15
gsea	15
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short-read	15
algorithm	14
application	14
chip-chip	14
cis-regulation	14
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genomics	14
ie	14
mrna	14
sketching	14
snp	14
web	14
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comparison	13
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functions	12
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python	11
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mining	9
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onto	9
pathways	9
r	9
refinement	9
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structure	9
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cancer	8
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java	8
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