maximilianh's alignment [19 articles] Export

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

	Annotated Alignments [My Copy] by Singh posted to alignment noalignment review by maximilianh on 2009-04-17 10:13:03 as
	The whole alignment and nothing but the alignment: the problem of spurious alignment flanks. [My Copy] Nucleic acids research (16 September 2008) by Martin C C. Frith, Yonil Park, Sergey L L. Sheetlin, John L L. Spouge posted to alignment by maximilianh on 2008-11-29 15:50:24 as along with 4 people and 1 group Neeperando cisevol sebastien_vigneau nuin BergmanLab
	NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences. [My Copy] Genomics (27 May 2008) by Dominic Rose, Jana Hertel, Kristin Reiche, Peter F F. Stadler, Jörg Hackermüller posted to alignment by maximilianh on 2008-06-03 11:00:37 as along with 1 person aprasad
	Combining Statistical Alignment and Phylogenetic Footprinting to Detect Regulatory Elements. [My Copy] Bioinformatics (18 March 2008) by R Satija, L Pachter, J Hein posted to alignment footprinting noalignment by maximilianh on 2008-05-07 15:29:24 as along with 6 people jo_davies druvus eckart_bindewald Stew gjuggler Ema
	ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species [My Copy] Nucl. Acids Res. (3 May 2008), gkn195. by Bart Hooghe, Paco Hulpiau, Frans van Roy, Pieter De Bleser posted to alignment conserved motif promoter by maximilianh on 2008-05-06 15:56:53 as along with 4 people isimpson idonaldson maralena guhjy
	Confidence in comparative genomics. [My Copy] Genome research, Vol. 18, No. 2. (1 February 2008), pp. 199-200. by Elliott H. Margulies posted to alignment by maximilianh on 2008-04-25 16:49:40 as along with 7 people natstreet druvus pengchy treangen djkt xingxu boudinot
	ReXSpecies--a tool for the analysis of the evolution of gene regulation across species. [My Copy] BMC evolutionary biology, Vol. 8 (14 April 2008), 111. by Stephan Struckmann, Marcos J. Araúzo-Bravo, Hans R. Schöler, Rolland A. Reinbold, Georg Fuellen posted to alignment cross-species-enhancer motif by maximilianh on 2008-04-16 22:32:02 as along with 3 people and 1 group isimpson sim82 cisevol cis-regulatory-evolution
	Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 28. (12 July 2005), pp. 9830-9835. by J. R. Hughes, J. F. Cheng, N. Ventress, et al.S. Prabhakar, K. Clark, E. Anguita, M. De Gobbi, P. de Jong, E. Rubin, D. R. Higgs posted to alignment cns cns-ranking enhancerprediction by maximilianh on 2008-03-05 10:24:56 as along with 1 person olympos
	Computation and Analysis of Genomic Multi-Sequence Alignments [My Copy] Annual Review of Genomics and Human Genetics, Vol. 8, No. 1. (9 May 2007), pp. 193-213. by Mathieu Blanchette posted to alignment by maximilianh on 2007-12-22 20:13:02 as along with 7 people and 1 group natstreet druvus treangen dpollard lilou nklee aprasad EisenLab
	Exploring Conservation of Transcription Factor Binding Sites with CONREAL. [My Copy] Methods Mol Biol, Vol. 395 (2007), pp. 437-448. by E. Berezikov, V. Guryev, E. Cuppen posted to alignment cns scanning by maximilianh on 2007-11-29 14:59:05 as along with 1 person nklee
	Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool. [My Copy] Methods Mol Biol, Vol. 395 (2007), pp. 319-328. by E. Barta posted to alignment conserved footprinting scanning by maximilianh on 2007-11-27 13:04:18 as
	Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements. [My Copy] Methods Mol Biol, Vol. 395 (2007), pp. 425-436. by P. V. Benos, D. L. Corcoran, E. Feingold posted to alignment cns footprinting scanning by maximilianh on 2007-11-27 13:02:58 as
	MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules [My Copy] PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e216. by Saurabh Sinha, Xin He posted to alignment discovery motif scanning by maximilianh on 2007-11-15 16:50:37 as along with 7 people and 2 groups ana dpollard cjeans zwang hpaces Ema uwe EisenLab cis-regulatory-evolution
	Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. [My Copy] Genome biology, Vol. 8, No. 10. (24 October 2007), R225. by Weichun Huang, Joseph R. Nevins, Uwe Ohler posted to alignment by maximilianh on 2007-11-04 00:17:53 as along with 5 people and 2 groups lusk dpollard djkt stajich Garamonfok EisenLab cis-regulatory-evolution
	Incorporating evolution of transcription factor binding sites into annotated alignments. [My Copy] J Biosci, Vol. 32, No. 5. (August 2007), pp. 841-850. by A. S. Bais, S. Grossmann, M. Vingron posted to alignment by maximilianh on 2007-10-09 18:18:53 as along with 1 person and 2 groups dpollard EisenLab cis-regulatory-evolution
	Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons. [My Copy] Trends in genetics : TIG, Vol. 22 (Apr 2006), pp. 187-193. by Elliott Margulies, Christina Chen, Eric Green posted to alignment fromconnotea by maximilianh on 2007-09-23 12:59:12 as
	Simultaneous alignment and annotation of cis-regulatory regions. [My Copy] Bioinformatics (Oxford, England), Vol. 23 (Jan 2007), pp. 44-49. by Abha Bais, Steffen Grossmann, Martin Vingron posted to alignment fromconnotea by maximilianh on 2007-09-23 12:59:11 as
	PROMALS: towards accurate multiple sequence alignments of distantly related proteins -- Pei and Grishin 23 (7): 802 -- Bioinformatics [My Copy] posted to alignment fromconnotea by maximilianh on 2007-09-23 12:59:10 as
	Multiple Non-Collinear TF-map Alignments of Promoter Regions [My Copy] BMC Bioinformatics, Vol. 8 (Apr 2007), pp. 138-138. by Enrique Blanco, Roderic Guigo, Xavier Messeguer posted to alignment fromconnotea by maximilianh on 2007-09-23 12:59:09 as

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fromconnotea	411
motif	172
discovery	125
duplicates	59
scanning	57
synteny	56
enhancer	55
tandem	53
syntenypaper	52
enhancerprediction	43
molecularbiologytechniques	41
combination	36
cns-differences	34
factors	32
cns	31
geneorder	29
cross-species-enhancer	28
noalignment	28
wnt	26
review	23
ncrna	22
conserved	21
phylogenomics	21
alignment	19
phylogeny	18
transcription	18
chipchip	17
promoter	17
ultraconserved	17
notconserved	16
rennes	16
repeated	16
cis-trans	15
otx	15
genome	14
pcr	14
whole	14
cluster	12
enhancerpromotercompatibility	12
insulator	12
disease	11
pwm	11
tools	11
websites	11
chromatin	10
ciona	10
cns-enhancer-screen	10
cns-ranking	10
mirna	10
pwmimprovement	10
randombreakage	10
cns-collaboration	9
dna	9
3dstructure	8
cns-similarity	8
genome-papers	8
pitx	8
promoters	8
application	7
conservation	7
genes	7
genomeregulatoryblocks	7
genomicregulatoryblocks	7
pwmcomparison	7
syntenytools	7
bidirectionalpromoters	6
enhanceosome	6
enhancer-screen	6
enhancer-vertebrate-invertebrate	6
long-range	6
orthology	6
phenotype	6
position	6
promoterprediction	6
redundancy	6
snp	6
chipseq	5
comparative	5
enhancer-and-repeats	5
enhancerdistances	5
genecoregulation	5
methylation	5
microrna	5
similarity	5
structure	5
textmining	5
validated	5
antisensetranscription	4
comparison	4
competition	4
enhancersharing	4
expression	4
footprinting	4
interchromosomal	4
introns	4
otxpaper	4
recognition	4
region	4
silencer	4
wholegenomescanning	4
cionapopulationgenetics	3
coding	3
composition	3
copy-number-variation	3
encode	3
enhancerincodingregion	3
enhancer-prediction	3
evoluation	3
factorclass	3
genometrees	3
go	3
interaction	3
inter-cns-distances	3
matrix	3
mirnaenhancer	3
model-species	3
mutations	3
myarticles	3
ncrnas	3
phylotypicstage	3
promoter-minimal	3
regions	3
regulatory	3
rna-binding	3
syntenyorientation	3
term_recognition	3
tf	3
thermodynamicalmodels	3
trainingset	3
3putr	2
ascidians	2
assayscisregwetlab	2
binding	2
bullshitarticles	2
cellsortingbasedanalysis	2
ciona-gene-annotation	2
cns-database	2
codingconservation	2
core	2
drosophila	2
enhancer-stage-specificity	2
factorinteractions	2
genomiccontext	2
grn	2
histones	2
jshypotheses	2
mammals	2
microarray	2
molecularbiologytools	2
ncrna-long	2
networks	2
of	2
pituitary	2
pluripotency	2
polymorphism	2
prediction	2
protocols	2
pvalue-multiplicity	2
rearrangement	2
regulatory-flexibility	2
replicationorigins	2
site-prediction	2
spacing	2
strengthofmatch	2
tfsynergy	2
ultraconserveddefinition	2
whyconserved	2
applicationbioinf	1
arx	1
autoregulation	1
bioinformatics	1
books	1
cell-cultures	1
ciona-gene-annotations	1
cisregdatabase	1
cns-difference	1
cns-enhance	1
cns-enhancer	1
decoy	1
degeneratesites	1
dlx	1
doublets	1
drosophia	1
drosphila	1
duplicatese	1
element	1
enhancer-contextanalysis	1
factorsclass	1
fastindexing	1
fugu	1
genefamilyfootprinting	1
genemodels	1
generalregulation	1
generegulatorynetworks	1
gibbs	1
grns	1
hmm	1
igh	1
impossible	1
insertionsdeletions	1
intra-primate	1
kernel	1
noaccess	1
nomotif	1
notconservedfunction	1
nucleosome	1
olfactoryreceptors	1
pax6	1
phylogenytools	1
positiveselection	1
primers	1
purificationfromdna	1
sites	1
smarts	1
statistics	1
suppressor	1
syntenypapers	1
transgenesis	1
tr-reviews	1
turnover	1
word	1
writing	1

maximilianh's alignment [19 articles] Export

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