maximilianh's fromconnotea [at least 200 articles] Export

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	De novo discovery of a tissue-specific gene regulatory module in a chordate. [My Copy] Genome research, Vol. 15 (Oct 2005), pp. 1315-1324. by David Johnson, Qing Zhou, Kasumi Yagi, Nori Satoh, Wing Wong, Arend Sidow posted to ciona fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans. [My Copy] Developmental cell, Vol. 6 (Jun 2004), pp. 757-770. by Adam Wenick, Oliver Hobert posted to ciona fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. [My Copy] Genome research, Vol. 12 (May 2002), pp. 701-712. by Debraj Guhathakurta, Lisanne Palomar, Gary Stormo, et al.Pat Tedesco, Thomas Johnson, David Walker, Gordon Lithgow, Stuart Kim, Christopher Link posted to rennes fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Computational prediction of novel components of lung transcriptional networks. [My Copy] Bioinformatics (Oxford, England), Vol. 23 (Jan 2007), pp. 21-29. by M. Martinez, Andrew Smith, Bilan Li, Michael Zhang, Kevin Harrod posted to rennes fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Systematic discovery of regulatory motifs in human promoters and 3[prime] UTRs by comparison of several mammals [My Copy] Nature, Vol. 434 (Mar 2005), pp. 338-345. by Xiaohui Xie, Jun Lu, E. Kulbokas, et al.Todd Golub, Vamsi Mootha, Kerstin L. Toh, Eric Lander, Manolis Kellis posted to rennes fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates [My Copy] Genome Biology, Vol. 6 (Dec 2005), pp. 104-104. by Laurence Ettwiller, Benedict Paten, Marcel Souren, Felix Loosli, Jochen Wittbrodt, Ewan Birney posted to rennes fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Identification of transcriptional regulatory elements in chemosensory receptor genes by probabilistic segmentation. [My Copy] Current biology : CB, Vol. 15 (Feb 2005), pp. 347-352. by Steven Mccarroll, Hao Li, Cornelia Bargmann posted to rennes fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Novel transcription regulatory elements in Caenorhabditis elegans muscle genes [My Copy] Genome Research, Vol. 14 (Dec 2004), pp. 2457-2468. by Debraj Guhathakurta, Lawrence Schriefer, Robert Waterston, Gary Stormo posted to rennes fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Transcriptional Control in the Segmentation Gene Network of Drosophila [My Copy] PLoS Biology, Vol. 2 (Sep 2004), pp. 271-271. by Mark Schroeder, Michael Pearce, John Fak, et al.Hongqing Fan, Ulrich Unnerstall, Eldon Emberly, Nikolaus Rajewsky, Eric Siggia, Ulrike Gaul posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome [My Copy] Proceedings of the National Academy of Sciences, Vol. 99 (Jan 2002), pp. 757-762. by Benjamin Berman, Yutaka Nibu, Barret Pfeiffer, et al.Pavel Tomancak, Susan Celniker, Michael Levine, Gerald Rubin, Michael Eisen posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. [My Copy] BMC bioinformatics, Vol. 3 (Oct 2002), pp. 30-30. by Nikolaus Rajewsky, Massimo Vergassola, Ulrike Gaul, Eric Siggia posted to cluster scanning fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Computational models for neurogenic gene expression in the Drosophila embryo. [My Copy] Current biology : CB, Vol. 16 (Jul 2006), pp. 1358-1365. by Robert Zinzen, Kate Senger, Mike Levine, Dmitri Papatsenko posted to expression prediction fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless. [My Copy] Genome research, Vol. 16 (Apr 2006), pp. 466-476. by Edwin Ostrin, Yumei Li, Kristi Hoffman, et al.Jing Liu, Keqing Wang, Li Zhang, Graeme Mardon, Rui Chen posted to genome whole fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Computational discovery of DNA motifs associated with cell type-specific gene expression in Ciona. [My Copy] Developmental biology, Vol. 276 (Dec 2004), pp. 563-580. by Takehiro Kusakabe, Reiko Yoshida, Yoko Ikeda, Motoyuki Tsuda posted to ciona fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. [My Copy] BMC genomics, Vol. 5 (xx 2004), pp. 99-99. by Albin Sandelin, Peter Bailey, Sara Bruce, et al.Pär Engström, Joanna Klos, Wyeth Wasserman, Johan Ericson, Boris Lenhard posted to conserved fromconnotea genomicregulatoryblocks ultraconserved by maximilianh on 2007-09-23 12:59:15 as
	Identification of regulatory regions which confer muscle-specific gene expression. [My Copy] Journal of molecular biology, Vol. 278 (Apr 1998), pp. 167-181. by W. W. Wasserman, J. W. Fickett posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Profiles of Growth Hormone (GH)-regulated Genes Reveal Time-dependent Responses and Identify a Mechanism for Regulation of Activating Transcription Factor 3 By GH [My Copy] Journal of Biological Chemistry, Vol. 281 (Feb 2006), pp. 4132-4141. by Jeffrey Huo, Richard Mceachin, Tracy Cui, et al.Nisha Duggal, Tsonwin Hai, David States, Jessica Schwartz posted to gibbs fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Evolutionary changes in cis and trans gene regulation. [My Copy] Nature, Vol. 430 (Jul 2004), pp. 85-88. by Patricia Wittkopp, Belinda Haerum, Andrew Clark posted to cis-trans fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	A regulatory code for neurogenic gene expression in the Drosophila embryo. [My Copy] Development (Cambridge, England), Vol. 131 (May 2004), pp. 2387-2394. by Michele Markstein, Robert Zinzen, Peter Markstein, et al.Ka P. Yee, Albert Erives, Angela Stathopoulos, Michael Levine posted to rennes fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. [My Copy] Genome biology, Vol. 5 (xx 2004), pp. 61-61. by Benjamin Berman, Barret Pfeiffer, Todd Laverty, et al.Steven Salzberg, Gerald Rubin, Michael Eisen, Susan Celniker posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	PLoS Computational Biology: Practical Strategies for Discovering Regulatory DNA Sequence Motifs [My Copy] posted to discovery motif fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Experimental validation of predicted mammalian erythroid cis-regulatory modules [My Copy] Genome Research (Oct 2006), pp. 5353806-5353806. by Hao Wang, Ying Zhang, Yong Cheng, et al.Yuepin Zhou, David King, James Taylor, Francesca Chiaromonte, Jyotsna Kasturi, Hanna Petrykowska, Brian Gibb, Christine Dorman, Webb Miller, Louis Dore, John Welch, Mitchell Weiss, Ross Hardison posted to validated fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	MicroRNAs preferentially target the genes with high transcriptional regulation complexity. [My Copy] Biochem Biophys Res Commun (Nov 2006) by Qinghua Cui, Zhenbao Yu, Youlian Pan, Enrico Purisima, Edwin Wang posted to microrna fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Conservation and divergence of the Emicro3' enhancer in the IGH locus of teleosts. [My Copy] Immunogenetics, Vol. 58 (Apr 2006), pp. 226-234. by Jun I. Hikima, Mara Lennard, Melanie Wilson, Norman Miller, L. Clem, Gregory Warr posted to igh fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Identification of Cis-regulatory elements in the mouse Pax9/Nkx2-9 genomic region: implication for evolutionary conserved synteny. [My Copy] Genetics, Vol. 165 (Sep 2003), pp. 235-242. by Fabio Santagati, Kuniya Abe, Volker Schmidt, et al.Thomas S. John, Misao Suzuki, Ken I. Yamamura, Kenji Imai posted to conserved regions fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Identification of genomic sites that bind the Drosophila suppressor of Hairy-wing insulator protein. [My Copy] Molecular and cellular biology, Vol. 26 (Aug 2006), pp. 5983-5993. by Timothy Parnell, Emily Kuhn, Brian Gilmore, Cecilia Helou, Marc Wold, Pamela Geyer posted to genome whole fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. [My Copy] Cell, Vol. 111 (Nov 2002), pp. 687-701. by Angelike Stathopoulos, Madeleine Van Drenth, Albert Erives, Michele Markstein, Michael Levine posted to genome whole fromconnotea by maximilianh on 2007-09-23 12:59:15 as
	Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells. [My Copy] PLoS computational biology, Vol. 2 (May 2006), pp. 53-53. by Anthony Philippakis, Brian Busser, Stephen Gisselbrecht, et al.Fangxue He, Beatriz Estrada, Alan Michelson, Martha Bulyk posted to drosophia fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. [My Copy] Genome research, Vol. 12 (Jul 2002), pp. 1019-1028. by Marc Halfon, Yonatan Grad, George Church, Alan Michelson posted to genome whole fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. [My Copy] Bioinformatics (Oxford, England), Vol. 20 (Nov 2004), pp. 2738-2750. by Yonatan Grad, Frederick Roth, Marc Halfon, George Church posted to cns similarity fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	DNA motifs in human and mouse proximal promoters predict tissue-specific expression. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 103 (Apr 2006), pp. 6275-6280. by Andrew Smith, Pavel Sumazin, Zhenyu Xuan, Michael Zhang posted to genome whole fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Regulation of Hypocretin (Orexin) Expression in Embryonic Zebrafish [My Copy] Journal of Biological Chemistry, Vol. 281 (Oct 2006), pp. 29753-29761. by Juliette Faraco, Lior Appelbaum, Wilfredo Marin, Stephanie Gaus, Philippe Mourrain, Emmanuel Mignot posted to core element fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Restriction of transgene expression to the B-lymphoid progeny of human lentivirally transduced CD34+ cells. [My Copy] Molecular therapy : the journal of the American Society of Gene Therapy, Vol. 10 (Jul 2004), pp. 45-56. by Thomas Moreau, Florence Bardin, Jean Imbert, Christian Chabannon, Cécile Tonnelle posted to region repeated fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs. [My Copy] BMC bioinformatics, Vol. 7 Suppl 4 (xx 2006), pp. 21-21. by Linyong Mao, W. Zheng posted to discovery motif fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	EXMOTIF: efficient structured motif extraction. [My Copy] Algorithms for molecular biology : AMB, Vol. 1 (xx 2006), pp. 21-21. by Yongqiang Zhang, Mohammed Zaki posted to discovery motif fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	SMOTIF: efficient structured pattern and profile motif search. [My Copy] Algorithms for molecular biology : AMB, Vol. 1 (xx 2006), pp. 22-22. by Yongqiang Zhang, Mohammed Zaki posted to combination fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster [My Copy] PLoS Computational Biology, Vol. 3 (Jan 2007), pp. 7-7. by Thomas Down, Casey Bergman, Jing Su, Tim Hubbard posted to genome whole fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Simultaneous alignment and annotation of cis-regulatory regions -- Bais et al. 23 (2): e44 -- Bioinformatics [My Copy] posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects -- Noto and Craven 23 (2): e156 -- Bioinformatics [My Copy] posted to discovery motif fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Predicting transcription factor affinities to DNA from a biophysical model -- Roider et al. 23 (2): 134 -- Bioinformatics [My Copy] posted to motif scanning fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	PEAKS: identification of regulatory motifs by their position in DNA sequences -- Bellora et al. 23 (2): 243 -- Bioinformatics [My Copy] posted to position fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Long-range downstream enhancers are essential for Pax6 expression. [My Copy] Developmental biology, Vol. 299 (Nov 2006), pp. 563-581. by Dirk Kleinjan, Anne Seawright, Sebastien Mella, et al.Catherine Carr, David Tyas, T. Simpson, John Mason, David Price, Veronica Van Heyningen posted to cns-enhancer-screen fromconnotea long-range mammals by maximilianh on 2007-09-23 12:59:14 as
	Multiple upstream modules regulate zebrafish myf5 expression. [My Copy] BMC developmental biology, Vol. 7 (xx 2007), pp. 1-1. by Yau H. Chen, Yun H. Wang, Min Y. Chang, et al.Cheng Y. Lin, Chih W. Weng, Monte Westerfield, Huai J. Tsai posted to enhancer fromconnotea by maximilianh on 2007-09-23 12:59:14 as
	Conserved distances between vertebrate highly conserved elements -- Sun et al. 15 (19): 2911 -- Human Molecular Genetics [My Copy] posted to inter-cns-distances fromconnotea by maximilianh on 2007-09-23 12:59:13 as
	MEDAKA - A MODEL ORGANISM FROM THE FAR EAST [My Copy] Nature Reviews Genetics, Vol. 3 (Jan 2002), pp. 53-64. by Joachim Wittbrodt, Akihiro Shima, Manfred Schartl posted to model-species fromconnotea by maximilianh on 2007-09-23 12:59:13 as
	Functional analysis of the chicken {delta}1-crystallin enhancer activity in Drosophila reveals remarkable evolutionary conservation between chicken and fly -- Blanco et al. 132 (8): 1895 -- Development [My Copy] posted to cross-species-enhancer fromconnotea by maximilianh on 2007-09-23 12:59:13 as
	Functional analysis of the sea urchin-derived arylsulfatase (Ars)-element in mammalian cells. [My Copy] Genes to cells : devoted to molecular & cellular mechanisms, Vol. 11 (Sep 2006), pp. 1009-1021. by Satoshi Watanabe, Sachiko Watanabe, Naoaki Sakamoto, Masahiro Sato, Koji Akasaka posted to cross-species-enhancer fromconnotea by maximilianh on 2007-09-23 12:59:13 as
	Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. [My Copy] Cell, Vol. 124 (Jan 2006), pp. 47-59. by Outi Hallikas, Kimmo Palin, Natalia Sinjushina, et al.Reetta Rautiainen, Juha Partanen, Esko Ukkonen, Jussi Taipale posted to validated fromconnotea by maximilianh on 2007-09-23 12:59:13 as
	Hoxb1 enhancer and control of rhombomere 4 expression: complex interplay between PREP1-PBX1-HOXB1 binding sites. [My Copy] Molecular and cellular biology, Vol. 25 (Oct 2005), pp. 8541-8552. by Elisabetta Ferretti, Francisco Cambronero, Stefan Tümpel, et al.Elena Longobardi, Leanne Wiedemann, Francesco Blasi, Robb Krumlauf posted to enhancer fromconnotea by maximilianh on 2007-09-23 12:59:13 as
	Schnurri transcription factors from Drosophila and vertebrates can mediate Bmp signaling through a phylogenetically conserved mechanism. [My Copy] Development (Cambridge, England), Vol. 133 (Oct 2006), pp. 4025-4034. by Li C. Yao, Ira Blitz, Daniel Peiffer, et al.Sopheap Phin, Ying Wang, Souichi Ogata, Ken Cho, Kavita Arora, Rahul Warrior posted to cross-species-enhancer fromconnotea by maximilianh on 2007-09-23 12:59:13 as

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fromconnotea	411
motif	171
discovery	124
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
comparative	5
enhancer-and-repeats	5
enhancerdistances	5
genecoregulation	5
methylation	5
microrna	5
similarity	5
structure	5
textmining	5
validated	5
antisensetranscription	4
chipseq	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 fromconnotea [at least 200 articles] Export

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