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

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#	Date / Author / Journal	LCS	GCS	LCR	CR
1	5698 Sawatzki HK, Cooper DN Understanding the recent evolution of the human genome: Insights from human-chimpanzee genome comparisons HUMAN MUTATION. 2007 FEB; 28 (2): 99-130	0	1	95	478
2	6370 Belancio VP, Hedges DJ, Deininger P Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health GENOME RESEARCH. 2008 MAR; 18 (3): 343-358	19	26	95	201
3	7250 Cordaux R, Batzer MA The impact of retrotransposons on human genome evolution NATURE REVIEWS GENETICS. 2009 OCT; 10 (10): 691-703	1	2	94	167
4	5975 Artamonova II, Gelfand MS Comparative genomics and evolution of alternative splicing: The pessimists' science CHEMICAL REVIEWS. 2007 AUG; 107 (8): 3407-3430	3	12	84	384
5	4022 Brosius J Echoes from the past - are we still in an RNP world? CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 8-24	7	17	72	302
6	5902 Babushok DV, Kazazian HH Progress in understanding the biology of the human mutagen LINE-1 HUMAN MUTATION. 2007 JUN; 28 (6): 527-539	17	31	64	160
7	3413 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution NATURE. 2004 APR 1; 428 (6982): 493-521	269	752	58	226
8	7311 Gogvadze E, Buzdin A Retroelements and their impact on genome evolution and functioning CELLULAR AND MOLECULAR LIFE SCIENCES. 2009 DEC; 66 (23): 3727-3742	0	0	57	157
9	7118 Oliver KR, Greene WK Transposable elements: powerful facilitators of evolution BIOESSAYS. 2009 JUL; 31 (7): 703-714	0	0	56	147
10	6362 Bohne A, Brunet F, Galiana-Arnoux D, Schultheis C, Volff JN Transposable elements as drivers of genomic and biological diversity in vertebrates CHROMOSOME RESEARCH. 2008 MAR; 16 (1): 203-215	10	19	53	109
#	Date / Author / Journal	LCS	GCS	LCR	CR
11	5553 Xing JC, Witherspoon DJ, Ray DA, Batzer MA, Jorde LB Mobile DNA elements in primate and human evolution AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY. 2007; : 2-19	0	0	52	214
12	5733 Babushok DV, Ostertag EM, Kazazian HH Current topics in genome evolution: Molecular mechanisms of new gene formation CELLULAR AND MOLECULAR LIFE SCIENCES. 2007 MAR; 64 (5): 542-554	3	28	52	131
13	5621 Buzdin A Human-specific endogenous retroviruses THESCIENTIFICWORLDJOURNAL. 2007; 7: 1848-1868	3	0	51	148
14	5863 Mattick JS A new paradigm for developmental biology JOURNAL OF EXPERIMENTAL BIOLOGY. 2007 MAY 1; 210 (9): 1526-1547	6	58	48	367
15	6192 Beauregard A, Curcio MJ, Belfort M The Take and Give Between Retrotransposable Elements and their Hosts ANNUAL REVIEW OF GENETICS. 2008; 42: 587-617	2	10	46	211
16	7340 Cohen CJ, Lock WM, Mager DL Endogenous retroviral LTRs as promoters for human genes: A critical assessment GENE. 2009 DEC 15; 448 (2): 105-114	0	0	44	137
17	1865 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. Initial sequencing and comparative analysis of the mouse genome NATURE. 2002 DEC 5; 420 (6915): 520-562	1083	2474	43	331
18	3953 Hillier LW, Miller W, Birney E, Warren W, Hardison RC, et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution NATURE. 2004 DEC 9; 432 (7018): 695-716	143	697	43	165
19	6106 Muotri AR, Marchetto MCN, Coufal NG, Gage FH The necessary junk: new functions for transposable elements HUMAN MOLECULAR GENETICS. 2007 OCT 15; 16: R159-R167	6	18	43	77
20	4579 Chen JM, Stenson PD, Cooper DN, Ferec C A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease HUMAN GENETICS. 2005 SEP; 117 (5): 411-427	34	52	42	133
#	Date / Author / Journal	LCS	GCS	LCR	CR
21	5557 Feschotte C, Pritham EJ DNA transposons and the evolution of eukaryotic genomes ANNUAL REVIEW OF GENETICS. 2007; 41: 331-368	13	48	42	236
22	2993 Miller W, Makova KD, Nekrutenko A, Hardison RC Comparative genomics ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2004; 5: 15-56	14	77	41	193
23	5974 Tang H Genome assembly, rearrangement, and repeats CHEMICAL REVIEWS. 2007 AUG; 107 (8): 3391-3406	0	1	41	154
24	6724 Pidpala OV, Yatsishina AP, Lukash LL Human Mobile Genetic Elements: Structure, Distribution and Functional Role CYTOLOGY AND GENETICS. 2008 NOV-DEC; 42 (6): 420-430	0	0	41	138
25	6755 Patrushev LI, Minkevich IG The Problem of the Eukaryotic Genome Size BIOCHEMISTRY-MOSCOW. 2008 DEC; 73 (13): 1519-1552	0	1	40	370
26	5294 Bailey JA, Eichler EE Primate segmental duplications: crucibles of evolution, diversity and disease NATURE REVIEWS GENETICS. 2006 JUL; 7 (7): 552-564	20	125	39	125
27	5655 Ray DA SINEs of progress: Mobile element applications to molecular ecology MOLECULAR ECOLOGY. 2007 JAN; 16 (1): 19-33	0	9	39	173
28	6470 Feschotte C Opinion - Transposable elements and the evolution of regulatory networks NATURE REVIEWS GENETICS. 2008 MAY; 9 (5): 397-405	16	42	39	105
29	6722 Blikstad V, Benachenhou F, Sperber GO, Blomberg J Evolution of human endogenous retroviral sequences: a conceptual account CELLULAR AND MOLECULAR LIFE SCIENCES. 2008 NOV; 65 (21): 3348-3365	3	8	39	184
30	4604 Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, et al. Initial sequence of the chimpanzee genome and comparison with the human genome NATURE. 2005 SEP 1; 437 (7055): 69-87	158	580	38	172
#	Date / Author / Journal	LCS	GCS	LCR	CR
31	6810 Marques-Bonet T, Ryder OA, Eichler EE Sequencing Primate Genomes: What Have We Learned? ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2009; 10: 355-386	0	0	37	169
32	6836 Rangwala SH, Zhang LL, Kazazian HH Many LINE1 elements contribute to the transcriptome of human somatic cells GENOME BIOLOGY. 2009; 10 (9): Art. No. R100	0	0	37	69
33	4520 Hedges DJ, Batzer MA From the margins of the genome: mobile elements shape primate evolution BIOESSAYS. 2005 AUG; 27 (8): 785-794	17	29	36	86
34	7205 Xing JC, Zhang YH, Han K, Salem AH, Sen SK, et al. Mobile elements create structural variation: Analysis of a complete human genome GENOME RESEARCH. 2009 SEP; 19 (9): 1516-1526	3	6	36	79
35	5760 Hedges DJ, Deininger PL Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS. 2007 MAR 1; 616 (1-2): 46-59	4	16	35	95
36	5818 Gasior SL, Preston G, Hedges DJ, Gilbert N, Moran JV, et al. Characterization of pre-insertion loci of de novo L1 insertions GENE. 2007 APR 1; 390 (1-2): 190-198	3	3	35	61
37	5896 Gingeras TR Origin of phenotypes: Genes and transcripts GENOME RESEARCH. 2007 JUN; 17 (6): 682-690	5	49	35	105
38	6619 Abrusan G, Giodano J, Warburton PE Analysis of Transposon Interruptions Suggests Selection for L1 Elements on the X Chromosome PLOS GENETICS. 2008 AUG; 4 (8): Art. No. e1000172	0	2	35	62
39	6640 Barbazuk WB, Fu Y, McGinnis KM Genome-wide analyses of alternative splicing in plants: Opportunities and challenges GENOME RESEARCH. 2008 SEP; 18 (9): 1381-1392	0	18	35	144
40	6771 Richard GF, Kerrest A, Dujon B Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS. 2008 DEC; 72 (4): 686-+	0	6	35	558
#	Date / Author / Journal	LCS	GCS	LCR	CR
41	6809 Duret L, Galtier N Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2009; 10: 285-311	0	0	34	147
42	4066 Kramerov DA, Vassetzky NS Short retroposons in eukaryotic genomes INTERNATIONAL REVIEW OF CYTOLOGY - A SURVEY OF CELL BIOLOGY, VOL 247. 2005; 247: 165-+	19	55	33	296
43	5293 Xing Y, Lee C Alternative splicing and RNA selection pressure - evolutionary consequences for eukaryotic genomes NATURE REVIEWS GENETICS. 2006 JUL; 7 (7): 499-509	21	89	33	143
44	5355 Munroe SH, Zhu J Overlapping transcripts, double-stranded RNA and antisense regulation: A genomic perspective CELLULAR AND MOLECULAR LIFE SCIENCES. 2006 SEP; 63 (18): 2102-2118	2	25	33	209
45	6084 Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. The diploid genome sequence of an individual human PLOS BIOLOGY. 2007 OCT; 5 (10): 2113-2144	2	15	33	106
46	2996 Enard W, Paabo S Comparative primate genomics ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2004; 5: 351-378	5	37	32	153
47	3556 Southan C Has the yo-yo stopped? - An assessment of human protein-coding gene number PROTEOMICS. 2004 JUN; 4 (6): 1712-1726	11	41	31	78
48	3826 Collins FS, Lander ES, Rogers J, Waterston RH, Int Human Genome Sequencing Conso Finishing the euchromatic sequence of the human genome NATURE. 2004 OCT 21; 431 (7011): 931-945	232	901	31	71
49	5759 Ray DA, Walker JA, Batzer MA Mobile element-based forensic genomics MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS. 2007 MAR 1; 616 (1-2): 24-33	2	4	31	109
50	5808 Konkel MK, Wang JX, Liang P, Batzer MA Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies GENE. 2007 APR 1; 390 (1-2): 28-38	2	3	31	75
#	Date / Author / Journal	LCS	GCS	LCR	CR
51	5921 Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project NATURE. 2007 JUN 14; 447 (7146): 799-816	72	671	31	128
52	6210 Urrutia AO, Ocana LB, Hurst LD Do Alu repeats drive the evolution of the primate transcriptome? GENOME BIOLOGY. 2008; 9 (2): Art. No. R25	2	6	31	75
53	2914 Copley RR, Goodstadt L, Ponting C Eukaryotic domain evolution inferred from genome comparisons CURRENT OPINION IN GENETICS & DEVELOPMENT. 2003 DEC; 13 (6): 623-628	5	18	30	47
54	2917 Deininger PL, Moran JV, Batzer MA, Kazazian HH Mobile elements and mammalian genome evolution CURRENT OPINION IN GENETICS & DEVELOPMENT. 2003 DEC; 13 (6): 651-658	83	136	30	59
55	4979 Babushok DV, Ostertag EM, Courtney CE, Choi JM, Kazazian HH L1 integration in a transgenic mouse model GENOME RESEARCH. 2006 FEB; 16 (2): 240-250	19	31	30	75
56	6409 Tomilin NV Regulation of mammalian gene expression by retroelements and non-coding tandem repeats BIOESSAYS. 2008 APR; 30 (4): 338-348	3	5	30	99
57	5804 Mills RE, Bennett EA, Iskow RC, Devine SE Which transposable elements are active in the human genome? TRENDS IN GENETICS. 2007 APR; 23 (4): 183-191	18	35	29	96
58	5962 Gu W, Ray DA, Walker JA, Barnes EW, Gentles AJ, et al. SINEs, evolution and genome structure in the opossum GENE. 2007 JUL 1; 396 (1): 46-58	1	4	29	73
59	6355 Worley KC, Weinstock GM, Gibbs RA Rats in the genomic era PHYSIOLOGICAL GENOMICS. 2008 FEB 19; 32 (3): 273-282	0	2	29	57
60	4826 Schulz WA, Steinhoff C, Florl AR Methylation of endogenous human retroelements in health and disease DNA METHYLATION: DEVELOPMENT, GENETIC DISEASE AND CANCER. 2006; 310: 211-250	9	27	28	169
#	Date / Author / Journal	LCS	GCS	LCR	CR
61	7015 Kroutter EN, Belancio VP, Wagstaff BJ, Roy-Engel AM The RNA Polymerase Dictates ORF1 Requirement and Timing of LINE and SINE Retrotransposition PLOS GENETICS. 2009 APR; 5 (4): Art. No. e1000458	1	2	28	68
62	3350 Kazazian HH Mobile elements: Drivers of genome evolution SCIENCE. 2004 MAR 12; 303 (5664): 1626-1632	146	410	27	84
63	4098 Han KD, Sen SK, Wang JX, Callinan PA, Lee JN, et al. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages NUCLEIC ACIDS RESEARCH. 2005; 33 (13): 4040-4052	27	36	27	57
64	4676 Sankaranarayanan K, Wassom JS Ionizing radiation and genetic risks - XIV. Potential research directions in the post-genome era based on knowledge of repair of radiation-induced DNA double-strand breaks in mammalian somatic cells and the origin of deletions associated with human genomic disorders MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS. 2005 OCT 15; 578 (1-2): 333-370	0	14	27	276
65	4860 Schulz WA L1 retrotransposons in human cancers JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY. 2006; : Art. No. 83672	0	9	27	109
66	5135 Seleme MDC, Vetter MR, Cordaux R, Bastone L, Batzer MA, et al. Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2006 APR 25; 103 (17): 6611-6616	14	19	27	57
67	5588 Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, et al. Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome GENOME BIOLOGY. 2007; 8 (6): Art. No. R127	16	31	27	57
68	5639 Schmegner C, Hoegel J, Vogel W, Assum G The rate, not the spectrum, of base pair substitutions changes at a GC-content transition in the human NF1 gene region: Implications for the evolution of the mammalian genome structure GENETICS. 2007 JAN; 175 (1): 421-428	0	2	27	51
69	5815 Eller CD, Regelson M, Merriman B, Nelson S, Horvath S, et al. Repetitive sequence environment distinguishes housekeeping genes GENE. 2007 APR 1; 390 (1-2): 153-165	2	8	27	139
70	5898 Zheng DY, Frankish A, Baertsch R, Kapranov P, Reymond A, et al. Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution GENOME RESEARCH. 2007 JUN; 17 (6): 839-851	8	20	27	74
#	Date / Author / Journal	LCS	GCS	LCR	CR
71	6956 Sinzelle L, Izsvak Z, Ivics Z Molecular domestication of transposable elements: From detrimental parasites to useful host genes CELLULAR AND MOLECULAR LIFE SCIENCES. 2009 MAR; 66 (6): 1073-1093	0	0	27	151
72	4775 Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog NATURE. 2005 DEC 8; 438 (7069): 803-819	100	470	26	119
73	5234 Webster MT, Axelsson E, Ellegren H Strong regional biases in nucleotide substitution in the chicken genome MOLECULAR BIOLOGY AND EVOLUTION. 2006 JUN; 23 (6): 1203-1216	9	27	26	75
74	5284 Sun M, Hurst LD, Carmichael GG, Chen J Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcription and organismic complexity GENOME RESEARCH. 2006 JUL; 16 (7): 922-933	1	17	26	64
75	5561 Blanchette M Computation and analysis of genomic multi-sequence alignments ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2007; 8: 193-213	0	5	26	134
76	5562 Jurka J, Kapitonov VV, Kohany O, Jurka MV Repetitive sequences in complex genomes: Structure and evolution ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2007; 8: 241-259	8	22	26	128
77	5595 Chen KF, Baxter T, Muir WM, Groenen MA, Schook LB Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa) INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES. 2007; 3 (3): 153-165	0	14	26	134
78	5730 Taft RJ, Pheasant M, Mattick JS The relationship between non-protein-coding DNA and eukaryotic complexity BIOESSAYS. 2007 MAR; 29 (3): 288-299	5	49	26	125
79	5817 Almeida LM, Silva IT, Silva WA, Castro JP, Riggs PK, et al. The contribution of transposable elements to Bos taurus gene structure GENE. 2007 APR 1; 390 (1-2): 180-189	1	7	26	80
80	5947 Portin P Evolution of man in the light of molecular genetics: a review. Part I. Our evolutionary history and genomics HEREDITAS. 2007 JUL; 144 (3): 80-95	0	1	26	130
#	Date / Author / Journal	LCS	GCS	LCR	CR
81	6193 Jern P, Coffin JM Effects of Retroviruses on Host Genome Function ANNUAL REVIEW OF GENETICS. 2008; 42: 709-732	6	12	26	131
82	6295 Holste D, Ohler U Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events PLOS COMPUTATIONAL BIOLOGY. 2008 JAN; 4 (1): Art. No. e21	0	0	26	73
83	6474 Duret L, Arndt PF The impact of recombination on nucleotide substitutions in the human genome PLOS GENETICS. 2008 MAY; 4 (5): Art. No. e1000071	3	24	26	91
84	6863 Irimia M, Rukov JL, Roy SW, Vinther J, Garcia-Fernandez J Quantitative regulation of alternative splicing in evolution and development BIOESSAYS. 2009 JAN; 31 (1): 40-50	0	2	26	98
85	7147 Piskurek O, Nishihara H, Okada N The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis GENE. 2009 JUL 15; 441 (1-2): 111-118	1	1	26	86
86	7298 Ray DA, Platt RN, Batzer MA Reading between the LINEs to see into the past TRENDS IN GENETICS. 2009 NOV; 25 (11): 475-479	0	0	26	49
87	3847 Stankiewicz P, Shaw CJ, Withers M, Inoue K, Lupski JR Serial segmental duplications during primate evolution result in complex human genome architecture GENOME RESEARCH. 2004 NOV; 14 (11): 2209-2220	15	56	25	82
88	3987 Stone EA, Cooper GM, Sidow A Trade-offs in detecting evolutionarily constrained sequence by comparative genomics ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2005; 6: 143-164	2	25	25	102
89	4214 Brookfield JFY The ecology of the genome - Mobile DNA elements and their hosts NATURE REVIEWS GENETICS. 2005 FEB; 6 (2): 128-136	16	44	25	90
90	4744 Brent MR Genome annotation past, present, and future: How to define an ORF at each locus GENOME RESEARCH. 2005 DEC; 15 (12): 1777-1786	5	42	25	70
#	Date / Author / Journal	LCS	GCS	LCR	CR
91	4933 Maksakova IA, Romanish MT, Gagnier L, Dunn CA, de Lagemaat LNV, et al. Retroviral elements and their hosts: Insertional mutagenesis in the mouse germ line PLOS GENETICS. 2006 JAN; 2 (1): Art. No. E2	0	43	25	128
92	5324 Pando MP, Kotraiah V, McGowan K, Bracco L, Einstein R Alternative isoform discrimination by the next generation of expression profiling microarrays EXPERT OPINION ON THERAPEUTIC TARGETS. 2006 AUG; 10 (4): 613-625	1	2	25	105
93	5450 Buzdin A, Kovalskaya-Alexandrova E, Gogvadze E, Sverdlov E At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription JOURNAL OF VIROLOGY. 2006 NOV; 80 (21): 10752-10762	7	12	25	48
94	6481 Lemaitre C, Sagot MF A small trip in the untranquil world of genomes - A survey on the detection and analysis of genome rearrangement breakpoints THEORETICAL COMPUTER SCIENCE. 2008 MAY 1; 395 (2-3): 171-192	0	0	25	96
95	6706 Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J Retrocopy contributions to the evolution of the human genome BMC GENOMICS. 2008 OCT 8; 9: Art. No. 466	1	3	25	75
96	6866 Beiter T, Reich E, Williams RW, Simon P Antisense transcription: A critical look in both directions CELLULAR AND MOLECULAR LIFE SCIENCES. 2009 JAN; 66 (1): 94-112	0	7	25	229
97	6948 Reeves GA, Talavera D, Thornton JM Genome and proteome annotation: organization, interpretation and integration JOURNAL OF THE ROYAL SOCIETY INTERFACE. 2009 FEB 6; 6 (31): 129-147	1	5	25	212
98	6971 Brady T, Lee YN, Ronen K, Malani N, Berry CC, et al. Integration target site selection by a resurrected human endogenous retrovirus GENES & DEVELOPMENT. 2009 MAR 1; 23 (5): 633-642	0	2	25	73
99	7146 Hirakawa M, Nishihara H, Kanehisa M, Okada N Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes GENE. 2009 JUL 15; 441 (1-2): 100-110	0	0	25	61
100	3911 Orth AP, Batalov S, Perrone M, Chanda SK The promise of genomics to identify novel therapeutic targets EXPERT OPINION ON THERAPEUTIC TARGETS. 2004 DEC; 8 (6): 587-596	3	25	24	81

Date / Author / Journal

LCS

GCS

LCR

5698 Sawatzki HK, Cooper DN

Understanding the recent evolution of the human genome: Insights from human-chimpanzee genome comparisons

HUMAN MUTATION. 2007 FEB; 28 (2): 99-130

478

6370 Belancio VP, Hedges DJ, Deininger P

Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health

GENOME RESEARCH. 2008 MAR; 18 (3): 343-358

201

7250 Cordaux R, Batzer MA

The impact of retrotransposons on human genome evolution

NATURE REVIEWS GENETICS. 2009 OCT; 10 (10): 691-703

167

5975 Artamonova II, Gelfand MS

Comparative genomics and evolution of alternative splicing: The pessimists' science

CHEMICAL REVIEWS. 2007 AUG; 107 (8): 3407-3430

384

4022 Brosius J

Echoes from the past - are we still in an RNP world?

CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 8-24

302

5902 Babushok DV, Kazazian HH

Progress in understanding the biology of the human mutagen LINE-1

HUMAN MUTATION. 2007 JUN; 28 (6): 527-539

160

3413 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, et al.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

NATURE. 2004 APR 1; 428 (6982): 493-521

269

752

226

7311 Gogvadze E, Buzdin A

Retroelements and their impact on genome evolution and functioning

CELLULAR AND MOLECULAR LIFE SCIENCES. 2009 DEC; 66 (23): 3727-3742

157

7118 Oliver KR, Greene WK

Transposable elements: powerful facilitators of evolution

BIOESSAYS. 2009 JUL; 31 (7): 703-714

147

6362 Bohne A, Brunet F, Galiana-Arnoux D, Schultheis C, Volff JN

Transposable elements as drivers of genomic and biological diversity in vertebrates

CHROMOSOME RESEARCH. 2008 MAR; 16 (1): 203-215

109

Date / Author / Journal

LCS

GCS

LCR

5553 Xing JC, Witherspoon DJ, Ray DA, Batzer MA, Jorde LB

Mobile DNA elements in primate and human evolution

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY. 2007; : 2-19

214

5733 Babushok DV, Ostertag EM, Kazazian HH

Current topics in genome evolution: Molecular mechanisms of new gene formation

CELLULAR AND MOLECULAR LIFE SCIENCES. 2007 MAR; 64 (5): 542-554

131

5621 Buzdin A

Human-specific endogenous retroviruses

THESCIENTIFICWORLDJOURNAL. 2007; 7: 1848-1868

148

5863 Mattick JS

A new paradigm for developmental biology

JOURNAL OF EXPERIMENTAL BIOLOGY. 2007 MAY 1; 210 (9): 1526-1547

367

6192 Beauregard A, Curcio MJ, Belfort M

The Take and Give Between Retrotransposable Elements and their Hosts

ANNUAL REVIEW OF GENETICS. 2008; 42: 587-617

211

7340 Cohen CJ, Lock WM, Mager DL

Endogenous retroviral LTRs as promoters for human genes: A critical assessment

GENE. 2009 DEC 15; 448 (2): 105-114

137

1865 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al.

Initial sequencing and comparative analysis of the mouse genome

NATURE. 2002 DEC 5; 420 (6915): 520-562

1083

2474

331

3953 Hillier LW, Miller W, Birney E, Warren W, Hardison RC, et al.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

NATURE. 2004 DEC 9; 432 (7018): 695-716

143

697

165

6106 Muotri AR, Marchetto MCN, Coufal NG, Gage FH

The necessary junk: new functions for transposable elements

HUMAN MOLECULAR GENETICS. 2007 OCT 15; 16: R159-R167

4579 Chen JM, Stenson PD, Cooper DN, Ferec C

A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease

HUMAN GENETICS. 2005 SEP; 117 (5): 411-427

133

Date / Author / Journal

LCS

GCS

LCR

5557 Feschotte C, Pritham EJ

DNA transposons and the evolution of eukaryotic genomes

ANNUAL REVIEW OF GENETICS. 2007; 41: 331-368

236

2993 Miller W, Makova KD, Nekrutenko A, Hardison RC

Comparative genomics

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2004; 5: 15-56

193

5974 Tang H

Genome assembly, rearrangement, and repeats

CHEMICAL REVIEWS. 2007 AUG; 107 (8): 3391-3406

154

6724 Pidpala OV, Yatsishina AP, Lukash LL

Human Mobile Genetic Elements: Structure, Distribution and Functional Role

CYTOLOGY AND GENETICS. 2008 NOV-DEC; 42 (6): 420-430

138

6755 Patrushev LI, Minkevich IG

The Problem of the Eukaryotic Genome Size

BIOCHEMISTRY-MOSCOW. 2008 DEC; 73 (13): 1519-1552

370

5294 Bailey JA, Eichler EE

Primate segmental duplications: crucibles of evolution, diversity and disease

NATURE REVIEWS GENETICS. 2006 JUL; 7 (7): 552-564

125

5655 Ray DA

SINEs of progress: Mobile element applications to molecular ecology

MOLECULAR ECOLOGY. 2007 JAN; 16 (1): 19-33

173

6470 Feschotte C

Opinion - Transposable elements and the evolution of regulatory networks

NATURE REVIEWS GENETICS. 2008 MAY; 9 (5): 397-405

105

6722 Blikstad V, Benachenhou F, Sperber GO, Blomberg J

Evolution of human endogenous retroviral sequences: a conceptual account

CELLULAR AND MOLECULAR LIFE SCIENCES. 2008 NOV; 65 (21): 3348-3365

184

4604 Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, et al.

Initial sequence of the chimpanzee genome and comparison with the human genome

NATURE. 2005 SEP 1; 437 (7055): 69-87

158

580

172

Date / Author / Journal

LCS

GCS

LCR

6810 Marques-Bonet T, Ryder OA, Eichler EE

Sequencing Primate Genomes: What Have We Learned?

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2009; 10: 355-386

169

6836 Rangwala SH, Zhang LL, Kazazian HH

Many LINE1 elements contribute to the transcriptome of human somatic cells

GENOME BIOLOGY. 2009; 10 (9): Art. No. R100

4520 Hedges DJ, Batzer MA

From the margins of the genome: mobile elements shape primate evolution

BIOESSAYS. 2005 AUG; 27 (8): 785-794

7205 Xing JC, Zhang YH, Han K, Salem AH, Sen SK, et al.

Mobile elements create structural variation: Analysis of a complete human genome

GENOME RESEARCH. 2009 SEP; 19 (9): 1516-1526

5760 Hedges DJ, Deininger PL

Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity

MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS. 2007 MAR 1; 616 (1-2): 46-59

5818 Gasior SL, Preston G, Hedges DJ, Gilbert N, Moran JV, et al.

Characterization of pre-insertion loci of de novo L1 insertions

GENE. 2007 APR 1; 390 (1-2): 190-198

5896 Gingeras TR

Origin of phenotypes: Genes and transcripts

GENOME RESEARCH. 2007 JUN; 17 (6): 682-690

105

6619 Abrusan G, Giodano J, Warburton PE

Analysis of Transposon Interruptions Suggests Selection for L1 Elements on the X Chromosome

PLOS GENETICS. 2008 AUG; 4 (8): Art. No. e1000172

6640 Barbazuk WB, Fu Y, McGinnis KM

Genome-wide analyses of alternative splicing in plants: Opportunities and challenges

GENOME RESEARCH. 2008 SEP; 18 (9): 1381-1392

144

6771 Richard GF, Kerrest A, Dujon B

Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS. 2008 DEC; 72 (4): 686-+

558

Date / Author / Journal

LCS

GCS

LCR

6809 Duret L, Galtier N

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2009; 10: 285-311

147

4066 Kramerov DA, Vassetzky NS

Short retroposons in eukaryotic genomes

INTERNATIONAL REVIEW OF CYTOLOGY - A SURVEY OF CELL BIOLOGY, VOL 247. 2005; 247: 165-+

296

5293 Xing Y, Lee C

Alternative splicing and RNA selection pressure - evolutionary consequences for eukaryotic genomes

NATURE REVIEWS GENETICS. 2006 JUL; 7 (7): 499-509

143

5355 Munroe SH, Zhu J

Overlapping transcripts, double-stranded RNA and antisense regulation: A genomic perspective

CELLULAR AND MOLECULAR LIFE SCIENCES. 2006 SEP; 63 (18): 2102-2118

209

6084 Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al.

The diploid genome sequence of an individual human

PLOS BIOLOGY. 2007 OCT; 5 (10): 2113-2144

106

2996 Enard W, Paabo S

Comparative primate genomics

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2004; 5: 351-378

153

3556 Southan C

Has the yo-yo stopped? - An assessment of human protein-coding gene number

PROTEOMICS. 2004 JUN; 4 (6): 1712-1726

3826 Collins FS, Lander ES, Rogers J, Waterston RH, Int Human Genome Sequencing Conso

Finishing the euchromatic sequence of the human genome

NATURE. 2004 OCT 21; 431 (7011): 931-945

232

901

5759 Ray DA, Walker JA, Batzer MA

Mobile element-based forensic genomics

MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS. 2007 MAR 1; 616 (1-2): 24-33

109

5808 Konkel MK, Wang JX, Liang P, Batzer MA

Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies

GENE. 2007 APR 1; 390 (1-2): 28-38

Date / Author / Journal

LCS

GCS

LCR

5921 Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

NATURE. 2007 JUN 14; 447 (7146): 799-816

671

128

6210 Urrutia AO, Ocana LB, Hurst LD

Do Alu repeats drive the evolution of the primate transcriptome?

GENOME BIOLOGY. 2008; 9 (2): Art. No. R25

2914 Copley RR, Goodstadt L, Ponting C

Eukaryotic domain evolution inferred from genome comparisons

CURRENT OPINION IN GENETICS & DEVELOPMENT. 2003 DEC; 13 (6): 623-628

2917 Deininger PL, Moran JV, Batzer MA, Kazazian HH

Mobile elements and mammalian genome evolution

CURRENT OPINION IN GENETICS & DEVELOPMENT. 2003 DEC; 13 (6): 651-658

136

4979 Babushok DV, Ostertag EM, Courtney CE, Choi JM, Kazazian HH

L1 integration in a transgenic mouse model

GENOME RESEARCH. 2006 FEB; 16 (2): 240-250

6409 Tomilin NV

Regulation of mammalian gene expression by retroelements and non-coding tandem repeats

BIOESSAYS. 2008 APR; 30 (4): 338-348

5804 Mills RE, Bennett EA, Iskow RC, Devine SE

Which transposable elements are active in the human genome?

TRENDS IN GENETICS. 2007 APR; 23 (4): 183-191

5962 Gu W, Ray DA, Walker JA, Barnes EW, Gentles AJ, et al.

SINEs, evolution and genome structure in the opossum

GENE. 2007 JUL 1; 396 (1): 46-58

6355 Worley KC, Weinstock GM, Gibbs RA

Rats in the genomic era

PHYSIOLOGICAL GENOMICS. 2008 FEB 19; 32 (3): 273-282

4826 Schulz WA, Steinhoff C, Florl AR

Methylation of endogenous human retroelements in health and disease

DNA METHYLATION: DEVELOPMENT, GENETIC DISEASE AND CANCER. 2006; 310: 211-250

169

Date / Author / Journal

LCS

GCS

LCR

7015 Kroutter EN, Belancio VP, Wagstaff BJ, Roy-Engel AM

The RNA Polymerase Dictates ORF1 Requirement and Timing of LINE and SINE Retrotransposition

PLOS GENETICS. 2009 APR; 5 (4): Art. No. e1000458

3350 Kazazian HH

Mobile elements: Drivers of genome evolution

SCIENCE. 2004 MAR 12; 303 (5664): 1626-1632

146

410

4098 Han KD, Sen SK, Wang JX, Callinan PA, Lee JN, et al.

Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages

NUCLEIC ACIDS RESEARCH. 2005; 33 (13): 4040-4052

4676 Sankaranarayanan K, Wassom JS

Ionizing radiation and genetic risks - XIV. Potential research directions in the post-genome era based on knowledge of repair of radiation-induced DNA double-strand breaks in mammalian somatic cells and the origin of deletions associated with human genomic disorders

MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS. 2005 OCT 15; 578 (1-2): 333-370

276

4860 Schulz WA

L1 retrotransposons in human cancers

JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY. 2006; : Art. No. 83672

109

5135 Seleme MDC, Vetter MR, Cordaux R, Bastone L, Batzer MA, et al.

Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2006 APR 25; 103 (17): 6611-6616

5588 Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, et al.

Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome

GENOME BIOLOGY. 2007; 8 (6): Art. No. R127

5639 Schmegner C, Hoegel J, Vogel W, Assum G

The rate, not the spectrum, of base pair substitutions changes at a GC-content transition in the human NF1 gene region: Implications for the evolution of the mammalian genome structure

GENETICS. 2007 JAN; 175 (1): 421-428

5815 Eller CD, Regelson M, Merriman B, Nelson S, Horvath S, et al.

Repetitive sequence environment distinguishes housekeeping genes

GENE. 2007 APR 1; 390 (1-2): 153-165

139

5898 Zheng DY, Frankish A, Baertsch R, Kapranov P, Reymond A, et al.

Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution

GENOME RESEARCH. 2007 JUN; 17 (6): 839-851

Date / Author / Journal

LCS

GCS

LCR

6956 Sinzelle L, Izsvak Z, Ivics Z

Molecular domestication of transposable elements: From detrimental parasites to useful host genes

CELLULAR AND MOLECULAR LIFE SCIENCES. 2009 MAR; 66 (6): 1073-1093

151

4775 Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, et al.

Genome sequence, comparative analysis and haplotype structure of the domestic dog

NATURE. 2005 DEC 8; 438 (7069): 803-819

100

470

119

5234 Webster MT, Axelsson E, Ellegren H

Strong regional biases in nucleotide substitution in the chicken genome

MOLECULAR BIOLOGY AND EVOLUTION. 2006 JUN; 23 (6): 1203-1216

5284 Sun M, Hurst LD, Carmichael GG, Chen J

Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcription and organismic complexity

GENOME RESEARCH. 2006 JUL; 16 (7): 922-933

5561 Blanchette M

Computation and analysis of genomic multi-sequence alignments

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2007; 8: 193-213

134

5562 Jurka J, Kapitonov VV, Kohany O, Jurka MV

Repetitive sequences in complex genomes: Structure and evolution

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2007; 8: 241-259

128

5595 Chen KF, Baxter T, Muir WM, Groenen MA, Schook LB

Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa)

INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES. 2007; 3 (3): 153-165

134

5730 Taft RJ, Pheasant M, Mattick JS

The relationship between non-protein-coding DNA and eukaryotic complexity

BIOESSAYS. 2007 MAR; 29 (3): 288-299

125

5817 Almeida LM, Silva IT, Silva WA, Castro JP, Riggs PK, et al.

The contribution of transposable elements to Bos taurus gene structure

GENE. 2007 APR 1; 390 (1-2): 180-189

5947 Portin P

Evolution of man in the light of molecular genetics: a review. Part I. Our evolutionary history and genomics

HEREDITAS. 2007 JUL; 144 (3): 80-95

130

Date / Author / Journal

LCS

GCS

LCR

6193 Jern P, Coffin JM

Effects of Retroviruses on Host Genome Function

ANNUAL REVIEW OF GENETICS. 2008; 42: 709-732

131

6295 Holste D, Ohler U

Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events

PLOS COMPUTATIONAL BIOLOGY. 2008 JAN; 4 (1): Art. No. e21

6474 Duret L, Arndt PF

The impact of recombination on nucleotide substitutions in the human genome

PLOS GENETICS. 2008 MAY; 4 (5): Art. No. e1000071

6863 Irimia M, Rukov JL, Roy SW, Vinther J, Garcia-Fernandez J

Quantitative regulation of alternative splicing in evolution and development

BIOESSAYS. 2009 JAN; 31 (1): 40-50

7147 Piskurek O, Nishihara H, Okada N

The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis

GENE. 2009 JUL 15; 441 (1-2): 111-118

7298 Ray DA, Platt RN, Batzer MA

Reading between the LINEs to see into the past

TRENDS IN GENETICS. 2009 NOV; 25 (11): 475-479

3847 Stankiewicz P, Shaw CJ, Withers M, Inoue K, Lupski JR

Serial segmental duplications during primate evolution result in complex human genome architecture

GENOME RESEARCH. 2004 NOV; 14 (11): 2209-2220

3987 Stone EA, Cooper GM, Sidow A

Trade-offs in detecting evolutionarily constrained sequence by comparative genomics

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2005; 6: 143-164

102

4214 Brookfield JFY

The ecology of the genome - Mobile DNA elements and their hosts

NATURE REVIEWS GENETICS. 2005 FEB; 6 (2): 128-136

4744 Brent MR

Genome annotation past, present, and future: How to define an ORF at each locus

GENOME RESEARCH. 2005 DEC; 15 (12): 1777-1786

Date / Author / Journal

LCS

GCS

LCR

4933 Maksakova IA, Romanish MT, Gagnier L, Dunn CA, de Lagemaat LNV, et al.

Retroviral elements and their hosts: Insertional mutagenesis in the mouse germ line

PLOS GENETICS. 2006 JAN; 2 (1): Art. No. E2

128

5324 Pando MP, Kotraiah V, McGowan K, Bracco L, Einstein R

Alternative isoform discrimination by the next generation of expression profiling microarrays

EXPERT OPINION ON THERAPEUTIC TARGETS. 2006 AUG; 10 (4): 613-625

105

5450 Buzdin A, Kovalskaya-Alexandrova E, Gogvadze E, Sverdlov E

At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription

JOURNAL OF VIROLOGY. 2006 NOV; 80 (21): 10752-10762

6481 Lemaitre C, Sagot MF

A small trip in the untranquil world of genomes - A survey on the detection and analysis of genome rearrangement breakpoints

THEORETICAL COMPUTER SCIENCE. 2008 MAY 1; 395 (2-3): 171-192

6706 Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J

Retrocopy contributions to the evolution of the human genome

BMC GENOMICS. 2008 OCT 8; 9: Art. No. 466

6866 Beiter T, Reich E, Williams RW, Simon P

Antisense transcription: A critical look in both directions

CELLULAR AND MOLECULAR LIFE SCIENCES. 2009 JAN; 66 (1): 94-112

229

6948 Reeves GA, Talavera D, Thornton JM

Genome and proteome annotation: organization, interpretation and integration

JOURNAL OF THE ROYAL SOCIETY INTERFACE. 2009 FEB 6; 6 (31): 129-147

212

6971 Brady T, Lee YN, Ronen K, Malani N, Berry CC, et al.

Integration target site selection by a resurrected human endogenous retrovirus

GENES & DEVELOPMENT. 2009 MAR 1; 23 (5): 633-642

7146 Hirakawa M, Nishihara H, Kanehisa M, Okada N

Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes

GENE. 2009 JUL 15; 441 (1-2): 100-110

100

3911 Orth AP, Batalov S, Perrone M, Chanda SK

The promise of genomics to identify novel therapeutic targets

EXPERT OPINION ON THERAPEUTIC TARGETS. 2004 DEC; 8 (6): 587-596

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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