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Fri Jul 16 11:16:14 2004

Initial sequencing and comparative analysis of the mouse genome
R.H. Waterston et al.
NATURE
420 (6915): 520-562 DEC 5 2002
and the citing papers

Nodes: 549
Authors: 2932, Journals: 196, Outer References: 18463
Collection span: 2002 - 2004
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#LCRNCRNodes / Authors / DateLCSGCS
118483 2004 NATURE 428(6982):464-466
Abbott A
The Renaissance rat
13
2213285 2003 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 100(6):3025-3026
Adams MD; Sutton GG; Smith HO; Myers EW; Venter JC
The independence of our genome assemblies
02
3150218 2003 MOLECULAR AND CELLULAR BIOLOGY 23(21):7648-7657
Adhikary S; Peukert K; Karsunky H; Beuger V; Lutz W; Elsasser HP; Moroy T; Eilers M
Miz1 is required for early embryonic development during gastrulation
00
417061 2003 CURRENT OPINION IN NEUROLOGY 16(4):451-458
Ahmad-Annuar A; Tabrizi SJ; Fisher EMC
Mouse models as a tool for understanding neurodegenerative diseases
02
5128182 2003 INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 12(3):391-397
Ahn SK
A bioinformatics-based approach for the prediction and identification of novel proteins potentially involved in phosphorylation signalling pathways
00
6221511 2004 NUCLEIC ACIDS RESEARCH 32():D523-D527
Akagi K; Suzuki T; Stephens RM; Jenkins NA; Copeland NG
RTCGD: retroviral tagged cancer gene database
03
712915 2003 AUTOIMMUNITY REVIEWS 2(4):177-180
Alarcon-Riquelme ME
Functional genomics in the study of autoimmune diseases
00
8134401 2004 GENOME RESEARCH 14(4):549-554
Alba MM; Guigo R
Comparative analysis of amino acid repeats in rodents and humans
22
91100178 2003 HUMAN MOLECULAR GENETICS 12(22):3025-3040
Amadou C; Younger RM; Sims S; Matthews LH; Rogers J; Kumanovics A; Ziegler A; Beck S; Lindahl KF
Co-duplication of olfactory receptor and MHC class I genes in the mouse major histocompatibility complex
02
1012866 2003 CYTOGENETIC AND GENOME RESEARCH 102(1-4):163-172
Amarger V; Erlandsson R; Pielberg G; Jeon JT; Andersson L
Comparative sequence analysis of the PRKAG3 region between human and pig: evolution of repetitive sequences and potential new exons
00
#LCRNCRNodes / Authors / DateLCSGCS
11141377 2004 GENES TO CELLS 9(4):331-344
Andachi Y
Caenorhabditis elegans T-box genes tbx-9 and tbx-8 are required for formation of hypodermis and body-wall muscle in embryogenesis
00
122107367 2004 FASEB JOURNAL 18(1):8-30
Andersen JN; Jansen PG; Echwald SM; Mortensen OH; Fukada T; Del Vecchio R; Tonks NK; Moller NPH
A genomic perspective on protein tyrosine phosphatases: gene structure, pseudogenes, and genetic disease linkage
02
135100496 2004 NATURE REVIEWS GENETICS 5(3):202-212
Andersson L; Georges M
Domestic-animal genomics: deciphering the genetics of complex traits
02
14112737 2003 CELLULAR AND MOLECULAR LIFE SCIENCES 60(8):1647-1658
Antequera F
Structure, function and evolution of CpG island promoters
12
15328177 2003 HUMAN MOLECULAR GENETICS 12(17):2201-2208
Armengol L; Pujana MA; Cheung J; Scherer SW; Estivill X
Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements
33
16351335 2004 ANNUAL REVIEW OF MEDICINE 55():1-13
Austin CP
The impact of the completed human genome sequence on the development of novel therapeutics for human disease
00
1717683 2003 EAR AND HEARING 24(4):332-341
Avraham KB
Mouse models for deafness: Lessons for the human inner ear and hearing loss
00
18171479 2004 MOLECULAR ENDOCRINOLOGY 18(1):1-12
Avsian-Kretchmer O; Hsueh AJW
Comparative genomic analysis of the eight-membered ring cystine knot-containing bone morphogenetic protein antagonists
02
19190449 2004 JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES 803(1):3-16
Baggerman G; Verleyen P; Clynen E; Huybrechts J; De Loof A; Schoofs L
Peptidomics
00
20836385 2004 GENOME BIOLOGY 5(4):-
Bailey JA; Baertsch R; Kent WJ; Haussler D; Eichler EE
Hotspots of mammalian chromosomal evolution
00
#LCRNCRNodes / Authors / DateLCSGCS
21851419 2004 GENOME RESEARCH 14(5):789-801
Bailey JA; Church DM; Ventura M; Rocchi M; Eichler EE
Analysis of segmental duplications and genome assembly in the mouse
00
223377 2003 AMERICAN JOURNAL OF HUMAN GENETICS 73(4):823-834
Bailey JA; Liu G; Eichler EE
An Alu transposition model for the origin and expansion of human segmental duplications
37
23235461 2004 JOURNAL OF VIROLOGY 78(11):5784-5798
Baillie GJ; van de Lagemaat LN; Baust C; Mager DL
Multiple groups of endogenous betaretroviruses in mice, rats, and other mammals
00
24118141 2003 GENOME RESEARCH 13(6B):1505-1519
Baldarelli RM; Hill DP; Blake JA; Adachi J; Furuno M; Bradt D; Corbani LE; Cousins S; Frazer KS; Qi D; Yang LL; Ramachandran S; Reed D; Zhu YX; Kasukawa T; Ringwald M; King BL; Maltais LJ; McKenzie LM; Schriml LM; Maglott D; Church DM; Pruitt K; Eppig JT; Richardson JE; Kadin JA; Bult CJ
Connecting sequence and biology in the laboratory mouse
36
2515676 2003 DNA AND CELL BIOLOGY 22(7):457-468
Balliet AG; Hollander MC; Fornace AJ; Hoffman B; Liebermann DA
Comparative analysis of the genetic structure and chromosomal mapping of the murine Gadd45g/CR6 gene
00
261107272 2003 PHYSIOLOGICAL GENOMICS 13(1):15-24
Barr MM
Super models
24
27129161 2003 GENOMICS 81(5):519-524
Barrans JD; Ip J; Lam CW; Hwang IL; Dzau VJ; Liew CC
Chromosomal distribution of the human cardiovascular transcriptome
00
2814144 2003 GENOME RESEARCH 13(6B):1552-1553
Batalov S; Fletcher CF
Exon structure analysis, ortholog identification, and SNP candidate screening by mapping mouse RIKEN sequences to multiple genome assemblies
00
29120731 2003 BLOOD 101(6):2099-2114
Baum C; Dullmann J; Li ZX; Fehse B; Meyer J; Williams DA; von Kalle C
Side effects of retroviral gene transfer into hematopoietic stem cells
038
30325489 2004 NATURE 429(6991):558-562
Bazykin GA; Kondrashov FA; Ogurtsov AY; Sunyaev S; Kondrashov AS
Positive selection at sites of multiple amino acid replacements since rat-mouse divergence
00
#LCRNCRNodes / Authors / DateLCSGCS
31287437 2004 GENOMICS 83(6):1012-1023
Beisel KW; Shiraki T; Morris KA; Pompeia C; Kachar B; Arakawa T; Bono H; Kawai J; Hayashizaki Y; Carninci P
Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library
00
321237536 2004 SCIENCE 304(5675):1321-1325
Bejerano G; Pheasant M; Makunin I; Stephen S; Kent WJ; Mattick JS; Haussler D
Ultraconserved elements in the human genome
00
33760488 2004 NATURE 429(6990):440-445
Bentley DR
Genomes for medicine
00
34150211 2003 MAMMALIAN GENOME 14(12):817-829
Bergstrom DE; Bergstrom RA; Munroe RJ; Lee BK; Browning VL; You Y; Eicher EM; Schimenti JC
Overlapping deletions spanning the proximal two-thirds of the mouse t complex
01
35158300 2003 PROTEIN ENGINEERING 16(12):881-888
Bhaduri A; Sowdhamini R
A genome-wide survey of human tyrosine phosphatases
00
3632627 2003 BIOCHEMICAL SOCIETY TRANSACTIONS 31():806-809
Bingle CD; Craven CJ
Comparative analysis of the PLUNC (palate, lung and nasal epithelium clone) protein families
12
37237527 2004 PROTEIN SCIENCE 13(2):422-430
Bingle CD; Leclair EE; Havard S; Bingle L; Gillingham P; Craven CJ
Phylogenetic and evolutionary analysis of the PLUNC gene family
00
3818506 2004 NUCLEIC ACIDS RESEARCH 32():D468-D470
Birney E; Andrews D; Bevan P; Caccamo M; Cameron G; Chen Y; Clarke L; Coates G; Cox T; Cuff J; Curwen V; Cutts T; Down T; Durbin R; Eyras E; Fernandez-Suarez XM; Gane P; Gibbins B; Gilbert J; Hammond M; Hotz H; Iyer V; Kahari A; Jekosch K; Kasprzyk A; Keefe D; Keenan S; Lehvaslaiho H; McVicker G; Melsopp C; Meidl P; Mongin E; Pettett R; Potter S; Proctor G; Rae M; Searle S; Slater G; Smedley D; Smith J; Spooner W; Stabenau A; Stalker J; Storey R; Ureta-Vidal A; Woodwark C; Clamp M; Hubbard T
Ensembl 2004
02
39427425 2004 GENOME RESEARCH 14(5):988-995
Birney E; Clamp M; Durbin R
GeneWise and genomewise
00
40726414 2004 GENOME RESEARCH 14(4):708-715
Blanchette M; Kent WJ; Riemer C; Elnitski L; Smit AFA; Roskin KM; Baertsch R; Rosenbloom K; Clawson H; Green ED; Haussler D; Miller W
Aligning multiple genomic sequences with the threaded blockset aligner
11
#LCRNCRNodes / Authors / DateLCSGCS
4114790 2003 FASEB JOURNAL 17(14):-
Blanco JG; Edick MJ; Relling MV
Etoposide induces chimeric Mll gene fusions
00
42212236 2003 NATURE 426(6965):395-396
Blaxter M
Comparative genomics - Two worms are better than one
12
43146531 2004 REPRODUCTION FERTILITY AND DEVELOPMENT 16(1-2):87-92
Blomberg LA; Zuelke KA
Serial analysis of gene expression (SAGE) during porcine embryo development
00
44145247 2003 NATURE REVIEWS GENETICS 4(4):309-314
Bochner BR
New technologies to assess genotype-phenotype relationships
011
45114304 2003 SCIENCE 299(5611):1391-1394
Boffelli D; McAuliffe J; Ovcharenko D; Lewis KD; Ovcharenko I; Pachter L; Rubin EM
Phylogenetic shadowing of primate sequences to find functional regions of the human genome
2548
461386504 2004 NATURE REVIEWS GENETICS 5(6):456-465
Boffelli D; Nobrega MA; Rubin EM
Comparative genomics at the vertebrate extremes
00
4745439 2004 HEREDITY 92(5):363-364
Bofkin L; Whelan S
Functional needles in a genomic haystack
00
48155185 2003 JOURNAL OF APPLIED PHYSIOLOGY 94(6):2502-2509
Bogue CW
Genetic models in applied physiology - Invited review: Functional genomics in the mouse: Powerful techniques for unraveling the basis of human development and disease
00
4929187 2003 JOURNAL OF APPLIED PHYSIOLOGY 95(4):1335-1337
Bogue M
Mouse Phenome Project: understanding human biology through mouse genetics and genomics
00
50133453 2004 JOURNAL OF MOLECULAR EVOLUTION 58(1):122-130
Boissinot SP; Roos C; Furano AV
Different rates of LINE-1 (L1) retrotransposon amplification and evolution in new world monkeys
00
#LCRNCRNodes / Authors / DateLCSGCS
51195198 2003 JOURNAL OF MEDICAL GENETICS 40(8):553-559
Bomprezzi R; Kovanen PE; Martin R
New approaches to investigating heterogeneity in complex traits
00
52532397 2004 GENOME RESEARCH 14(4):507-516
Bourque G; Pevzner PA; Tesler G
Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes
11
53183447 2004 JOURNAL OF BONE AND MINERAL RESEARCH 19(4):587-599
Bouxsein ML; Uchiyama T; Rosen CJ; Shultz KL; Donahue LR; Turner CH; Sen S; Churchill GA; Muller R; Beamer WG
Mapping quantitative trait loci for vertebral trabecular bone volume fraction and microarchitecture in mice
00
54130226 2003 NATURE 422(6930):433-438
Bowers JE; Chapman BA; Rong JK; Paterson AH
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
128
55147109 2003 GENOME BIOLOGY 4(7):-
Brachat S; Dietrich FS; Voegeli S; Zhang ZH; Stuart L; Lerch A; Gates K; Gaffney T; Philippsen P
Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii
05
56124123 2003 GENOME RESEARCH 13(1):97-102
Bray N; Dubchak I; Pachter L
AVID: A global alignment program
1737
5736258 2003 NUCLEIC ACIDS RESEARCH 31(13):3525-3526
Bray N; Pachter L
MAVID multiple alignment server
610
58150445 2004 JOURNAL OF BIOLOGICAL CHEMISTRY 279(23):24467-24476
Broer A; Klingel K; Kowalczuk S; Rasko JEJ; Cavanaugh J; Broer S
Molecular cloning of mouse amino acid transport system B-0, a neutral amino acid transporter related to Hartnup disorder
00
59726412 2004 GENOME RESEARCH 14(4):685-692
Brudno M; Poliakov A; Salamov A; Cooper GM; Sidow A; Rubin EM; Solovyev V; Batzoglou S; Dubchak I
Automated whole-genome multiple alignment of rat, mouse, and human
11
60345465 2004 MAMMALIAN GENOME 15(5):344-351
Buchner DA; Seburn KL; Frankel WN; Meisler MH
Three ENU-induced neurological mutations in the pore loop of sodium channel Scn8a (Na(v)1.6) and a genetically linked retinal mutation, rd13
00
#LCRNCRNodes / Authors / DateLCSGCS
61136164 2003 GENOMICS 82(4):452-459
Buchner DA; Trudeau M; George AL; Sprunger LK; Meisler MH
High-resolution mapping of the sodium channel modifier Scnm1 on mouse chromosome 3 and identification of a 1.3-kb recombination hot spot
00
621111244 2003 NATURE REVIEWS GENETICS 4(3):195-205
Buer J; Balling R
Mice, microbes and models of infection
05
6329508 2004 NUCLEIC ACIDS RESEARCH 32():D476-D481
Bult CJ; Blake JA; Richardson JE; Kadin JA; Eppig JT
The Mouse Genome Database (MGD): integrating biology with the genome
02
647125381 2004 GENOME BIOLOGY 5(1):-
Bulyk ML
Computational prediction of transcription-factor binding site locations
00
65161359 2004 DIFFERENTIATION 72(2-3):92-102
Calegari F; Marzesco AM; Kittler R; Buchholz F; Huttner WB
Tissue-specific RNA interference in post-implantation mouse embryos using directional electroporation and whole embryo culture
00
6624500 2004 NATURE REVIEWS GENETICS 5(5):327-327
Campbell N
Year of the rat
00
67127107 2003 GENOME BIOLOGY 4(3):-
Canestro C; Bassham S; Postlethwait JH
Seeing chordate evolution through the Ciona genome sequence
01
6812111 2003 AMERICAN SCIENTIST 91(3):234-241
Caporale LH
Foresight in genome evolution
00
6948538 2003 CELLULAR MICROBIOLOGY 5(12):861-873
Carlton JM
Genome sequencing and comparative genomics of tropical disease pathogens
00
70169533 2004 RNA-A PUBLICATION OF THE RNA SOCIETY 10(5):828-840
Carmel I; Tal S; Vig I; Ast G
Comparative analysis detects dependencies among the 5 ' splice-site positions
11
#LCRNCRNodes / Authors / DateLCSGCS
71164132 2003 GENOME RESEARCH 13(6B):1273-1289
Carninci P; Waki K; Shiraki T; Konno H; Shibata K; Itoh M; Aizawa K; Arakawa T; Ishii Y; Sasaki D; Bono H; Kondo S; Sugahara Y; Saito R; Osato N; Fukuda S; Sato K; Watahiki A; Hirozane-Kishikawa T; Nakamura M; Shibata Y; Yasunishi A; Kikuchi N; Yoshiki A; Kusakabe M; Gustincich S; Beisel K; Pavan W; Aidinis V; Nakagawara A; Held WA; Iwata H; Kono T; Nakauchi H; Lyons P; Wells C; Hume DA; Fagiolini M; Hensch TK; Brinkmeier M; Camper S; Hirota J; Mombaerts P; Muramatsu M; Okazaki Y; Kawai J; Hayashizaki Y
Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia
311
72192228 2003 NATURE 422(6934):849-857
Carroll SB
Genetics and the making of Homo sapiens
114
73362420 2004 GENOME RESEARCH 14(5):802-811
Castillo-Davis CI; Kondrashov FA; Hartl DL; Kulathinal RJ
The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint
00
745196443 2004 JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 37(1):93-106
Castrillo JO; Oliver SG
Yeast as a touchstone in post-genomic research: Strategies for integrative analysis in functional genomics
00
75349350 2004 CELL 116(4):499-509
Cawley S; Bekiranov S; Ng HH; Kapranov P; Sekinger EA; Kampa D; Piccolboni A; Sementchenko V; Cheng J; Williams AJ; Wheeler R; Wong B; Drenkow J; Yamanaka M; Patel S; Brubaker S; Tammana H; Helt G; Struhl K; Gingeras TR
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
17
76313256 2003 NUCLEIC ACIDS RESEARCH 31(13):3507-3509
Cawley S; Pachter L; Alexandersson M
SLAM web server for comparative gene finding and alignment
01
77489476 2004 MOLECULAR BIOLOGY AND EVOLUTION 21(6):1014-1023
Chamary JV; Hurst LD
Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: Evidence for selectively driven codon usage
00
78124372 2004 GENE 330():19-27
Chavanas S; Mechin MC; Takahara H; Kawada A; Nachat R; Serre G; Simon M
Comparative analysis of the mouse and human peptidylarginine deiminase gene clusters reveals highly conserved non-coding segments and a new human gene, PADI6
00
79113411 2004 GENOME RESEARCH 14(4):679-684
Chen R; Sodergren E; Weinstock GM; Gibbs RA
Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project
11
80242492 2004 NATURE GENETICS 36(3):304-312
Chen WSV; Delrow J; Corrin PD; Frazier JP; Soriano P
Identification and validation of PDGF transcriptional targets by microarray-coupled gene-trap mutagenesis
00
#LCRNCRNodes / Authors / DateLCSGCS
8112148 2003 CURRENT BIOLOGY 13(24):2206-2211
Chen XG; Smith JD; Shi H; Yang DD; Flavell RA; Wolin SL
The Ro autoantigen binds misfolded U2 small nuclear RNAs and assists mammalian cell survival after UV irradiation
11
82293454 2004 JOURNAL OF MOLECULAR MEDICINE-JMM 82(4):232-239
Chen XG; Wolin SL
The Ro 60 kDa autoantigen: insights into cellular function and role in autoimmunity
00
83140212 2003 MAMMALIAN GENOME 14(12):859-865
Chen YJ; Yu P; Luo JC; Jiang Y
Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT
00
84834269 2003 PHARMACOGENOMICS 4(5):571-582
Cheng JF; Pennacchio LA
Comparative and functional analysis of cardiovascular-related genes
00
85144111 2003 GENOME BIOLOGY 4(8):-
Cheung J; Wilson MD; Zhang JJ; Khaja R; MacDonald JR; Heng HHQ; Koop BF; Scherer SW
Recent segmental and gene duplications in the mouse genome
06
8625342 2004 BMC BIOINFORMATICS 5():-
Chi B; deLeeuw RJ; Coe BP; MacAulay C; Lam WL
SeeGH - A software tool for visualization of whole genome array comparative genomic hybridization data
00
8717369 2003 DEVELOPMENT GENES AND EVOLUTION 213(5-6):291-302
Chiba S; Awazu S; Itoh M; Chin-Bow ST; Satoh N; Satou Y; Hastings KEM
A genomewide survey of developmentally relevant genes in Ciona intestinalis - IX. Genes for muscle structural proteins
03
88133433 2004 GENOMICS 83(4):636-646
Choi IC; Oh JS; Cho BN; Ahnn JH; Jung YK; Kim DH; Cho CH
Characterization and comparative genomic analysis of intronless Adams with testicular gene expression
00
89326339 2004 BIOINFORMATICS 20(7):1053-1059
Choi KP; Zeng FF; Zhang LX
Good spaced seeds for homology search
00
90126389 2004 GENOME RESEARCH 14(1):188-196
Chung YJ; Jonkers J; Kitson H; Fiegler H; Humphray S; Scott C; Hunt S; Yu Y; Nishijima I; Velds A; Holstege H; Carter N; Bradley A
A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization
00
#LCRNCRNodes / Authors / DateLCSGCS
91253160 2003 GENOME RESEARCH 13(12):2747-2753
Clark MS; Edwards YJK; Peterson D; Clifton SW; Thompson AJ; Sasaki M; Suzuki Y; Kikuchi K; Watabe S; Kawakami K; Sugano S; Elgar G; Johnson SL
Fugu ESTs: New resources for transcription analysis and genome annotation
00
92130430 2004 GENOMICS 83(3):373-383
Clark RM; Dalgliesh GL; Endres D; Gomez M; Taylor J; Bidichandani SI
Expansion of GAA triplet repeats in the human genome: unique origin of the FRDA mutation at the center of an Alu
00
93144227 2003 NATURE 422(6934):835-847
Collins FS; Green ED; Guttmacher AE; Guyer MS
A vision for the future of genomics research
1488
9411030 2003 BIOTECHNIQUES 34(6):1136-+
Conrad M; Brielmeier M; Wurst W; Bornkamm GW
Optimized vector for conditional gene targeting in mouse embryonic stem cells
00
95134273 2003 PHYSIOLOGICAL GENOMICS 14(1):73-82
Conte C; Ebeling M; Marcuz A; Nef P; Andres-Barquin PJ
Evolutionary relationships of the Tas2r receptor gene families in mouse and human
01
96156200 2003 JOURNAL OF MOLECULAR BIOLOGY 333(5):1045-1059
Contreras-Moreira B; Johnsson PF; Bates PA
Structural context of exons in protein domains: Implications for protein modelling and design
00
97729400 2004 GENOME RESEARCH 14(4):539-548
Cooper GM; Brudno M; Stone EA; Dubchak I; Batzoglou S; Sidow A
Characterization of evolutionary rates and constraints in three mammalian genomes
22
9874652 2003 CURRENT OPINION IN GENETICS & DEVELOPMENT 13(6):604-610
Cooper GM; Sidow A
Genomic regulatory regions: insights from comparative sequence analysis
11
9954755 2003 CURRENT OPINION IN GENETICS & DEVELOPMENT 13(6):623-628
Copley RR; Goodstadt L; Ponting C
Eukaryotic domain evolution inferred from genome comparisons
12
10013194 2003 GENE 310():215-220
Costas J; Casares F; Vieira J
Turnover of binding sites for transcription factors involved in early Drosophila development
13

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