bertelsen's software [44 articles] Export

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

	Linear model for fast background subtraction in oligonucleotide microarrays [My Copy] Algorithms for Molecular Biology, Vol. 4, No. 1. (2009), 15. by K. Myriam Kroll, Gerard Barkema, Enrico Carlon posted to software preprocessing oligonucleotide model microarray linear background algorithm by bertelsen on 2009-11-23 22:04:40 as along with 1 person renatomilani
	The Basic Immune Simulator: An agent-based model to study the interactions between innate and adaptive immunity [My Copy] Theoretical Biology and Medical Modelling, Vol. 4, No. 1. (27 September 2007), 39. by Virginia Folcik, Gary An, Charles Orosz posted to viral-infection software simulation model immune-system agent-based by bertelsen on 2009-11-23 21:35:30 as along with 5 people ogurcan tomhebbron gokhan jayster4 johnpeterwalsh
	Building Blocks For Variational Bayesian Learning Of Latent Variable Models [My Copy] Journal of Machine Learning Research, Vol. 8 (2007), pp. 155-201. by Tapani Raiko, Harri Valpola, Markus Harva, Juha Karhunen posted to variational-inference tool software latent bayesian by bertelsen on 2009-10-13 17:06:10 as along with 1 person rorymulvaney
	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
	FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions [My Copy] Genome Biology, Vol. 10, No. 4. (2009), R39. by Jessica Severin, Andrew Waterhouse, Hideya Kawaji, et al.Timo Lassmann, Erik van Nimwegen, Piotr Balwierz, Michiel de Hoon, David Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten Daub, Alistair Forrest posted to transcription-factor transcription software regulator promoters network mirna integrating gene-regulation gene-expression database by bertelsen on 2009-09-27 16:12:38 as along with 10 people jfr Garamonfok rdiaz YukaH ealloza guhjy pengchy natstreet druvus dolchan
	Writing DNA with GenoCAD. [My Copy] Nucleic acids research, Vol. 37, No. Web Server issue. (1 July 2009), pp. W40-47. by Michael J. Czar, Yizhi Cai, Jean Peccoud posted to synthetic-biology software overview dna design by bertelsen on 2009-09-25 12:21:12 as along with 8 people operon dchughes JamesBarger genocad peccoud Vincent_Rouilly grahamc GustavoLacerda
	puma: a Bioconductor package for propagating uncertainty in microarray analysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 211. by Richard Pearson, Xuejun Liu, Guido Sanguinetti, Marta Milo, Neil Lawrence, Magnus Rattray posted to uncertainty software microarray bioconductor bayesian analysis by bertelsen on 2009-09-02 21:48:47 as along with 8 people and 1 group zufar rdiaz Stew guhjy lwaldron brianb barriot neils Bioinformatics - CRUK
	Standards and ontologies in computational systems biology. [My Copy] Essays in biochemistry, Vol. 45 (2008), pp. 211-222. by Herbert M. Sauro, Frank T. Bergmann posted to visualization tool systems-biology standard software ontology modelling languages computational by bertelsen on 2009-09-01 17:38:13 as along with 2 people jonathancooper jmuhlich
	Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation [My Copy] Theoretical Biology and Medical Modelling, Vol. 5, No. 1. (27 May 2008), 11. by Gary An posted to systemic-computation software multi-scale modular modeling introduction inflammation dynamic agent-based by bertelsen on 2009-09-01 16:09:18 as
	The Systems Biology Graphical Notation [My Copy] Nature Biotechnology, Vol. 27, No. 8. (07 August 2009), pp. 735-741. by Nicolas L. Novere, Michael Hucka, Huaiyu Mi, et al.Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit I. Aladjem, Sarala M. Wimalaratne, Frank T. Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji, Lu Li, Yukiko Matsuoka, Alice Villeger, Sarah E. Boyd, Laurence Calzone, Melanie Courtot, Ugur Dogrusoz, Tom C. Freeman, Akira Funahashi, Samik Ghosh, Akiya Jouraku, Sohyoung Kim, Fedor Kolpakov, Augustin Luna, Sven Sahle, Esther Schmidt, Steven Watterson, Guanming Wu, Igor Goryanin, Douglas B. Kell, Chris Sander, Herbert Sauro, Jacky L. Snoep, Kurt Kohn, Hiroaki Kitano posted to visualization tool systems-biology standard software regulation networks languages interactis graphical-modelling biochemical by bertelsen on 2009-08-31 15:39:29 as along with 38 people and 3 groups singhsh greg tonamswish pablocarb josepe abc623 daforerog abhishek_tiwari robertrentzsch ngehlenborg pekrau thegoose fgibson Borelli thomaskelder pmendes dullhunk polivares chasmand brianb roys torfinnnome guhjy Zephyrus lenov reyez allysonlister apocapoc renatomilani VGreiff druvus sjcockell jandot megraw leliavski frohike fpattyn jhyang Orengo Group Journal Picks Journal picks Neuroblastoma
	LibSBML: an API library for SBML. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 6. (15 March 2008), pp. 880-881. by Benjamin J. Bornstein, Sarah M. Keating, Akiya Jouraku, Michael Hucka posted to systems-biology software python library by bertelsen on 2009-08-31 15:26:05 as along with 10 people silverballer47 jvb allysonlister schwartzjmc agomez guhjy dullhunk lenov maralena pmendes
	Grid Cellware: the first grid-enabled tool for modelling and simulating cellular processes [My Copy] Bioinformatics, Vol. 21, No. 7. (1 April 2005), pp. 1284-1287. by Pawan K. Dhar, Tan C. Meng, Sandeep Somani, et al.Li Ye, Kishore Sakharkar, Arun Krishnan, Azmi B. M. Ridwan, Sebastian H. Wah, Mandar Chitre, Zhu Hao posted to tool systems-biology software simulation processes modelling grid by bertelsen on 2009-08-31 14:52:52 as along with 3 people mchitre jmeppley kalvala
	Genomes2Drugs: identifies target proteins and lead drugs from proteome data. [My Copy] PloS one, Vol. 4, No. 7. (10 July 2009), e6195. by David Toomey, Heinrich C. Hoppe, Marian P. Brennan, Kevin B. Nolan, Anthony J. Chubb posted to tool software drug-discovery drug by bertelsen on 2009-08-25 10:58:03 as along with 3 people guhjy brianb sjcockell
	R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses [My Copy] Bioinformatics, Vol. 23, No. 5. (1 March 2007), pp. 641-643. by Brian S. Yandell, Tapan Mehta, Samprit Banerjee, et al.Daniel Shriner, Ramprasad Venkataraman, Jee Y. Moon, Whipple W. Neely, Hao Wu, Randy von Smith, Nengjun Yi posted to quantitative-trait-loci software r mcmc bayesian by bertelsen on 2009-08-15 17:52:47 as along with 2 people Ayest medic0747
	Building biomedical web communities using a semantically aware content management system. [My Copy] Briefings in bioinformatics, Vol. 10, No. 2. (1 March 2009), pp. 129-138. by Sudeshna Das, Lisa Girard, Tom Green, Louis Weitzman, Alister Lewis-Bowen, Tim Clark posted to biomedical community content-management-system management scientific semantic-web software tool by bertelsen on 2009-07-23 17:01:48 as along with 8 people jfr artaban421 dbk guhjy fgibson allysonlister natstreet druvus
	BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. [My Copy] Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006), pp. W472-476. by Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, et al.David Montaner, Eva Alloza, Juan M. Vaquerizas, Lucía Conde, Christian Blaschke, Javier Vera, Joaquín Dopazo posted to annotation functional-genomics software systems-biology by bertelsen on 2009-07-20 14:15:45 as along with 5 people and 2 groups daforerog rschulz marcius ealloza Garamonfok BioinfoCIPF SGU-CIPF
	WebArray: an online platform for microarray data analysis [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005), 306. by Xiaoqin Xia, Michael Mcclelland, Yipeng Wang posted to analysis microarray software webservices by bertelsen on 2009-07-20 13:10:27 as along with 4 people natstreet angelicabtto daforerog rdiaz
	Network legos: building blocks of cellular wiring diagrams. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 15, No. 7. (September 2008), pp. 829-844. by T. M. Murali, C. G. Rivera posted to disease gene-expression integrating large-scale methodology modules network software top-down by bertelsen on 2009-07-08 23:24:26 as along with 7 people druvus guhjy jfr sjcockell tmmurali lptolik RamuAnandakrishnan
	A-MADMAN: annotation-based microarray data meta-analysis tool. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (29 June 2009), 201. by Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, et al.Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi posted to annotation gene-expression large-scale meta-analysis microarray normalization software tool by bertelsen on 2009-07-08 11:59:05 as along with 6 people and 1 group daforerog ptrobajo dswan guhjy shikin neils Bioinformatics
	Installing and configuring CMap. [My Copy] Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.], Vol. Chapter 9 (March 2007) by B. Faga posted to biology software web by bertelsen on 2009-07-04 19:22:16 as
	BFRM: Bayesian factor regression modelling [My Copy] Bulletin of the International Society for Bayesian Analysis, Vol. 14 (2007), pp. 4-5. by Q. Wang, C. Carvalho, J. E. Lucas, M. West posted to bayesian factor-analysis regression software sparse by bertelsen on 2009-06-01 02:27:26 as
	DAVID gene ID conversion tool. [My Copy] Bioinformation, Vol. 2, No. 10. (2008), pp. 428-430. by Da Wei a. . W. Huang, Brad T. Sherman, Robert Stephens, Michael W. Baseler, H. Clifford Lane, Richard A. Lempicki posted to bioinformatics conversion databases identification software tool by bertelsen on 2009-05-18 15:07:28 as along with 3 people jfr daforerog guhjy
	Biopython: freely available Python tools for computational molecular biology and bioinformatics [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1422-1423. by Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, et al.Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon posted to bioinformatics biology biopython computational molecular python software by bertelsen on 2009-05-04 09:13:14 as along with 38 people and 9 groups eesruiz Geknitics pekrau Sergey_gerbek hwright jfr karinaecomp applebyb klexa rdiaz FabienneGranier thegoose oteri cmzmasek jwm guhjy AlexBateman daforerog ltitodem Thaverkamp sobolevnrm psique dswan neils dullhunk Vincent_Rouilly gwallau brianb jorisslob svenrahmann jmeppley VGreiff sjcockell druvus jago kshameer operon svozil Systems_Biology Computational_Systems_Biology Structural Biology Group TorVergata Journal picks baker-group Bioinformatics Software-Architecture OER_Open_Educational_Resources Method_Engineering_Services
	Sparse Matrix Implementation in Octave [My Copy] (3 Apr 2006) by David Bateman, Andy Adler posted to octave opensource software sparse by bertelsen on 2009-03-27 16:02:50 as along with 1 person belonesox
	Ultrafast and memory-efficient alignment of short DNA sequences to the human genome [My Copy] Genome Biology, Vol. 10, No. 3. (2009), R25. by Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg posted to alignment genome human oligonucleotide promoter software by bertelsen on 2009-03-27 15:47:22 as along with 36 people and 4 groups jfr hzoltan cthachuk darshan fstrozzi adijr debasis bozdagd polivares torfinnnome n00c talponer jmcq rschulz ghattem operon humburg idonaldson mmartin skembel dquest heliopais djkt GeeSharpMinor darian semrich dakelley idoerg vmsr hpaces admash pdexheimer mhamada fpattyn natstreet druvus BergmanLab SIMR bioinformatics iSEEM Notre Dame Bioinformatics
	bioNMF: a versatile tool for non-negative matrix factorization in biology [My Copy] BMC Bioinformatics, Vol. 7 (28 July 2006), 366. by Alberto Pascual-Montano, Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M. Carazo, Roberto D. Pascual-Marqui posted to biology clustering matrix-factorization nonnegative software tool by bertelsen on 2009-03-13 14:47:12 as along with 1 person jfr
	Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_2. (1 July 2008), pp. W341-346. by Fatima Al-Shahrour, Jose Carbonell, Pablo Minguez, et al.Stefan Goetz, Ana Conesa, Joaquin Tarraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquin Dopazo posted to analysis functional-genomics ontology pathway software tool by bertelsen on 2009-03-12 15:49:40 as along with 3 people sgoetz neils balicea
	Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research [My Copy] Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3674-3676. by Ana Conesa, Stefan Gotz, Juan M. Garcia-Gomez, Javier Terol, Manuel Talon, Montserrat Robles posted to alignment annotation go ontology sequence software tool by bertelsen on 2009-03-12 15:24:27 as along with 10 people seb1 Thaverkamp karinlag nlapalu fbristow Garamonfok sgoetz talponer imelda aconesa
	Basic local alignment search tool. [My Copy] Journal of molecular biology, Vol. 215, No. 3. (5 October 1990), pp. 403-410. by S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman posted to alignment comparison sequence software tool by bertelsen on 2009-03-12 15:23:20 as along with 77 people and 6 groups VGreiff richter80 krapnik azazello rshe mtaschuk sjcockell niallhaslam djohnson thegoose humburg timhubbard pachorip n00c maria_hauser rpetrenko parnell yylin esyoun APRegier idoerg Neeperando robert85 thegoose2 daforerog mcbla coela alessandroparini Blackbeard florisbuijzen laurabailey treangen pwais mmartin tharris dmp camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront caporaso michC myui BioNica CitoJam rabio timflutre lusk cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti ashaytan benwei granujilla C. elegans / WormBase dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
	ProbCD: enrichment analysis accounting for categorization uncertainty [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Ricardo Vencio, Ilya Shmulevich posted to annotation enrichment-analysis go microarray ontology probabilistic software uncertainty by bertelsen on 2009-03-12 14:23:56 as along with 4 people and 1 group druvus sobolevnrm heliopais barriot baker-group
	BayGO: Bayesian analysis of ontology term enrichment in microarray data. [My Copy] BMC Bioinformatics, Vol. 7 (2006) by R. Z. Vêncio, T. Koide, S. L. Gomes, C. A. Pereira posted to analysis bayesian enrichment-analysis microarray ontology r software by bertelsen on 2009-03-12 14:18:52 as along with 2 people jfr cmzmasek
	Building blocks for variational Bayesian learning of latent variable models [My Copy] Journal of Machine Learning Research, Vol. 8 (2006), pp. 155-201. by Abteknillinen Korkeakoulu, Tekniska Högskolan, Universite De, et al.Tapani Raiko, Tapani Raiko, Harri Valpola, Harri Valpola, Markus Harva, Markus Harva, Juha Karhunen, Juha Karhunen posted to bayesian latent learning machine-learning models python software variational by bertelsen on 2009-03-05 15:18:36 as
	False discovery rate, sensitivity and sample size for microarray studies [My Copy] Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 3017-3024. by Yudi Pawitan, Stefan Michiels, Serge Koscielny, Arief Gusnanto, Alexander Ploner posted to discovery false fdr microarray sample-size sensitivity software by bertelsen on 2009-02-23 14:02:15 as along with 6 people zoex_99 jperkins guhjy ugengma shikin wirawan
	PYCHEM: a multivariate analysis package for python. [My Copy] Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2565-2566. by R. M. Jarvis, D. Broadhurst, H. Johnson, N. M. O'Boyle, R. Goodacre posted to analysis multivariate python software statistical by bertelsen on 2009-02-14 21:17:16 as along with 1 person plofje
	MPI for Python [My Copy] Journal of Parallel and Distributed Computing, Vol. 65, No. 9. (September 2005), pp. 1108-1115. by Lisandro Dalcin, Rodrigo Paz, Mario Storti posted to interface multiple parallel processes python software tool by bertelsen on 2009-02-14 21:11:12 as along with 3 people mabi fpalm josepe
	Modular Toolkit for Data Processing (MDP): A Python Data Processing Framework. [My Copy] Frontiers in neuroinformatics, Vol. 2 (2008) by Tiziano Zito, Niko Wilbert, Laurenz Wiskott, Pietro Berkes posted to data python software tool by bertelsen on 2009-02-14 21:00:55 as along with 2 people rawphi sdaehne
	SPRINT: A new parallel framework for R [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 558. by Jon Hill, Matthew Hambley, Thorsten Forster, et al.Muriel Mewissen, Terence Sloan, Florian Scharinger, Arthur Trew, Peter Ghazal posted to interface microarray parallel r software by bertelsen on 2009-01-30 16:20:33 as along with 21 people and 1 group coela jfr rdiaz barry guhjy skembel fpattyn Yanno pkonings natstreet druvus lptolik paszkows nuin cisevol irinamohorianu kvjanos kshameer jmeppley GeeSharpMinor pengchy BergmanLab
	Identifying differentially expressed subnetworks with MMG. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 23. (1 December 2008), pp. 2792-2793. by J. Noirel, G. Sanguinetti, P. C. Wright posted to analysis data expression graphs networks proteomics quantitative regulation software by bertelsen on 2008-11-19 12:59:13 as along with 11 people zufar pauldobson jfr sg45653 pengchy behindtherabbit roys jiayi369 tmmurali guhjy rdiaz
	A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data [My Copy] BMC Bioinformatics, Vol. 9 (13 November 2008), 480. by Luca Corradi, Marco Fato, Ivan Porro, Silvia Scaglione, Livia Torterolo posted to analysis cluster computing data gene-expression grid microarray software by bertelsen on 2008-11-19 12:22:43 as along with 3 people jfr guhjy pengchy
	Array-A-Lizer: A serial DNA microarray quality analyzer [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (2004) by Andreas Petri, Jan Fleckner, Mads Matthiessen posted to analysis microarray quality software by bertelsen on 2008-10-22 22:20:30 as
	JCLEC: a Java framework for evolutionary computation [My Copy] Soft Computing - A Fusion of Foundations, Methodologies and Applications, Vol. 12, No. 4. (28 February 2008), pp. 381-392. by Sebastián Ventura, Cristóbal Romero, Amelia Zafra, José Delgado, César Hervás posted to algorithms computation evolution evolutionary-computation java object-oriented-design optimization software tool by bertelsen on 2008-09-17 10:07:10 as along with 2 people and 3 groups axeltan nojhan Evolutionary Computation Software EvolutionaryComputation Metaheuristics
	The Vmatch large scale sequence analysis software [My Copy] (11 October 2007) by Stefan Kurtz posted to analysis sequence software by bertelsen on 2008-06-25 00:00:52 as
	Accounting for probe-level noise in principal component analysis of microarray data. [My Copy] Bioinformatics, Vol. 21, No. 19. (2005), pp. 3748-54. by G. Sanguinetti, M. Milo, M. Rattray, N. D. Lawrence posted to algorithms analysis analysismethods array bayesian binfbib component data expression gene genetic import interpretation models oligonucleotide principal processes profilingmethods sequence software statistical stochastic by bertelsen on 2007-06-19 17:46:12 as

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microarray	223
analysis	129
review	125
gene-expression	124
systems-biology	95
bayesian	92
cancer	78
expression	59
networks	57
affymetrix	48
gene	46
annotation	44
functional-genomics	44
software	44
biology	42
tool	42
model	40
network	38
regulation	38
modelling	36
data	34
bioinformatics	31
disease	29
modeling	29
pathway	28
genechip	27
models	27
rna	27
human	26
polyadenylation	26
drug-discovery	25
clustering	24
multi-scale	24
oligonucleotide	24
gene-regulation	23
ontology	23
biochemical	22
probe	22
inference	21
degradation	20
differential	20
molecular	20
mrna	20
probability	20
transcription	20
dynamic	19
factor-analysis	19
database	18
integrative	18
probe-level	18
stochastic	18
chemical	17
mathematical	17
probabilistic	17
simulation	17
dirichlet-process	16
function	16
integration	16
kinetic	16
nonparametric	16
algorithm	15
comparison	15
computational	15
drug	15
experiment	15
genome	15
genomics	15
high-throughput	15
r	15
sampling	15
sequence	15
statistical	15
structure	15
theory	15
enrichment-analysis	14
gastric	14
noise	14
normalization	14
prediction	14
python	14
regression	14
array	13
biochemical-systems-theory	13
bioconductor	13
classification	13
control	13
framework	13
go	13
interpretation	13
mirna	13
pathways	13
personalized-medicine	13
phenotype	13
protein	13
statistics	13
therapy	13
algorithms	12
clinical	12
complexity	12
hierarchical	12
latent	12
mechanism	12
modules	12
promoter	12
transcriptome	12
computational-biology	11
distribution	11
evolution	11
non-protein-coding	11
oncogenesis	11
quality	11
sparse	11
tumour	11
alternative	10
genetic	10
integrating	10
mcmc	10
mixture	10
modular	10
proteomics	10
quantitative	10
systems	10
test	10
uncertainty	10
3-utr	9
biomedical	9
biophysics	9
cell-biology	9
data-integration	9
design	9
diagnostic	9
discovery	9
dna	9
hypothesis	9
information	9
interactions	9
large-scale	9
machine-learning	9
method	9
methodology	9
multiple	9
quality-control	9
selection	9
s-system	9
therapeutic	9
transcription-factor	9
visualization	9
background	8
experimental-design	8
heterogeneity	8
hybridization	8
ica	8
insilico	8
linear	8
measure	8
methods	8
overview	8
rnai	8
synthetic-biology	8
systemic-computation	8
time-series	8
transcripts	8
utr	8
agent-based	7
binary	7
development	7
drug-target	7
emergent-properties	7
infection	7
invivo	7
mapping	7
multivariate	7
organization	7
pathology	7
physiology	7
rats	7
specificity	7
tiling	7
time-course	7
translation	7
webservices	7
application	6
cdna	6
chip-chip	6
computation	6
computing	6
databases	6
epigenetic	6
evolutionary-computation	6
feature	6
genetics	6
graphs	6
mammalian	6
matrix-factorization	6
metabolomics	6
nonlinear	6
pathway-analysis	6
pattern	6
pre-processing	6
primary	6
prior	6
processes	6
profiles	6
reactions	6
reverse-engineering	6
rna-seq	6
scientific	6
sequencing	6
summary	6
thermodynamics	6
tumor	6
upt	6
apoptosis	5
baysian	5
bias	5
binfbib	5
biomarker	5
book	5
cell-cycle	5
comparative	5
correction	5
dependence	5
encode	5
environment	5
error	5
eukaryotic	5
false	5
gaussian	5
gene-function	5
genome-wide	5
gibbs	5
identification	5
import	5
invitro	5
kidney	5
localization	5
measurement	5
medical	5
membrane	5
metabolic-network	5
ncrna	5
nmd	5
nonsense-mediated	5
normal	5
ontologies	5
optimization	5
pca	5
physical	5
process	5
profiling	5
profilingmethods	5
protein-expression	5
quality-assessment	5
quantitative-trait-loci	5
sensitivity	5
signal	5
simulations	5
splicing	5
synthesis	5
time	5
topological	5
treatment	5
truncated	5
unknown	5
variation	5
variational	5
5-utr	4
animals	4
approximation	4
biomolecular	4
cage	4
cell	4
circuits	4
co-expression	4
co-regulation	4
decay	4
diversity	4
dynamics	4
endolymphatic-sac	4
entropy	4
estimation	4
exons	4
exploratory	4
filtering	4
gastric-cancer-group	4
gene-set-analysis	4
global	4
graphical-modelling	4
grid	4
guide	4
high-dimensional	4
hybrid	4
inflammation	4
inhibitors	4
inner-ear	4
interface	4
knowledge-based	4
literature	4
local	4
map	4
mechanistic	4
metabolic-control-analysis	4
mice	4
mining	4
mixtures	4
motif	4
nested	4
ode	4
ordinal	4
pharmacogenomic	4
philosophy	4
physics	4
post-transcriptional	4
power-laws	4
prognosis	4
sequence-analysis	4
signals	4
signature	4
signatures	4
standard	4
steady-state	4
survey	4
tissue-specific	4
toxoplasma	4
transcript	4
transformation	4
web	4
accuracy	3
adjustment	3
affinity	3
affy	3
alignment	3
amplification	3
analysismethods	3
assessment	3
associations	3
automatic	3
bacteria	3
beta	3
calibration	3
cell-lines	3
characteristics	3
chemical-master-equation	3
chemotherapy	3
chip-seq	3
chromatin	3
chromosomal-expression	3
combinatorial	3
component	3
correlation	3
dataset	3
differential-equation	3
differentiation	3
dirichlet	3
distributions	3
dynamical-systems	3
enzyme	3
evaluation	3
exchangeability	3
fdr	3
gene-circuits	3
generalized	3
genes	3
genotyping	3
histological	3
hmm	3
humans	3
identifiability	3
independence	3
interference	3
introduction	3
languages	3
learning	3
management	3
medicine	3
metastatic	3
model-selection	3
modularity	3
multinomial	3
natural	3
nonnegative	3
nuclear	3
parasitology	3
pattern-recognition	3
performance	3
perturbation	3
polymerase	3
random	3
ranking	3
regulators	3
renormalization-group-analysis	3
repository	3
reproducibility	3
resonance	3
resource	3
robust	3
signaling-system	3
signal-transduction	3
snp	3
stochastic-resonance	3
structural-biology	3
tumorigenesis	3
unsupervised	3
3	2
5	2
acid	2
anatomy	2
approximate	2
approximations	2
behaviour	2
benchmark	2
biopython	2
buffet	2
cdf	2
cell-migration	2
cell-population	2
cells	2
chromosome-wide	2
comment	2
community	2
constraint-based-modelling	2
copy-number-variation	2
cox-theorem	2
cross-hybridization	2
cross-laboratory	2
cross-platform	2
cross-study	2
cytoplasmic	2
definition	2
density	2
detection	2
deterministic	2
difference	2
distance	2
dsrna	2
epithelial	2
evidence	2
exon	2
false-discovery	2
for:birte	2
format	2
foundations	2
fractal	2
game-theory	2
gamma	2
generative	2
genotype	2
grid-computing	2
health	2
heart	2
heterogeneous	2
homologous	2
image-processing	2
immune-system	2
indian	2
internet	2
isoform	2
knowledgebase	2
kullback-leibler	2
lasso	2
logic	2
lung	2
mage	2
mass_spectroscopy	2
matlab	2
matrix	2
matroid	2
memory	2
metabolic	2
methylation	2
miame	2
mismatch	2
missing-value	2
mitochondria	2
molecular-connectivity-map	2
multi-target	2
mutations	2
neuroscience	2
nonequilibrium	2
non-specific	2
nucleic	2
numerical	2
octave	2
oncogene-addiction	2
opensource	2
organ	2
parallel	2
parts	2
p-bodies	2
perspective	2
pharmacogenomics	2
phenome	2
physiome	2
pipelines	2
plant	2
plausibility	2
poly	2
post-transcription	2
preprocessing	2

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