HistCite - Initial sequencing and analysis of the human genome (Lander)

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#	Date / Author / Journal	LCS	GCS	LCR	CR
301	4590 Gilbert N, Lutz S, Morrish TA, Moran JV Multiple fates of L1 retrotransposition intermediates in cultured human cells MOLECULAR AND CELLULAR BIOLOGY. 2005 SEP; 25 (17): 7780-7795	40	61	17	77
302	4657 Dehal P, Boore JL Two rounds of whole genome duplication in the ancestral vertebrate PLOS BIOLOGY. 2005 OCT; 3 (10): Art. No. e314	0	218	17	51
303	4670 Ray DA, Batzer MA Tracking Alu evolution in New World primates BMC EVOLUTIONARY BIOLOGY. 2005 OCT 6; 5: Art. No. 51	5	8	17	82
304	4757 Zhang XHF, Leslie CS, Chasin LA Computational searches for splicing signals METHODS. 2005 DEC; 37 (4): 292-305	2	16	17	67
305	4885 GuhaThakurta D Computational identification of transcriptional regulatory elements in DNA sequence NUCLEIC ACIDS RESEARCH. 2006; 34 (12): 3585-3598	1	32	17	187
306	4943 Wang JX, Song L, Gonder MK, Azrak S, Ray DA, et al. Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms GENE. 2006 JAN 3; 365: 11-20	11	13	17	50
307	4973 Sainz J, Rovensky P, Gudjonsson SA, Thorleifsson G, Stefansson K, et al. Segmental duplication density decrease with distance to human-mouse breaks of synteny EUROPEAN JOURNAL OF HUMAN GENETICS. 2006 FEB; 14 (2): 216-221	1	3	17	23
308	5000 Nguyen DQ, Webber C, Ponting CP Bias of selection on human copy-number variants PLOS GENETICS. 2006 FEB; 2 (2): Art. No. e20	0	77	17	61
309	5055 Shih ACC, Lee DT, Lin L, Peng CL, Chen SH, et al. SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools BMC BIOINFORMATICS. 2006 MAR 2; 7: Art. No. 103	1	6	17	49
310	5093 Costantini M, Clay O, Auletta F, Bernardi G An isochore map of human chromosomes GENOME RESEARCH. 2006 APR; 16 (4): 536-541	11	48	17	44
#	Date / Author / Journal	LCS	GCS	LCR	CR
311	5228 Khelifi A, Meunier J, Duret L, Mouchiroud D GC content evolution of the human and mouse genomes: Insights from the study of processed pseudogenes in regions of different recombination rates JOURNAL OF MOLECULAR EVOLUTION. 2006 JUN; 62 (6): 745-752	6	14	17	70
312	5247 Polak P, Domany E Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes BMC GENOMICS. 2006 JUN 1; 7: Art. No. 133	11	27	17	53
313	5463 Gaffney DJ, Keightley PD Genomic selective constraints in murid noncoding DNA PLOS GENETICS. 2006 NOV; 2 (11): Art. No. e204	0	27	17	54
314	5523 Kordis D, Lovsin N, Gubensek F Phylogenomic analysis of the L1 retrotransposons in Deuterostomia SYSTEMATIC BIOLOGY. 2006 DEC; 55 (6): 886-901	3	8	17	48
315	5586 Mahony S, Corcoran DL, Feingold E, Benos PV Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome GENOME BIOLOGY. 2007; 8 (5): Art. No. r84	0	7	17	71
316	5828 Han K, Konkel MK, Xing J, Wang H, Lee J, et al. Mobile DNA in old world monkeys: A glimpse through the rhesus macaque genome SCIENCE. 2007 APR 13; 316 (5822): 238-240	14	20	17	27
317	6030 Goodier JL, Zhang L, Vetter MR, Kazazian HH LINE-1 ORF1 protein localizes in stress granules with other RNA-Binding proteins, including components of RNA interference RNA-induced silencing complex MOLECULAR AND CELLULAR BIOLOGY. 2007 SEP; 27 (18): 6469-6483	8	19	17	87
318	6086 Han K, Lee J, Meyer TJ, Wang J, Sen SK, et al. Alu recombination-mediated structural deletions in the chimpanzee genome PLOS GENETICS. 2007 OCT; 3 (10): 1939-1949	6	15	17	56
319	6157 Siepel A, Diekhans M, Brejova B, Langton L, Stevens M, et al. Targeted discovery of novel human exons by comparative genomics GENOME RESEARCH. 2007 DEC; 17 (12): 1763-1773	1	14	17	63
320	6287 Levy A, Sela N, Ast G TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates NUCLEIC ACIDS RESEARCH. 2008 JAN; 36: D47-D52	2	5	17	41
#	Date / Author / Journal	LCS	GCS	LCR	CR
321	6337 Irimia M, Rukov JL, Penny D, Garcia-Fernandez J, Vinther J, et al. Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis MOLECULAR BIOLOGY AND EVOLUTION. 2008 FEB; 25 (2): 375-382	3	13	17	50
322	6372 Ji XL, Zhao SY DA and Xiao-two giant and composite LTR-retrotransposon-like elements identified in the human genome GENOMICS. 2008 MAR; 91 (3): 249-258	1	2	17	39
323	6376 Tripathi M, Chauhan UK, Tripathi P, Agrawal S Role of Alu element in detecting population diversity INTERNATIONAL JOURNAL OF HUMAN GENETICS. 2008 MAR-JUN; 8 (1-2): 61-74	0	0	17	80
324	6585 Elgar G, Vavouri T Tuning in to the signals: noncoding sequence conservation in vertebrate genornes TRENDS IN GENETICS. 2008 JUL; 24 (7): 344-352	0	6	17	63
325	6740 Chen LL, Carmichael GG Gene regulation by SINES and inosines Biological consequences of A-to-I editing of Alu element inverted repeats CELL CYCLE. 2008 NOV 1; 7 (21): 3294-3301	0	2	17	89
326	6748 Kechris K, Yang YH, Yeh RF Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays BMC GENOMICS. 2008 NOV 20; 9: Art. No. 551	0	0	17	74
327	6851 Wang JR, Bowen NJ, Marino-Ramirez L, Jordan IK A c-Myc regulatory subnetwork from human transposable element sequences MOLECULAR BIOSYSTEMS. 2009; 5 (12): 1831-1839	0	0	17	41
328	7047 Liu GE, Alkan C, Jiang L, Zhao SY, Eichler EE Comparative analysis of Alu repeats in primate genomes GENOME RESEARCH. 2009 MAY; 19 (5): 876-885	0	0	17	36
329	7123 Horard B, Eymery A, Fourel G, Vassetzky N, Puechberty J, et al. Global analysis of DNA methylation and transcription of human repetitive sequences EPIGENETICS. 2009 JUL; 4 (5): 339-350	0	0	17	71
330	7168 Zhao FQ, Qi J, Schuster SC Tracking the past: Interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius GENOME RESEARCH. 2009 AUG; 19 (8): 1384-1392	1	2	17	47
#	Date / Author / Journal	LCS	GCS	LCR	CR
331	7248 Kramerov DA, Vasetskii NS Short Interspersed Repetitive Sequences as a Phylogenetic Tool MOLECULAR BIOLOGY. 2009 OCT; 43 (5): 735-746	0	0	17	74
332	1904 Tishkoff SA, Verrelli BC Patterns of human genetic diversity: Implications for human evolutionary history and disease ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2003; 4: 293-340	8	116	16	304
333	1927 Rudd MK, Schueler MG, Willard HF Sequence organization and functional annotation of human centromeres COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY. 2003; 68: 141-149	3	11	16	78
334	2152 Guy J, Hearn T, Crosier M, Mudge J, Viggiano L, et al. Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p GENOME RESEARCH. 2003 FEB; 13 (2): 159-172	15	35	16	71
335	2551 Nahon JL Birth of 'human-specific' genes during primate evolution GENETICA. 2003 JUL; 118 (2-3): 193-208	5	23	16	117
336	2734 Wang J, Li ST, Zhang Y, Zheng HK, Xu Z, et al. Vertebrate gene predictions and the problem of large genes NATURE REVIEWS GENETICS. 2003 SEP; 4 (9): 741-749	1	21	16	39
337	2915 Jackson M Duplicate, decouple, disperse: the evolutionary transience of human centromeric regions CURRENT OPINION IN GENETICS & DEVELOPMENT. 2003 DEC; 13 (6): 629-635	4	10	16	42
338	3059 Schadt EE, Edwards SW, GuhaThakurta D, Holder D, Ying L, et al. A comprehensive transcript index of the human genome generated using microarrays and computational approaches GENOME BIOLOGY. 2004; 5 (10): Art. No. R73	10	58	16	48
339	3601 Boissinot S, Entezam A, Young L, Munson PJ, Furano AV The Insertional history of an active family of L1 retrotransposons in humans GENOME RESEARCH. 2004 JUL; 14 (7): 1221-1231	28	35	16	35
340	4019 Locke DP, Jiang Z, Pertz LM, Misceo D, Archidiacono N, et al. Molecular evolution of the human chromosome 15 pericentromeric region CYTOGENETIC AND GENOME RESEARCH. 2005; 108 (1-3): 73-82	4	8	16	44
#	Date / Author / Journal	LCS	GCS	LCR	CR
341	4083 Vinogradov AE Noncoding DNA, isochores and gene expression: nucleosome formation potential NUCLEIC ACIDS RESEARCH. 2005; 33 (2): 559-563	6	35	16	62
342	4089 Fehlbaum P, Guihal C, Bracco L, Cochet O A microarray configuration to quantify expression levels and relative abundance of splice variants NUCLEIC ACIDS RESEARCH. 2005; 33 (5): Art. No. e47	8	36	16	48
343	4290 Margulies EH, Maduro VVB, Thomas PJ, Tomkins JP, Amemiya CT, et al. Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2005 MAR 1; 102 (9): 3354-3359	11	48	16	37
344	4374 Ferreri GC, Liscinsky DM, Mack JA, Eldridge MDB, O'Neill RJ Retention of latent centromeres in the mammalian genome JOURNAL OF HEREDITY. 2005 MAY; 96 (3): 217-224	1	16	16	59
345	4528 Gaffney DJ, Keightley PD The scale of mutational variation in the murid genome GENOME RESEARCH. 2005 AUG; 15 (8): 1086-1094	10	38	16	49
346	4686 Khil PR, Camerini-Otero RD Molecular features and functional constraints in the evolution of the mammalian X chromosome CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY. 2005 NOV-DEC; 40 (6): 313-330	1	5	16	128
347	4874 Farkash EA, Kao GD, Horman SR, Prak ETL Gamma radiation increases endonuclease-dependent L1 retrotransposition in a cultured cell assay NUCLEIC ACIDS RESEARCH. 2006; 34 (4): 1196-1204	3	10	16	46
348	4915 Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, et al. Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes GENOME RESEARCH. 2006 JAN; 16 (1): 55-65	17	113	16	45
349	4949 Sugano T, Kajikawa M, Okada N Isolation and characterization of retrotransposition-competent LINEs from zebrafish GENE. 2006 JAN 3; 365: 74-82	4	9	16	35
350	5010 Lemischka IR, Pritsker M Alternative splicing increases complexity of stem cell transcriptome CELL CYCLE. 2006 FEB 15; 5 (4): 347-351	0	6	16	56
#	Date / Author / Journal	LCS	GCS	LCR	CR
351	5124 Gasior SL, Wakeman TP, Xu B, Deininger PL The human LINE-1 retrotransposon creates DNA double-strand breaks JOURNAL OF MOLECULAR BIOLOGY. 2006 APR 14; 357 (5): 1383-1393	20	41	16	88
352	5147 Byrne KP, Blanc G Computational analyses of ancient polyploidy CURRENT BIOINFORMATICS. 2006 MAY; 1 (2): 131-146	0	1	16	124
353	5176 Sikela JM The jewels of our genome: The search for the genomic changes underlying the evolutionarily unique capacities of the human brain PLOS GENETICS. 2006 MAY; 2 (5): Art. No. e80	0	18	16	76
354	5319 Ryan FP Genomic creativity and natural selection: a modern synthesis BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY. 2006 AUG; 88 (4): 655-672	0	9	16	199
355	5323 Pan YL Advances in the discovery of cis-regulatory elements CURRENT BIOINFORMATICS. 2006 AUG; 1 (3): 321-336	0	4	16	209
356	5345 Muckenfuss H, Hamdorf M, Held U, Perkovic M, Lower J, et al. APOBEC3 proteins inhibit human LINE-1 retrotransposition JOURNAL OF BIOLOGICAL CHEMISTRY. 2006 AUG 4; 281 (31): 22161-22172	18	87	16	74
357	5462 Berry C, Hannenhalli S, Leipzig J, Bushman FD Selection of target sites for mobile DNA integration in the human genome PLOS COMPUTATIONAL BIOLOGY. 2006 NOV; 2 (11): Art. No. e157	0	27	16	46
358	5468 Abrusan G, Krambeck HJ Competition may determine the diversity of transposable elements THEORETICAL POPULATION BIOLOGY. 2006 NOV; 70 (3): 364-375	4	8	16	65
359	5563 Griffiths-Jones S Annotating noncoding RNA genes ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2007; 8: 279-298	2	18	16	102
360	5638 Gonzalez J, Casals F, Ruiz A Testing chromosomal phylogenies and inversion breakpoint reuse in Drosophila GENETICS. 2007 JAN; 175 (1): 167-177	0	4	16	75
#	Date / Author / Journal	LCS	GCS	LCR	CR
361	5666 Romanish MT, Lock WM, van de Lagemaat LN, Dunn CA, Mager DL Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution PLOS GENETICS. 2007 JAN; 3 (1): Art. No. e10	7	15	16	71
362	5689 Mueller M, Martens L, Apweiler R Annotating the human proteome: Beyond establishing a parts list BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS. 2007 FEB; 1774 (2): 175-191	3	10	16	184
363	5786 Pace JK, Feschotte C The evolutionary history of human DNA transposons: Evidence for intense activity in the primate lineage GENOME RESEARCH. 2007 APR; 17 (4): 422-432	18	29	16	58
364	5893 Piriyapongsa J, Marino-Ramirez L, Jordan IK Origin and evolution of human microRNAs from transposable elements GENETICS. 2007 JUN; 176 (2): 1323-1337	9	37	16	79
365	5925 Honda H, Ichiyanagi K, Suzuki J, Ono T, Koyama H, et al. A new system for analyzing LINE retrotransposition in the chicken DT40 cell line widely used for reverse genetics GENE. 2007 JUN 15; 395 (1-2): 116-124	0	2	16	37
366	5942 Goodstadt L, Heger A, Webber C, Ponting CP An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes GENOME RESEARCH. 2007 JUL; 17 (7): 969-981	5	12	16	72
367	5963 Garcia-Perez JL, Marchetto MCN, Muotri AR, Coufal NG, Gage FH, et al. LINE-1 retrotransposition in human embryonic stem cells HUMAN MOLECULAR GENETICS. 2007 JUL 1; 16 (13): 1569-1577	7	13	16	45
368	6090 Sorek R The birth of new exons: Mechanisms and evolutionary consequences RNA-A PUBLICATION OF THE RNA SOCIETY. 2007 OCT; 13 (10): 1603-1608	8	24	16	37
369	6119 Pontius JU, Mullikin JC, Smith DR, Lindblad-Toh K, Gnerre S, et al. Initial sequence and comparative analysis of the cat genome GENOME RESEARCH. 2007 NOV; 17 (11): 1675-1689	10	47	16	102
370	6144 Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK Evaluating the protein coding potential of exonized transposable element sequences BIOLOGY DIRECT. 2007 NOV 26; 2: Art. No. 31	3	9	16	59
#	Date / Author / Journal	LCS	GCS	LCR	CR
371	6217 Han L, Su B, Li WH, Zhao ZM CpG island density and its correlations with genomic features in mammalian genomes GENOME BIOLOGY. 2008; 9 (5): Art. No. R79	1	9	16	46
372	6260 Kazazian HH, Seleme MDC, Babushok DV, Ostertag DM, Vetter MR, et al. Human diversity and L1 retrotransposon biology: Creation of new genes and individual variation in retrotransposition potential RETROTRANSPOSITION, DIVERSITY AND THE BRAIN. 2008; : 43-52	0	0	16	35
373	6384 Newman JC, Bailey AD, Fan HY, Pavelitz T, Weiner AM An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome PLOS GENETICS. 2008 MAR; 4 (3): Art. No. e1000031	1	5	16	79
374	6421 Bradley BJ Reconstructing phylogenies and phenotypes: a molecular view of human evolution JOURNAL OF ANATOMY. 2008 APR; 212 (4): 337-353	0	10	16	203
375	6424 Lagerstrom MC, Schioth HB Structural diversity of G protein-coupled receptors and significance for drug discovery NATURE REVIEWS DRUG DISCOVERY. 2008 APR; 7 (4): 339-357	3	67	16	254
376	6435 Chiba H, Yamashita R, Kinoshita K, Nakai K Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs BMC GENOMICS. 2008 APR 2; 9: Art. No. 152	0	1	16	52
377	6452 Ryazansky SS, Gvozdev VA Small RNAs and cancerogenesis BIOCHEMISTRY-MOSCOW. 2008 MAY; 73 (5): 514-527	0	3	16	204
378	6467 Ram O, Schwartz S, Ast G Multifactorial interplay controls the splicing profile of Alu-derived exons MOLECULAR AND CELLULAR BIOLOGY. 2008 MAY; 28 (10): 3513-3525	0	8	16	50
379	6545 Putnam NH, Butts T, Ferrier DEK, Furlong RF, Hellsten U, et al. The amphioxus genome and the evolution of the chordate karyotype NATURE. 2008 JUN 19; 453 (7198): 1064-U3	6	142	16	80
380	6701 Floris M, Orsini M, Thanaraj TA Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing BMC GENOMICS. 2008 OCT 2; 9: Art. No. 453	0	0	16	60
#	Date / Author / Journal	LCS	GCS	LCR	CR
381	6723 Stocking C, Kozak CA Murine endogenous retroviruses CELLULAR AND MOLECULAR LIFE SCIENCES. 2008 NOV; 65 (21): 3383-3398	0	3	16	150
382	6768 Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, et al. Active Alu retrotransposons in the human genome GENOME RESEARCH. 2008 DEC; 18 (12): 1875-1883	7	8	16	41
383	6827 Wang XF, Jin X, Wang XY, Liu J, Feng JJ, et al. Effects of L1-ORF2 fragments on green fluorescent protein gene expression GENETICS AND MOLECULAR BIOLOGY. 2009; 32 (4): 688-696	0	0	16	35
384	6830 Balasubramanian S, Zheng DY, Liu YJ, Fang G, Frankish A, et al. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes GENOME BIOLOGY. 2009; 10 (1): Art. No. R2	0	2	16	40
385	6876 Srinivasan S, Bingham JL, Johnson D The ABCs of human alternative splicing: A review of ATP-binding cassette transporter splicing CURRENT OPINION IN DRUG DISCOVERY & DEVELOPMENT. 2009 JAN; 12 (1): 149-158	0	0	16	73
386	6946 Derrien T, Theze J, Vaysse A, Andre C, Ostrander EA, et al. Revisiting the missing protein-coding gene catalog of the domestic dog BMC GENOMICS. 2009 FEB 4; 10: Art. No. 62	0	0	16	60
387	6952 Tong CB, Guo BC, He SP Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation BMC GENOMICS. 2009 FEB 19; 10: Art. No. 83	0	0	16	58
388	7014 Pang GSY, Wang JB, Wang ZH, Lee CGL Predicting potentially functional SNPs in drug-response genes PHARMACOGENOMICS. 2009 APR; 10 (4): 639-653	0	0	16	157
389	7170 Walters RD, Kugel JF, Goodrich JA InvAluable Junk: The Cellular Impact and Function of Alu and B2 RNAs IUBMB LIFE. 2009 AUG; 61 (8): 831-837	0	0	16	64
390	7173 Novick PA, Basta H, Floumanhaft M, McClure MA, Boissinot S The Evolutionary Dynamics of Autonomous Non-LTR Retrotransposons in the Lizard Anolis Carolinensis Shows More Similarity to Fish Than Mammals MOLECULAR BIOLOGY AND EVOLUTION. 2009 AUG; 26 (8): 1811-1822	1	2	16	57
#	Date / Author / Journal	LCS	GCS	LCR	CR
391	7188 Adelson DL, Raison JM, Edgar RC Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2009 AUG 4; 106 (31): 12855-12860	0	0	16	51
392	7278 Lewin HA, Larkin DM, Pontius J, O'Brien SJ Every genome sequence needs a good map GENOME RESEARCH. 2009 NOV; 19 (11): 1925-1928	0	2	16	37
393	118 Weinberg RA A question of strategy TRENDS IN BIOCHEMICAL SCIENCES. 2001 APR; 26 (4): 207-208	0	1	15	31
394	1942 Stankiewicz P, Inoue K, Bi W, Walz K, Park SS, et al. Genomic disorders: Genome architecture results in susceptibility to DNA rearrangements causing common human traits COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY. 2003; 68: 445-454	2	13	15	81
395	2094 Boright AP, Kere J, Scherer SW Genomics and pediatric research PEDIATRIC RESEARCH. 2003 JAN; 53 (1): 4-9	0	0	15	60
396	2573 Puente XS, Sanchez LM, Overall CM, Lopez-Otin C Human and mouse proteases: A comparative genomic approach NATURE REVIEWS GENETICS. 2003 JUL; 4 (7): 544-558	14	232	15	143
397	2830 Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, et al. The DNA sequence and analysis of human chromosome 6 NATURE. 2003 OCT 23; 425 (6960): 805-U1	29	77	15	49
398	2865 Long M, Betran E, Thornton K, Wang W The origin of new genes: Glimpses from the young and old NATURE REVIEWS GENETICS. 2003 NOV; 4 (11): 865-875	24	202	15	122
399	2911 Sankoff D Rearrangements and chromosomal evolution CURRENT OPINION IN GENETICS & DEVELOPMENT. 2003 DEC; 13 (6): 583-587	4	23	15	55
400	3252 Leveugle M, Prat K, Popovici C, Birnbaum D, Coulier F Phylogenetic analysis of Ciona intestinalis gene superfamilies supports the hypothesis of successive gene expansions JOURNAL OF MOLECULAR EVOLUTION. 2004 FEB; 58 (2): 168-181	4	25	15	90

Date / Author / Journal

LCS

GCS

LCR

301

4590 Gilbert N, Lutz S, Morrish TA, Moran JV

Multiple fates of L1 retrotransposition intermediates in cultured human cells

MOLECULAR AND CELLULAR BIOLOGY. 2005 SEP; 25 (17): 7780-7795

302

4657 Dehal P, Boore JL

Two rounds of whole genome duplication in the ancestral vertebrate

PLOS BIOLOGY. 2005 OCT; 3 (10): Art. No. e314

218

303

4670 Ray DA, Batzer MA

Tracking Alu evolution in New World primates

BMC EVOLUTIONARY BIOLOGY. 2005 OCT 6; 5: Art. No. 51

304

4757 Zhang XHF, Leslie CS, Chasin LA

Computational searches for splicing signals

METHODS. 2005 DEC; 37 (4): 292-305

305

4885 GuhaThakurta D

Computational identification of transcriptional regulatory elements in DNA sequence

NUCLEIC ACIDS RESEARCH. 2006; 34 (12): 3585-3598

187

306

4943 Wang JX, Song L, Gonder MK, Azrak S, Ray DA, et al.

Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

GENE. 2006 JAN 3; 365: 11-20

307

4973 Sainz J, Rovensky P, Gudjonsson SA, Thorleifsson G, Stefansson K, et al.

Segmental duplication density decrease with distance to human-mouse breaks of synteny

EUROPEAN JOURNAL OF HUMAN GENETICS. 2006 FEB; 14 (2): 216-221

308

5000 Nguyen DQ, Webber C, Ponting CP

Bias of selection on human copy-number variants

PLOS GENETICS. 2006 FEB; 2 (2): Art. No. e20

309

5055 Shih ACC, Lee DT, Lin L, Peng CL, Chen SH, et al.

SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools

BMC BIOINFORMATICS. 2006 MAR 2; 7: Art. No. 103

310

5093 Costantini M, Clay O, Auletta F, Bernardi G

An isochore map of human chromosomes

GENOME RESEARCH. 2006 APR; 16 (4): 536-541

Date / Author / Journal

LCS

GCS

LCR

311

5228 Khelifi A, Meunier J, Duret L, Mouchiroud D

GC content evolution of the human and mouse genomes: Insights from the study of processed pseudogenes in regions of different recombination rates

JOURNAL OF MOLECULAR EVOLUTION. 2006 JUN; 62 (6): 745-752

312

5247 Polak P, Domany E

Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes

BMC GENOMICS. 2006 JUN 1; 7: Art. No. 133

313

5463 Gaffney DJ, Keightley PD

Genomic selective constraints in murid noncoding DNA

PLOS GENETICS. 2006 NOV; 2 (11): Art. No. e204

314

5523 Kordis D, Lovsin N, Gubensek F

Phylogenomic analysis of the L1 retrotransposons in Deuterostomia

SYSTEMATIC BIOLOGY. 2006 DEC; 55 (6): 886-901

315

5586 Mahony S, Corcoran DL, Feingold E, Benos PV

Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome

GENOME BIOLOGY. 2007; 8 (5): Art. No. r84

316

5828 Han K, Konkel MK, Xing J, Wang H, Lee J, et al.

Mobile DNA in old world monkeys: A glimpse through the rhesus macaque genome

SCIENCE. 2007 APR 13; 316 (5822): 238-240

317

6030 Goodier JL, Zhang L, Vetter MR, Kazazian HH

LINE-1 ORF1 protein localizes in stress granules with other RNA-Binding proteins, including components of RNA interference RNA-induced silencing complex

MOLECULAR AND CELLULAR BIOLOGY. 2007 SEP; 27 (18): 6469-6483

318

6086 Han K, Lee J, Meyer TJ, Wang J, Sen SK, et al.

Alu recombination-mediated structural deletions in the chimpanzee genome

PLOS GENETICS. 2007 OCT; 3 (10): 1939-1949

319

6157 Siepel A, Diekhans M, Brejova B, Langton L, Stevens M, et al.

Targeted discovery of novel human exons by comparative genomics

GENOME RESEARCH. 2007 DEC; 17 (12): 1763-1773

320

6287 Levy A, Sela N, Ast G

TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates

NUCLEIC ACIDS RESEARCH. 2008 JAN; 36: D47-D52

Date / Author / Journal

LCS

GCS

LCR

321

6337 Irimia M, Rukov JL, Penny D, Garcia-Fernandez J, Vinther J, et al.

Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis

MOLECULAR BIOLOGY AND EVOLUTION. 2008 FEB; 25 (2): 375-382

322

6372 Ji XL, Zhao SY

DA and Xiao-two giant and composite LTR-retrotransposon-like elements identified in the human genome

GENOMICS. 2008 MAR; 91 (3): 249-258

323

6376 Tripathi M, Chauhan UK, Tripathi P, Agrawal S

Role of Alu element in detecting population diversity

INTERNATIONAL JOURNAL OF HUMAN GENETICS. 2008 MAR-JUN; 8 (1-2): 61-74

324

6585 Elgar G, Vavouri T

Tuning in to the signals: noncoding sequence conservation in vertebrate genornes

TRENDS IN GENETICS. 2008 JUL; 24 (7): 344-352

325

6740 Chen LL, Carmichael GG

Gene regulation by SINES and inosines Biological consequences of A-to-I editing of Alu element inverted repeats

CELL CYCLE. 2008 NOV 1; 7 (21): 3294-3301

326

6748 Kechris K, Yang YH, Yeh RF

Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays

BMC GENOMICS. 2008 NOV 20; 9: Art. No. 551

327

6851 Wang JR, Bowen NJ, Marino-Ramirez L, Jordan IK

A c-Myc regulatory subnetwork from human transposable element sequences

MOLECULAR BIOSYSTEMS. 2009; 5 (12): 1831-1839

328

7047 Liu GE, Alkan C, Jiang L, Zhao SY, Eichler EE

Comparative analysis of Alu repeats in primate genomes

GENOME RESEARCH. 2009 MAY; 19 (5): 876-885

329

7123 Horard B, Eymery A, Fourel G, Vassetzky N, Puechberty J, et al.

Global analysis of DNA methylation and transcription of human repetitive sequences

EPIGENETICS. 2009 JUL; 4 (5): 339-350

330

7168 Zhao FQ, Qi J, Schuster SC

Tracking the past: Interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius

GENOME RESEARCH. 2009 AUG; 19 (8): 1384-1392

Date / Author / Journal

LCS

GCS

LCR

331

7248 Kramerov DA, Vasetskii NS

Short Interspersed Repetitive Sequences as a Phylogenetic Tool

MOLECULAR BIOLOGY. 2009 OCT; 43 (5): 735-746

332

1904 Tishkoff SA, Verrelli BC

Patterns of human genetic diversity: Implications for human evolutionary history and disease

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2003; 4: 293-340

116

304

333

1927 Rudd MK, Schueler MG, Willard HF

Sequence organization and functional annotation of human centromeres

COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY. 2003; 68: 141-149

334

2152 Guy J, Hearn T, Crosier M, Mudge J, Viggiano L, et al.

Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p

GENOME RESEARCH. 2003 FEB; 13 (2): 159-172

335

2551 Nahon JL

Birth of 'human-specific' genes during primate evolution

GENETICA. 2003 JUL; 118 (2-3): 193-208

117

336

2734 Wang J, Li ST, Zhang Y, Zheng HK, Xu Z, et al.

Vertebrate gene predictions and the problem of large genes

NATURE REVIEWS GENETICS. 2003 SEP; 4 (9): 741-749

337

2915 Jackson M

Duplicate, decouple, disperse: the evolutionary transience of human centromeric regions

CURRENT OPINION IN GENETICS & DEVELOPMENT. 2003 DEC; 13 (6): 629-635

338

3059 Schadt EE, Edwards SW, GuhaThakurta D, Holder D, Ying L, et al.

A comprehensive transcript index of the human genome generated using microarrays and computational approaches

GENOME BIOLOGY. 2004; 5 (10): Art. No. R73

339

3601 Boissinot S, Entezam A, Young L, Munson PJ, Furano AV

The Insertional history of an active family of L1 retrotransposons in humans

GENOME RESEARCH. 2004 JUL; 14 (7): 1221-1231

340

4019 Locke DP, Jiang Z, Pertz LM, Misceo D, Archidiacono N, et al.

Molecular evolution of the human chromosome 15 pericentromeric region

CYTOGENETIC AND GENOME RESEARCH. 2005; 108 (1-3): 73-82

Date / Author / Journal

341

Noncoding DNA, isochores and gene expression: nucleosome formation potential

NUCLEIC ACIDS RESEARCH. 2005; 33 (2): 559-563

342

4089 Fehlbaum P, Guihal C, Bracco L, Cochet O

A microarray configuration to quantify expression levels and relative abundance of splice variants

NUCLEIC ACIDS RESEARCH. 2005; 33 (5): Art. No. e47

343

4290 Margulies EH, Maduro VVB, Thomas PJ, Tomkins JP, Amemiya CT, et al.

Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2005 MAR 1; 102 (9): 3354-3359

344

4374 Ferreri GC, Liscinsky DM, Mack JA, Eldridge MDB, O'Neill RJ

Retention of latent centromeres in the mammalian genome

JOURNAL OF HEREDITY. 2005 MAY; 96 (3): 217-224

345

4528 Gaffney DJ, Keightley PD

The scale of mutational variation in the murid genome

GENOME RESEARCH. 2005 AUG; 15 (8): 1086-1094

346

4686 Khil PR, Camerini-Otero RD

Molecular features and functional constraints in the evolution of the mammalian X chromosome

CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY. 2005 NOV-DEC; 40 (6): 313-330

128

347

4874 Farkash EA, Kao GD, Horman SR, Prak ETL

Gamma radiation increases endonuclease-dependent L1 retrotransposition in a cultured cell assay

NUCLEIC ACIDS RESEARCH. 2006; 34 (4): 1196-1204

348

4915 Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, et al.

Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes

GENOME RESEARCH. 2006 JAN; 16 (1): 55-65

113

349

4949 Sugano T, Kajikawa M, Okada N

Isolation and characterization of retrotransposition-competent LINEs from zebrafish

GENE. 2006 JAN 3; 365: 74-82

350

5010 Lemischka IR, Pritsker M

Alternative splicing increases complexity of stem cell transcriptome

CELL CYCLE. 2006 FEB 15; 5 (4): 347-351

Date / Author / Journal

LCS

GCS

LCR

351

5124 Gasior SL, Wakeman TP, Xu B, Deininger PL

The human LINE-1 retrotransposon creates DNA double-strand breaks

JOURNAL OF MOLECULAR BIOLOGY. 2006 APR 14; 357 (5): 1383-1393

352

5147 Byrne KP, Blanc G

Computational analyses of ancient polyploidy

CURRENT BIOINFORMATICS. 2006 MAY; 1 (2): 131-146

124

353

5176 Sikela JM

The jewels of our genome: The search for the genomic changes underlying the evolutionarily unique capacities of the human brain

PLOS GENETICS. 2006 MAY; 2 (5): Art. No. e80

354

5319 Ryan FP

Genomic creativity and natural selection: a modern synthesis

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY. 2006 AUG; 88 (4): 655-672

199

355

5323 Pan YL

Advances in the discovery of cis-regulatory elements

CURRENT BIOINFORMATICS. 2006 AUG; 1 (3): 321-336

209

356

5345 Muckenfuss H, Hamdorf M, Held U, Perkovic M, Lower J, et al.

APOBEC3 proteins inhibit human LINE-1 retrotransposition

JOURNAL OF BIOLOGICAL CHEMISTRY. 2006 AUG 4; 281 (31): 22161-22172

357

5462 Berry C, Hannenhalli S, Leipzig J, Bushman FD

Selection of target sites for mobile DNA integration in the human genome

PLOS COMPUTATIONAL BIOLOGY. 2006 NOV; 2 (11): Art. No. e157

358

5468 Abrusan G, Krambeck HJ

Competition may determine the diversity of transposable elements

THEORETICAL POPULATION BIOLOGY. 2006 NOV; 70 (3): 364-375

359

5563 Griffiths-Jones S

Annotating noncoding RNA genes

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2007; 8: 279-298

102

360

5638 Gonzalez J, Casals F, Ruiz A

Testing chromosomal phylogenies and inversion breakpoint reuse in Drosophila

GENETICS. 2007 JAN; 175 (1): 167-177

Date / Author / Journal

LCS

GCS

LCR

361

5666 Romanish MT, Lock WM, van de Lagemaat LN, Dunn CA, Mager DL

Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution

PLOS GENETICS. 2007 JAN; 3 (1): Art. No. e10

362

5689 Mueller M, Martens L, Apweiler R

Annotating the human proteome: Beyond establishing a parts list

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS. 2007 FEB; 1774 (2): 175-191

184

363

5786 Pace JK, Feschotte C

The evolutionary history of human DNA transposons: Evidence for intense activity in the primate lineage

GENOME RESEARCH. 2007 APR; 17 (4): 422-432

364

5893 Piriyapongsa J, Marino-Ramirez L, Jordan IK

Origin and evolution of human microRNAs from transposable elements

GENETICS. 2007 JUN; 176 (2): 1323-1337

365

5925 Honda H, Ichiyanagi K, Suzuki J, Ono T, Koyama H, et al.

A new system for analyzing LINE retrotransposition in the chicken DT40 cell line widely used for reverse genetics

GENE. 2007 JUN 15; 395 (1-2): 116-124

366

5942 Goodstadt L, Heger A, Webber C, Ponting CP

An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes

GENOME RESEARCH. 2007 JUL; 17 (7): 969-981

367

5963 Garcia-Perez JL, Marchetto MCN, Muotri AR, Coufal NG, Gage FH, et al.

LINE-1 retrotransposition in human embryonic stem cells

HUMAN MOLECULAR GENETICS. 2007 JUL 1; 16 (13): 1569-1577

368

6090 Sorek R

The birth of new exons: Mechanisms and evolutionary consequences

RNA-A PUBLICATION OF THE RNA SOCIETY. 2007 OCT; 13 (10): 1603-1608

369

6119 Pontius JU, Mullikin JC, Smith DR, Lindblad-Toh K, Gnerre S, et al.

Initial sequence and comparative analysis of the cat genome

GENOME RESEARCH. 2007 NOV; 17 (11): 1675-1689

102

370

6144 Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK

Evaluating the protein coding potential of exonized transposable element sequences

BIOLOGY DIRECT. 2007 NOV 26; 2: Art. No. 31

Date / Author / Journal

LCS

GCS

LCR

371

6217 Han L, Su B, Li WH, Zhao ZM

CpG island density and its correlations with genomic features in mammalian genomes

GENOME BIOLOGY. 2008; 9 (5): Art. No. R79

372

6260 Kazazian HH, Seleme MDC, Babushok DV, Ostertag DM, Vetter MR, et al.

Human diversity and L1 retrotransposon biology: Creation of new genes and individual variation in retrotransposition potential

RETROTRANSPOSITION, DIVERSITY AND THE BRAIN. 2008; : 43-52

373

6384 Newman JC, Bailey AD, Fan HY, Pavelitz T, Weiner AM

An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome

PLOS GENETICS. 2008 MAR; 4 (3): Art. No. e1000031

374

6421 Bradley BJ

Reconstructing phylogenies and phenotypes: a molecular view of human evolution

JOURNAL OF ANATOMY. 2008 APR; 212 (4): 337-353

203

375

6424 Lagerstrom MC, Schioth HB

Structural diversity of G protein-coupled receptors and significance for drug discovery

NATURE REVIEWS DRUG DISCOVERY. 2008 APR; 7 (4): 339-357

254

376

6435 Chiba H, Yamashita R, Kinoshita K, Nakai K

Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs

BMC GENOMICS. 2008 APR 2; 9: Art. No. 152

377

6452 Ryazansky SS, Gvozdev VA

Small RNAs and cancerogenesis

BIOCHEMISTRY-MOSCOW. 2008 MAY; 73 (5): 514-527

204

378

6467 Ram O, Schwartz S, Ast G

Multifactorial interplay controls the splicing profile of Alu-derived exons

MOLECULAR AND CELLULAR BIOLOGY. 2008 MAY; 28 (10): 3513-3525

379

6545 Putnam NH, Butts T, Ferrier DEK, Furlong RF, Hellsten U, et al.

The amphioxus genome and the evolution of the chordate karyotype

NATURE. 2008 JUN 19; 453 (7198): 1064-U3

142

380

6701 Floris M, Orsini M, Thanaraj TA

Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing

BMC GENOMICS. 2008 OCT 2; 9: Art. No. 453

Date / Author / Journal

LCS

GCS

LCR

381

6723 Stocking C, Kozak CA

Murine endogenous retroviruses

CELLULAR AND MOLECULAR LIFE SCIENCES. 2008 NOV; 65 (21): 3383-3398

150

382

6768 Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, et al.

Active Alu retrotransposons in the human genome

GENOME RESEARCH. 2008 DEC; 18 (12): 1875-1883

383

6827 Wang XF, Jin X, Wang XY, Liu J, Feng JJ, et al.

Effects of L1-ORF2 fragments on green fluorescent protein gene expression

GENETICS AND MOLECULAR BIOLOGY. 2009; 32 (4): 688-696

384

6830 Balasubramanian S, Zheng DY, Liu YJ, Fang G, Frankish A, et al.

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes

GENOME BIOLOGY. 2009; 10 (1): Art. No. R2

385

6876 Srinivasan S, Bingham JL, Johnson D

The ABCs of human alternative splicing: A review of ATP-binding cassette transporter splicing

CURRENT OPINION IN DRUG DISCOVERY & DEVELOPMENT. 2009 JAN; 12 (1): 149-158

386

6946 Derrien T, Theze J, Vaysse A, Andre C, Ostrander EA, et al.

Revisiting the missing protein-coding gene catalog of the domestic dog

BMC GENOMICS. 2009 FEB 4; 10: Art. No. 62

387

6952 Tong CB, Guo BC, He SP

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

BMC GENOMICS. 2009 FEB 19; 10: Art. No. 83

388

7014 Pang GSY, Wang JB, Wang ZH, Lee CGL

Predicting potentially functional SNPs in drug-response genes

PHARMACOGENOMICS. 2009 APR; 10 (4): 639-653

157

389

7170 Walters RD, Kugel JF, Goodrich JA

InvAluable Junk: The Cellular Impact and Function of Alu and B2 RNAs

IUBMB LIFE. 2009 AUG; 61 (8): 831-837

390

7173 Novick PA, Basta H, Floumanhaft M, McClure MA, Boissinot S

The Evolutionary Dynamics of Autonomous Non-LTR Retrotransposons in the Lizard Anolis Carolinensis Shows More Similarity to Fish Than Mammals

MOLECULAR BIOLOGY AND EVOLUTION. 2009 AUG; 26 (8): 1811-1822

Date / Author / Journal

LCS

GCS

LCR

391

7188 Adelson DL, Raison JM, Edgar RC

Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2009 AUG 4; 106 (31): 12855-12860

392

7278 Lewin HA, Larkin DM, Pontius J, O'Brien SJ

Every genome sequence needs a good map

GENOME RESEARCH. 2009 NOV; 19 (11): 1925-1928

393

118 Weinberg RA

A question of strategy

TRENDS IN BIOCHEMICAL SCIENCES. 2001 APR; 26 (4): 207-208

394

1942 Stankiewicz P, Inoue K, Bi W, Walz K, Park SS, et al.

Genomic disorders: Genome architecture results in susceptibility to DNA rearrangements causing common human traits

COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY. 2003; 68: 445-454

395

2094 Boright AP, Kere J, Scherer SW

Genomics and pediatric research

PEDIATRIC RESEARCH. 2003 JAN; 53 (1): 4-9

396

2573 Puente XS, Sanchez LM, Overall CM, Lopez-Otin C

Human and mouse proteases: A comparative genomic approach

NATURE REVIEWS GENETICS. 2003 JUL; 4 (7): 544-558

232

143

397

2830 Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, et al.

The DNA sequence and analysis of human chromosome 6

NATURE. 2003 OCT 23; 425 (6960): 805-U1

398

2865 Long M, Betran E, Thornton K, Wang W

The origin of new genes: Glimpses from the young and old

NATURE REVIEWS GENETICS. 2003 NOV; 4 (11): 865-875

202

122

399

2911 Sankoff D

Rearrangements and chromosomal evolution

CURRENT OPINION IN GENETICS & DEVELOPMENT. 2003 DEC; 13 (6): 583-587

400

3252 Leveugle M, Prat K, Popovici C, Birnbaum D, Coulier F

Phylogenetic analysis of Ciona intestinalis gene superfamilies supports the hypothesis of successive gene expansions

JOURNAL OF MOLECULAR EVOLUTION. 2004 FEB; 58 (2): 168-181

Initial sequencing and analysis of the human genome (Lander) The papers citing Lander ES, et al. "Initial sequencing and analysis of the human genome." NATURE. 2001 FEB 15; 409 (6822): 860-921	Historiographs	Glossary HistCite Guide About Grand Totals: LCS 38623, GCS 253809, CR 422506 Collection span: 2000 - 2010
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