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

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#	Date / Author / Journal	LCS	GCS	LCR	CR
101	4023 Biemont C, Vieira C What transposable elements tell us about genome organization and evolution: the case of Drosophila CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 25-34	6	20	24	176
102	4366 Shapiro JA, von Sternberg R Why repetitive DNA is essential to genome function BIOLOGICAL REVIEWS. 2005 MAY; 80 (2): 227-250	4	19	24	247
103	4592 Gregory TR Synergy between sequence and size in large-scale genomics NATURE REVIEWS GENETICS. 2005 SEP; 6 (9): 699-708	10	41	24	111
104	5087 Singh R, Robida MD, Karimpour S Building biological complexity with limited genes CURRENT GENOMICS. 2006 APR; 7 (2): 97-114	1	3	24	195
105	5095 Wang JX, Song L, Grover D, Azrak S, Batzer MA, et al. DbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans HUMAN MUTATION. 2006 APR; 27 (4): 323-329	14	18	24	56
106	5385 Carninci P Tagging mammalian transcription complexity TRENDS IN GENETICS. 2006 SEP; 22 (9): 501-510	6	35	24	75
107	5516 Weber MJ Mammalian small nucleolar RNAs are mobile genetic elements PLOS GENETICS. 2006 DEC; 2 (12): Art. No. e205	0	21	24	79
108	5711 Kost-Alimova M, Imreh S Modeling non-random deletions in cancer SEMINARS IN CANCER BIOLOGY. 2007 FEB; 17 (1): 19-30	1	9	24	91
109	5799 Slotkin RK, Martienssen R Transposable elements and the epigenetic regulation of the genome NATURE REVIEWS GENETICS. 2007 APR; 8 (4): 272-285	18	127	24	145
110	5807 Lee J, Cordaux R, Han KD, Wang JX, Hedges DJ, et al. Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons GENE. 2007 APR 1; 390 (1-2): 18-27	4	5	24	53
#	Date / Author / Journal	LCS	GCS	LCR	CR
111	5881 Schumann GG APOBEC3 proteins: major players in intracellular defence against LINE-1-mediated retrotransposition BIOCHEMICAL SOCIETY TRANSACTIONS. 2007 JUN; 35: 637-642	3	6	24	50
112	6336 Karro JE, Peifer M, Hardison RC, Kollmann M, von Grunberg HH Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure MOLECULAR BIOLOGY AND EVOLUTION. 2008 FEB; 25 (2): 362-374	1	5	24	53
113	6653 Ponting CP The functional repertoires of metazoan genomes NATURE REVIEWS GENETICS. 2008 SEP; 9 (9): 689-698	0	8	24	94
114	6698 Lin L, Shen SH, Tye A, Cai JJ, Jiang P, et al. Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues PLOS GENETICS. 2008 OCT; 4 (10): Art. No. e1000225	4	6	24	70
115	7270 Kandul NP, Noor MAF Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3 BMC GENETICS. 2009 OCT 19; 10: Art. No. 67	0	0	24	99
116	3443 Bailey JA, Church DM, Ventura M, Rocchi M, Eichler EE Analysis of segmental duplications and genome assembly in the mouse GENOME RESEARCH. 2004 MAY; 14 (5): 789-801	17	52	23	51
117	4013 Ryder OA Conservation genomics: applying whole genome studies to species conservation efforts CYTOGENETIC AND GENOME RESEARCH. 2005; 108 (1-3): 6-15	2	9	23	90
118	4024 Dewannieux M, Heidmann T LINEs, SINEs and processed pseudogenes: parasitic strategies for genome modeling CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 35-48	2	13	23	147
119	4519 Han JS, Boeke JD LINEA retrotransposons: modulators of quantity and quality of mammalian gene expression? BIOESSAYS. 2005 AUG; 27 (8): 775-784	36	56	23	85
120	5502 Ding WY, Lin L, Cheh B, Dai JW L1 elements, processed pseudogenes and retrogenes in mammalian genomes IUBMB LIFE. 2006 DEC; 58 (12): 677-685	0	2	23	61
#	Date / Author / Journal	LCS	GCS	LCR	CR
121	6404 Pozzoli U, Menozzi G, Fumagalli M, Cereda M, Comi GP, et al. Both selective and neutral processes drive GC content evolution in the human genome BMC EVOLUTIONARY BIOLOGY. 2008 MAR 27; 8: Art. No. 99	0	3	23	53
122	6924 Koszul R, Fischer G A prominent role for segmental duplications in modeling Eukaryotic genomes COMPTES RENDUS BIOLOGIES. 2009 FEB-MAR; 332 (2-3): 254-266	0	1	23	102
123	7057 Pace JK, Sen SK, Batzer MA, Feschotte C Repair-Mediated Duplication by Capture of Proximal Chromosomal DNA Has Shaped Vertebrate Genome Evolution PLOS GENETICS. 2009 MAY; 5 (5): Art. No. e1000469	0	0	23	63
124	7109 Lin L, Jiang P, Shen SH, Sato S, Davidson BL, et al. Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes HUMAN MOLECULAR GENETICS. 2009 JUN 15; 18 (12): 2204-2214	0	1	23	57
125	7110 Gogvadze E, Stukacheva E, Buzdin A, Sverdlov E Human-Specific Modulation of Transcriptional Activity Provided by Endogenous Retroviral Insertions JOURNAL OF VIROLOGY. 2009 JUN 15; 83 (12): 6098-6105	2	2	23	44
126	7137 Venner S, Feschotte C, Biemont C Dynamics of transposable elements: towards a community ecology of the genome TRENDS IN GENETICS. 2009 JUL; 25 (7): 317-323	0	0	23	86
127	7280 Damert A, Raiz J, Horn AV, Lower J, Wang H, et al. 5 '-Transducing SVA retrotransposon groups spread efficiently throughout the human genome GENOME RESEARCH. 2009 NOV; 19 (11): 1992-2008	2	2	23	56
128	7316 Bourque G Transposable elements in gene regulation and in the evolution of vertebrate genomes CURRENT OPINION IN GENETICS & DEVELOPMENT. 2009 DEC; 19 (6): 607-612	0	0	23	63
129	1902 Ashurst JL, Collins JE Gene annotation: Prediction and testing ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2003; 4: 69-88	17	34	22	101
130	2676 Eichler EE, Sankoff D Structural dynamics of eukaryotic chromosome evolution SCIENCE. 2003 AUG 8; 301 (5634): 793-797	33	155	22	60
#	Date / Author / Journal	LCS	GCS	LCR	CR
131	3652 Suzuki M, Hayashizaki Y Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs BIOESSAYS. 2004 AUG; 26 (8): 833-843	5	27	22	115
132	3776 Zhao SY, Shetty J, Hou LH, Delcher A, Zhu BL, et al. Human, mouse, and rat genome large-scale rearrangements: Stability versus speciation GENOME RESEARCH. 2004 OCT; 14 (10A): 1851-1860	9	42	22	62
133	3848 Blakesley RW, Hansen NF, Mullikin JC, Thomas PJ, McDowell JC, et al. An intermediate grade of finished genomic sequence suitable for comparative analyses GENOME RESEARCH. 2004 NOV; 14 (11): 2235-2244	12	34	22	50
134	3988 Giallourakis C, Henson C, Reich M, Xie XH, Mootha VK Disease gene discovery through integrative genomics ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2005; 6: 381-406	0	18	22	117
135	4045 Ohshima K, Okada N SINEs and LINEs: symbionts of eukaryotic genomes with a common tail CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 475-490	17	39	22	165
136	4405 Zheng DY, Zhang ZL, Harrison PM, Karro J, Carriero N, et al. Integrated pseudogene annotation for human chromosome 22: Evidence for transcription JOURNAL OF MOLECULAR BIOLOGY. 2005 MAY 27; 349 (1): 27-45	11	34	22	46
137	4597 Hedges DJ, Cordaux R, Xing J, Witherspoon DJ, Rogers AR, et al. Modeling the amplification dynamics of human Alu retrotransposons PLOS COMPUTATIONAL BIOLOGY. 2005 SEP; 1 (4): Art. No. e44	0	9	22	61
138	4743 Little PFR Structure and function of the human genome GENOME RESEARCH. 2005 DEC; 15 (12): 1759-1766	1	9	22	54
139	4776 Wang H, Xing J, Grover D, Hedges DJ, Han KD, et al. SVA elements: A hominid-specific retroposon family JOURNAL OF MOLECULAR BIOLOGY. 2005 DEC 9; 354 (4): 994-1007	26	36	22	47
140	4842 Sironi M, Menozzi G, Comi GP, Cereda M, Cagliani R, et al. Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns GENOME BIOLOGY. 2006; 7 (12): Art. No. R120	4	7	22	64
#	Date / Author / Journal	LCS	GCS	LCR	CR
141	5127 Temple G, Lamesch P, Milstein S, Hill DE, Wagner L, et al. From genome to proteome: developing expression clone resources for the human genome HUMAN MOLECULAR GENETICS. 2006 APR 15; 15: R31-R43	2	14	22	89
142	5252 Liu GE, Matukumalli LK, Sonstegard TS, Shade LL, Van Tassell CP Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences BMC GENOMICS. 2006 JUN 7; 7: Art. No. 140	1	8	22	59
143	5272 Sen SK, Han KD, Wang JX, Lee J, Wang H, et al. Human genomic deletions mediated by recombination between Alu elements AMERICAN JOURNAL OF HUMAN GENETICS. 2006 JUL; 79 (1): 41-53	30	59	22	60
144	5531 An WF, Han JS, Wheelan SJ, Davis ES, Coombes CE, et al. Active retrotransposition by a synthetic L1 element in mice PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2006 DEC 5; 103 (49): 18662-18667	9	16	22	68
145	5910 Sen SK, Huang CT, Han K, Batzer MA Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome NUCLEIC ACIDS RESEARCH. 2007 JUN; 35 (11): 3741-3751	4	11	22	65
146	5930 Buzdin A, Gogvadze E, Lebrun MH Chimeric retrogenes suggest a role for the nucleolus in LINE amplification FEBS LETTERS. 2007 JUN 26; 581 (16): 2877-2882	2	4	22	57
147	5938 Hasler J, Samuelsson T, Strub K Useful 'junk': Alu RNAs in the human transcriptome CELLULAR AND MOLECULAR LIFE SCIENCES. 2007 JUL; 64 (14): 1793-1800	8	25	22	80
148	6088 Cogburn LA, Porter TE, Duclos MJ, Simon J, Burgess SC, et al. Functional genomics of the chicken - A model organism POULTRY SCIENCE. 2007 OCT; 86 (10): 2059-2094	0	14	22	322
149	6714 Wegmann D, Dupanloup I, Excoffier L Width of Gene Expression Profile Drives Alternative Splicing PLOS ONE. 2008 OCT 31; 3 (10): Art. No. e3587	0	2	22	59
150	6996 Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die? GENOME RESEARCH. 2009 APR; 19 (4): 545-555	2	3	22	46
#	Date / Author / Journal	LCS	GCS	LCR	CR
151	7122 Singh R, Knight R Systems Biology: Understanding Function from Genes to Networks CURRENT PROTEOMICS. 2009 JUL; 6 (2): 93-103	0	0	22	165
152	2998 Borevitz JO, Ecker JR Plant genomics: The third wave ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2004; 5: 443-477	0	28	21	173
153	3474 Eichler EE, Clark RA, She XW An assessment of the sequence gaps: Unfinished business in a finished human genome NATURE REVIEWS GENETICS. 2004 MAY; 5 (5): 345-354	15	56	21	73
154	3660 Zhang ZL, Gerstein M Large-scale analysis of pseudogenes in the human genome CURRENT OPINION IN GENETICS & DEVELOPMENT. 2004 AUG; 14 (4): 328-335	9	52	21	57
155	4040 Hua-Van A, Le Rouzic A, Maisonhaute C, Capy P Abundance, distribution and dynamics of retrotransposable elements and transposons: similarities and differences CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 426-440	9	25	21	154
156	4349 Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4 NATURE. 2005 APR 7; 434 (7034): 724-731	8	21	21	50
157	4769 Coghlan A, Eichler EE, Oliver SG, Paterson AH, Stein L Chromosome evolution in eukaryotes: a multi-kingdom perspective TRENDS IN GENETICS. 2005 DEC; 21 (12): 673-682	2	41	21	133
158	4834 Guigo R, Flicek P, Abril JF, Reymond A, Lagarde J, et al. EGASP: the human ENCODE genome annotation assessment project GENOME BIOLOGY. 2006; 7: Art. No. S2	5	30	21	73
159	4846 Witherspoon DJ, Marchani EE, Watkins WS, Ostler CT, Wooding SP, et al. Human population genetic structure and diversity inferred from polymorphic L1 (LINE-1) and Alu insertions HUMAN HEREDITY. 2006; 62 (1): 30-46	4	14	21	92
160	4876 Belancio VP, Hedges DJ, Deininger P LINE-1 RNA splicing and influences on mammalian gene expression NUCLEIC ACIDS RESEARCH. 2006; 34 (5): 1512-1521	27	39	21	56
#	Date / Author / Journal	LCS	GCS	LCR	CR
161	4941 Holste D, Huo G, Tung V, Burge CB HOLLYWOOD: a comparative relational database of alternative splicing NUCLEIC ACIDS RESEARCH. 2006 JAN 1; 34: D56-D62	9	36	21	57
162	5064 Chen FC, Chen CJ, Ho JY, Chuang TJ Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat BMC BIOINFORMATICS. 2006 MAR 15; 7: Art. No. 136	3	16	21	49
163	5116 Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, et al. Heterotachy in mammalian promoter evolution PLOS GENETICS. 2006 APR; 2 (4): Art. No. e30	0	37	21	47
164	5419 Abrusan G, Krambeck HJ The distribution of L1 and Alu retroelements in relation to GC content on human sex chromosomes is consistent with the ectopic recombination model JOURNAL OF MOLECULAR EVOLUTION. 2006 OCT; 63 (4): 484-492	4	9	21	51
165	5810 Fablet M, Rebollo R, Biemont C, Vieira C The evolution of retrotransposon regulatory regions and its consequences on the Drosophila melanogaster and Homo sapiens host genomes GENE. 2007 APR 1; 390 (1-2): 84-91	1	2	21	86
166	5943 Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, et al. Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica GENOME RESEARCH. 2007 JUL; 17 (7): 992-1004	20	36	21	66
167	6115 Bergman CM, Quesneville H Discovering and detecting transposable elements in genome sequences BRIEFINGS IN BIOINFORMATICS. 2007 NOV; 8 (6): 382-392	1	7	21	81
168	6248 Haas BJ Analysis of Alternative Splicing in Plants with Bioinformatics Tools NUCLEAR PRE-MRNA PROCESSING IN PLANTS. 2008; 326: 17-37	0	3	21	69
169	6514 Akagi K, Li JF, Stephens RM, Volfovsky N, Symer DE Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition GENOME RESEARCH. 2008 JUN; 18 (6): 869-880	0	4	21	49
170	6695 Lee JY, Ji Z, Tian B Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3 '-end of genes NUCLEIC ACIDS RESEARCH. 2008 OCT; 36 (17): 5581-5590	5	7	21	61
#	Date / Author / Journal	LCS	GCS	LCR	CR
171	6940 Novikova OS, Blinov AG Origin, evolution, and distribution of different groups of non-LTR retrotransposons among eukaryotes RUSSIAN JOURNAL OF GENETICS. 2009 FEB; 45 (2): 129-138	0	0	21	85
172	1334 Stankiewicz P, Lupski JR Molecular-evolutionary mechanisms for genomic disorders CURRENT OPINION IN GENETICS & DEVELOPMENT. 2002 JUN; 12 (3): 312-319	22	81	20	78
173	1978 Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, et al. Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates GENOME BIOLOGY. 2003; 4 (11): Art. No. R74	30	55	20	62
174	2924 Zhang ZL, Harrison PM, Liu Y, Gerstein M Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human genome GENOME RESEARCH. 2003 DEC; 13 (12): 2541-2558	43	132	20	96
175	3395 Wasserman WW, Sandelin A Applied bioinformatics for the identification of regulatory elements NATURE REVIEWS GENETICS. 2004 APR; 5 (4): 276-287	18	263	20	98
176	3471 Garcia-Blanco MA, Baraniak AP, Lasda EL Alternative splicing in disease and therapy NATURE BIOTECHNOLOGY. 2004 MAY; 22 (5): 535-546	20	180	20	187
177	3509 Bentley DR Genomes for medicine NATURE. 2004 MAY 27; 429 (6990): 440-445	4	27	20	60
178	3603 Sogayar MC, Camargo AA, Bettoni F, Carraro DM, Pires LC, et al. A transcript finishing initiative for closing gaps in the human transcriptome GENOME RESEARCH. 2004 JUL; 14 (7): 1413-1423	2	10	20	66
179	3775 Bennettt EA, Coleman LE, Tsui C, Pittard WS, Devine SE Natural genetic variation caused by transposable elements in humans GENETICS. 2004 OCT; 168 (2): 933-951	37	52	20	73
180	3786 Mallon AM, Wilming L, Weekes J, Gilbert JGR, Ashurst J, et al. Organization and evolution of a gene-rich region of the mouse genome: A 12.7-Mb region deleted in the Del(13)Svea36H mouse GENOME RESEARCH. 2004 OCT; 14 (10A): 1888-1901	2	14	20	96
#	Date / Author / Journal	LCS	GCS	LCR	CR
181	4033 Brandt J, Veith AM, Volff JN A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 307-317	5	15	20	78
182	4106 Brosius J Disparity, adaptation, exaptation, bookkeeping, and contingency at the genome level PALEOBIOLOGY. 2005; 31 (2): 1-16	3	5	20	175
183	4223 Johnson JM, Edwards S, Shoemaker D, Schadt EE Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments TRENDS IN GENETICS. 2005 FEB; 21 (2): 93-102	17	121	20	48
184	4483 Horvath JE, Gulden CL, Vallente RU, Eichler MY, Ventura M, et al. Punctuated duplication seeding events during the evolution of human chromosome 2p11 GENOME RESEARCH. 2005 JUL; 15 (7): 914-927	3	19	20	56
185	4572 van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates GENOME RESEARCH. 2005 SEP; 15 (9): 1243-1249	18	37	20	49
186	4742 Varki A, Altheide TK Comparing the human and chimpanzee genomes: Searching for needles in a haystack GENOME RESEARCH. 2005 DEC; 15 (12): 1746-1758	3	46	20	133
187	4857 Chen JM, Ferec C, Cooper DN LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease: Mutation detection bias and multiple mechanisms of target gene disruption JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY. 2006; : Art. No. 56182	0	11	20	76
188	4882 Buzdin A, Kovalskaya-Alexandrova E, Gogvadze E, Sverdlov E GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats NUCLEIC ACIDS RESEARCH. 2006; 34 (9): Art. No. e67	4	9	20	44
189	4994 Chamary JV, Parmley JL, Hurst LD Hearing silence: non-neutral evolution at synonymous sites in mammals NATURE REVIEWS GENETICS. 2006 FEB; 7 (2): 98-108	13	136	20	131
190	5198 Cordaux R, Lee J, Dinoso L, Batzer MA Recently integrated Alu retrotransposons are essentially neutral residents of the human genome GENE. 2006 MAY 24; 373: 138-144	10	14	20	37
#	Date / Author / Journal	LCS	GCS	LCR	CR
191	5342 Schibler L, Roig A, Mahe MF, Laurent P, Hayes H, et al. High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution BMC GENOMICS. 2006 AUG 1; 7: Art. No. 194	3	18	20	53
192	5542 Duret L, Eyre-Walker A, Galtier N A new perspective on isochore evolution GENE. 2006 DEC 30; 385: 71-74	6	31	20	35
193	5676 Ellegren H Characteristics, causes and evolutionary consequences of male-biased mutation PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 2007 JAN 7; 274 (1606): 1-10	3	21	20	111
194	5820 Song MZ, Boissinot S Selection against LINE-1 retrotransposons results principally from their ability to mediate ectopic recombination GENE. 2007 APR 1; 390 (1-2): 206-213	11	12	20	45
195	5957 Giordano J, Ge YC, Gelfand Y, Abrusan G, Benson G, et al. Evolutionary history of mammalian transposons determined by genome-wide defragmentation PLOS COMPUTATIONAL BIOLOGY. 2007 JUL; 3 (7): Art. No. e137	0	11	20	37
196	6034 Ichiyanagi K, Nishihara H, Duvernell DD, Okada N Acquisition of endonuclease specificity during evolution of L1 retrotransposon MOLECULAR BIOLOGY AND EVOLUTION. 2007 SEP; 24 (9): 2009-2015	2	3	20	44
197	6161 Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, et al. A unified classification system for eukaryotic transposable elements NATURE REVIEWS GENETICS. 2007 DEC; 8 (12): 973-982	21	92	20	93
198	6212 McGuire AM, Pearson MD, Neafsey DE, Galagan JE Cross-kingdom patterns of alternative splicing and splice recognition GENOME BIOLOGY. 2008; 9 (3): Art. No. R50	4	8	20	86
199	6275 Abrusan G, Krambeck HJ, Junier T, Giordano J, Warburton PE Biased distributions and decay of long interspersed nuclear elements in the chicken genome GENETICS. 2008 JAN; 178 (1): 573-581	4	5	20	48
200	6342 Rodriguez J, Vives L, Jorda M, Morales C, Munoz M, et al. Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells NUCLEIC ACIDS RESEARCH. 2008 FEB; 36 (3): 770-784	3	11	20	74

Date / Author / Journal

LCS

GCS

LCR

101

4023 Biemont C, Vieira C

What transposable elements tell us about genome organization and evolution: the case of Drosophila

CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 25-34

176

102

4366 Shapiro JA, von Sternberg R

Why repetitive DNA is essential to genome function

BIOLOGICAL REVIEWS. 2005 MAY; 80 (2): 227-250

247

103

4592 Gregory TR

Synergy between sequence and size in large-scale genomics

NATURE REVIEWS GENETICS. 2005 SEP; 6 (9): 699-708

111

104

5087 Singh R, Robida MD, Karimpour S

Building biological complexity with limited genes

CURRENT GENOMICS. 2006 APR; 7 (2): 97-114

195

105

5095 Wang JX, Song L, Grover D, Azrak S, Batzer MA, et al.

DbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans

HUMAN MUTATION. 2006 APR; 27 (4): 323-329

106

5385 Carninci P

Tagging mammalian transcription complexity

TRENDS IN GENETICS. 2006 SEP; 22 (9): 501-510

107

5516 Weber MJ

Mammalian small nucleolar RNAs are mobile genetic elements

PLOS GENETICS. 2006 DEC; 2 (12): Art. No. e205

108

5711 Kost-Alimova M, Imreh S

Modeling non-random deletions in cancer

SEMINARS IN CANCER BIOLOGY. 2007 FEB; 17 (1): 19-30

109

5799 Slotkin RK, Martienssen R

Transposable elements and the epigenetic regulation of the genome

NATURE REVIEWS GENETICS. 2007 APR; 8 (4): 272-285

127

145

110

5807 Lee J, Cordaux R, Han KD, Wang JX, Hedges DJ, et al.

Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons

GENE. 2007 APR 1; 390 (1-2): 18-27

Date / Author / Journal

111

APOBEC3 proteins: major players in intracellular defence against LINE-1-mediated retrotransposition

BIOCHEMICAL SOCIETY TRANSACTIONS. 2007 JUN; 35: 637-642

112

6336 Karro JE, Peifer M, Hardison RC, Kollmann M, von Grunberg HH

Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure

MOLECULAR BIOLOGY AND EVOLUTION. 2008 FEB; 25 (2): 362-374

113

6653 Ponting CP

The functional repertoires of metazoan genomes

NATURE REVIEWS GENETICS. 2008 SEP; 9 (9): 689-698

114

6698 Lin L, Shen SH, Tye A, Cai JJ, Jiang P, et al.

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

PLOS GENETICS. 2008 OCT; 4 (10): Art. No. e1000225

115

7270 Kandul NP, Noor MAF

Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3

BMC GENETICS. 2009 OCT 19; 10: Art. No. 67

116

3443 Bailey JA, Church DM, Ventura M, Rocchi M, Eichler EE

Analysis of segmental duplications and genome assembly in the mouse

GENOME RESEARCH. 2004 MAY; 14 (5): 789-801

117

4013 Ryder OA

Conservation genomics: applying whole genome studies to species conservation efforts

CYTOGENETIC AND GENOME RESEARCH. 2005; 108 (1-3): 6-15

118

4024 Dewannieux M, Heidmann T

LINEs, SINEs and processed pseudogenes: parasitic strategies for genome modeling

CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 35-48

147

119

4519 Han JS, Boeke JD

LINEA retrotransposons: modulators of quantity and quality of mammalian gene expression?

BIOESSAYS. 2005 AUG; 27 (8): 775-784

120

5502 Ding WY, Lin L, Cheh B, Dai JW

L1 elements, processed pseudogenes and retrogenes in mammalian genomes

IUBMB LIFE. 2006 DEC; 58 (12): 677-685

Date / Author / Journal

LCS

GCS

LCR

121

6404 Pozzoli U, Menozzi G, Fumagalli M, Cereda M, Comi GP, et al.

Both selective and neutral processes drive GC content evolution in the human genome

BMC EVOLUTIONARY BIOLOGY. 2008 MAR 27; 8: Art. No. 99

122

6924 Koszul R, Fischer G

A prominent role for segmental duplications in modeling Eukaryotic genomes

COMPTES RENDUS BIOLOGIES. 2009 FEB-MAR; 332 (2-3): 254-266

102

123

7057 Pace JK, Sen SK, Batzer MA, Feschotte C

Repair-Mediated Duplication by Capture of Proximal Chromosomal DNA Has Shaped Vertebrate Genome Evolution

PLOS GENETICS. 2009 MAY; 5 (5): Art. No. e1000469

124

7109 Lin L, Jiang P, Shen SH, Sato S, Davidson BL, et al.

Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes

HUMAN MOLECULAR GENETICS. 2009 JUN 15; 18 (12): 2204-2214

125

7110 Gogvadze E, Stukacheva E, Buzdin A, Sverdlov E

Human-Specific Modulation of Transcriptional Activity Provided by Endogenous Retroviral Insertions

JOURNAL OF VIROLOGY. 2009 JUN 15; 83 (12): 6098-6105

126

7137 Venner S, Feschotte C, Biemont C

Dynamics of transposable elements: towards a community ecology of the genome

TRENDS IN GENETICS. 2009 JUL; 25 (7): 317-323

127

7280 Damert A, Raiz J, Horn AV, Lower J, Wang H, et al.

5 '-Transducing SVA retrotransposon groups spread efficiently throughout the human genome

GENOME RESEARCH. 2009 NOV; 19 (11): 1992-2008

128

7316 Bourque G

Transposable elements in gene regulation and in the evolution of vertebrate genomes

CURRENT OPINION IN GENETICS & DEVELOPMENT. 2009 DEC; 19 (6): 607-612

129

1902 Ashurst JL, Collins JE

Gene annotation: Prediction and testing

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2003; 4: 69-88

101

130

2676 Eichler EE, Sankoff D

Structural dynamics of eukaryotic chromosome evolution

SCIENCE. 2003 AUG 8; 301 (5634): 793-797

155

Date / Author / Journal

LCS

GCS

LCR

131

3652 Suzuki M, Hayashizaki Y

Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs

BIOESSAYS. 2004 AUG; 26 (8): 833-843

115

132

3776 Zhao SY, Shetty J, Hou LH, Delcher A, Zhu BL, et al.

Human, mouse, and rat genome large-scale rearrangements: Stability versus speciation

GENOME RESEARCH. 2004 OCT; 14 (10A): 1851-1860

133

3848 Blakesley RW, Hansen NF, Mullikin JC, Thomas PJ, McDowell JC, et al.

An intermediate grade of finished genomic sequence suitable for comparative analyses

GENOME RESEARCH. 2004 NOV; 14 (11): 2235-2244

134

3988 Giallourakis C, Henson C, Reich M, Xie XH, Mootha VK

Disease gene discovery through integrative genomics

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2005; 6: 381-406

117

135

4045 Ohshima K, Okada N

SINEs and LINEs: symbionts of eukaryotic genomes with a common tail

CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 475-490

165

136

4405 Zheng DY, Zhang ZL, Harrison PM, Karro J, Carriero N, et al.

Integrated pseudogene annotation for human chromosome 22: Evidence for transcription

JOURNAL OF MOLECULAR BIOLOGY. 2005 MAY 27; 349 (1): 27-45

137

4597 Hedges DJ, Cordaux R, Xing J, Witherspoon DJ, Rogers AR, et al.

Modeling the amplification dynamics of human Alu retrotransposons

PLOS COMPUTATIONAL BIOLOGY. 2005 SEP; 1 (4): Art. No. e44

138

4743 Little PFR

Structure and function of the human genome

GENOME RESEARCH. 2005 DEC; 15 (12): 1759-1766

139

4776 Wang H, Xing J, Grover D, Hedges DJ, Han KD, et al.

SVA elements: A hominid-specific retroposon family

JOURNAL OF MOLECULAR BIOLOGY. 2005 DEC 9; 354 (4): 994-1007

140

4842 Sironi M, Menozzi G, Comi GP, Cereda M, Cagliani R, et al.

Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns

GENOME BIOLOGY. 2006; 7 (12): Art. No. R120

Date / Author / Journal

LCS

GCS

LCR

141

5127 Temple G, Lamesch P, Milstein S, Hill DE, Wagner L, et al.

From genome to proteome: developing expression clone resources for the human genome

HUMAN MOLECULAR GENETICS. 2006 APR 15; 15: R31-R43

142

5252 Liu GE, Matukumalli LK, Sonstegard TS, Shade LL, Van Tassell CP

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences

BMC GENOMICS. 2006 JUN 7; 7: Art. No. 140

143

5272 Sen SK, Han KD, Wang JX, Lee J, Wang H, et al.

Human genomic deletions mediated by recombination between Alu elements

AMERICAN JOURNAL OF HUMAN GENETICS. 2006 JUL; 79 (1): 41-53

144

5531 An WF, Han JS, Wheelan SJ, Davis ES, Coombes CE, et al.

Active retrotransposition by a synthetic L1 element in mice

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2006 DEC 5; 103 (49): 18662-18667

145

5910 Sen SK, Huang CT, Han K, Batzer MA

Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome

NUCLEIC ACIDS RESEARCH. 2007 JUN; 35 (11): 3741-3751

146

5930 Buzdin A, Gogvadze E, Lebrun MH

Chimeric retrogenes suggest a role for the nucleolus in LINE amplification

FEBS LETTERS. 2007 JUN 26; 581 (16): 2877-2882

147

5938 Hasler J, Samuelsson T, Strub K

Useful 'junk': Alu RNAs in the human transcriptome

CELLULAR AND MOLECULAR LIFE SCIENCES. 2007 JUL; 64 (14): 1793-1800

148

6088 Cogburn LA, Porter TE, Duclos MJ, Simon J, Burgess SC, et al.

Functional genomics of the chicken - A model organism

POULTRY SCIENCE. 2007 OCT; 86 (10): 2059-2094

322

149

6714 Wegmann D, Dupanloup I, Excoffier L

Width of Gene Expression Profile Drives Alternative Splicing

PLOS ONE. 2008 OCT 31; 3 (10): Art. No. e3587

150

6996 Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL

Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die?

GENOME RESEARCH. 2009 APR; 19 (4): 545-555

Date / Author / Journal

LCS

GCS

LCR

151

7122 Singh R, Knight R

Systems Biology: Understanding Function from Genes to Networks

CURRENT PROTEOMICS. 2009 JUL; 6 (2): 93-103

165

152

2998 Borevitz JO, Ecker JR

Plant genomics: The third wave

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2004; 5: 443-477

173

153

3474 Eichler EE, Clark RA, She XW

An assessment of the sequence gaps: Unfinished business in a finished human genome

NATURE REVIEWS GENETICS. 2004 MAY; 5 (5): 345-354

154

3660 Zhang ZL, Gerstein M

Large-scale analysis of pseudogenes in the human genome

CURRENT OPINION IN GENETICS & DEVELOPMENT. 2004 AUG; 14 (4): 328-335

155

4040 Hua-Van A, Le Rouzic A, Maisonhaute C, Capy P

Abundance, distribution and dynamics of retrotransposable elements and transposons: similarities and differences

CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 426-440

154

156

4349 Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, et al.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

NATURE. 2005 APR 7; 434 (7034): 724-731

157

4769 Coghlan A, Eichler EE, Oliver SG, Paterson AH, Stein L

Chromosome evolution in eukaryotes: a multi-kingdom perspective

TRENDS IN GENETICS. 2005 DEC; 21 (12): 673-682

133

158

4834 Guigo R, Flicek P, Abril JF, Reymond A, Lagarde J, et al.

EGASP: the human ENCODE genome annotation assessment project

GENOME BIOLOGY. 2006; 7: Art. No. S2

159

4846 Witherspoon DJ, Marchani EE, Watkins WS, Ostler CT, Wooding SP, et al.

Human population genetic structure and diversity inferred from polymorphic L1 (LINE-1) and Alu insertions

HUMAN HEREDITY. 2006; 62 (1): 30-46

160

4876 Belancio VP, Hedges DJ, Deininger P

LINE-1 RNA splicing and influences on mammalian gene expression

NUCLEIC ACIDS RESEARCH. 2006; 34 (5): 1512-1521

Date / Author / Journal

LCS

GCS

LCR

161

4941 Holste D, Huo G, Tung V, Burge CB

HOLLYWOOD: a comparative relational database of alternative splicing

NUCLEIC ACIDS RESEARCH. 2006 JAN 1; 34: D56-D62

162

5064 Chen FC, Chen CJ, Ho JY, Chuang TJ

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat

BMC BIOINFORMATICS. 2006 MAR 15; 7: Art. No. 136

163

5116 Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, et al.

Heterotachy in mammalian promoter evolution

PLOS GENETICS. 2006 APR; 2 (4): Art. No. e30

164

5419 Abrusan G, Krambeck HJ

The distribution of L1 and Alu retroelements in relation to GC content on human sex chromosomes is consistent with the ectopic recombination model

JOURNAL OF MOLECULAR EVOLUTION. 2006 OCT; 63 (4): 484-492

165

5810 Fablet M, Rebollo R, Biemont C, Vieira C

The evolution of retrotransposon regulatory regions and its consequences on the Drosophila melanogaster and Homo sapiens host genomes

GENE. 2007 APR 1; 390 (1-2): 84-91

166

5943 Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, et al.

Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica

GENOME RESEARCH. 2007 JUL; 17 (7): 992-1004

167

6115 Bergman CM, Quesneville H

Discovering and detecting transposable elements in genome sequences

BRIEFINGS IN BIOINFORMATICS. 2007 NOV; 8 (6): 382-392

168

6248 Haas BJ

Analysis of Alternative Splicing in Plants with Bioinformatics Tools

NUCLEAR PRE-MRNA PROCESSING IN PLANTS. 2008; 326: 17-37

169

6514 Akagi K, Li JF, Stephens RM, Volfovsky N, Symer DE

Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition

GENOME RESEARCH. 2008 JUN; 18 (6): 869-880

170

6695 Lee JY, Ji Z, Tian B

Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3 '-end of genes

NUCLEIC ACIDS RESEARCH. 2008 OCT; 36 (17): 5581-5590

Date / Author / Journal

LCS

GCS

LCR

171

6940 Novikova OS, Blinov AG

Origin, evolution, and distribution of different groups of non-LTR retrotransposons among eukaryotes

RUSSIAN JOURNAL OF GENETICS. 2009 FEB; 45 (2): 129-138

172

1334 Stankiewicz P, Lupski JR

Molecular-evolutionary mechanisms for genomic disorders

CURRENT OPINION IN GENETICS & DEVELOPMENT. 2002 JUN; 12 (3): 312-319

173

1978 Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, et al.

Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates

GENOME BIOLOGY. 2003; 4 (11): Art. No. R74

174

2924 Zhang ZL, Harrison PM, Liu Y, Gerstein M

Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human genome

GENOME RESEARCH. 2003 DEC; 13 (12): 2541-2558

132

175

3395 Wasserman WW, Sandelin A

Applied bioinformatics for the identification of regulatory elements

NATURE REVIEWS GENETICS. 2004 APR; 5 (4): 276-287

263

176

3471 Garcia-Blanco MA, Baraniak AP, Lasda EL

Alternative splicing in disease and therapy

NATURE BIOTECHNOLOGY. 2004 MAY; 22 (5): 535-546

180

187

177

3509 Bentley DR

Genomes for medicine

NATURE. 2004 MAY 27; 429 (6990): 440-445

178

3603 Sogayar MC, Camargo AA, Bettoni F, Carraro DM, Pires LC, et al.

A transcript finishing initiative for closing gaps in the human transcriptome

GENOME RESEARCH. 2004 JUL; 14 (7): 1413-1423

179

3775 Bennettt EA, Coleman LE, Tsui C, Pittard WS, Devine SE

Natural genetic variation caused by transposable elements in humans

GENETICS. 2004 OCT; 168 (2): 933-951

180

3786 Mallon AM, Wilming L, Weekes J, Gilbert JGR, Ashurst J, et al.

Organization and evolution of a gene-rich region of the mouse genome: A 12.7-Mb region deleted in the Del(13)Svea36H mouse

GENOME RESEARCH. 2004 OCT; 14 (10A): 1888-1901

Date / Author / Journal

LCS

GCS

LCR

181

4033 Brandt J, Veith AM, Volff JN

A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes

CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 307-317

182

4106 Brosius J

Disparity, adaptation, exaptation, bookkeeping, and contingency at the genome level

PALEOBIOLOGY. 2005; 31 (2): 1-16

175

183

4223 Johnson JM, Edwards S, Shoemaker D, Schadt EE

Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments

TRENDS IN GENETICS. 2005 FEB; 21 (2): 93-102

121

184

4483 Horvath JE, Gulden CL, Vallente RU, Eichler MY, Ventura M, et al.

Punctuated duplication seeding events during the evolution of human chromosome 2p11

GENOME RESEARCH. 2005 JUL; 15 (7): 914-927

185

4572 van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL

Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates

GENOME RESEARCH. 2005 SEP; 15 (9): 1243-1249

186

4742 Varki A, Altheide TK

Comparing the human and chimpanzee genomes: Searching for needles in a haystack

GENOME RESEARCH. 2005 DEC; 15 (12): 1746-1758

133

187

4857 Chen JM, Ferec C, Cooper DN

LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease: Mutation detection bias and multiple mechanisms of target gene disruption

JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY. 2006; : Art. No. 56182

188

4882 Buzdin A, Kovalskaya-Alexandrova E, Gogvadze E, Sverdlov E

GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats

NUCLEIC ACIDS RESEARCH. 2006; 34 (9): Art. No. e67

189

4994 Chamary JV, Parmley JL, Hurst LD

Hearing silence: non-neutral evolution at synonymous sites in mammals

NATURE REVIEWS GENETICS. 2006 FEB; 7 (2): 98-108

136

131

190

5198 Cordaux R, Lee J, Dinoso L, Batzer MA

Recently integrated Alu retrotransposons are essentially neutral residents of the human genome

GENE. 2006 MAY 24; 373: 138-144

Date / Author / Journal

LCS

GCS

LCR

191

5342 Schibler L, Roig A, Mahe MF, Laurent P, Hayes H, et al.

High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution

BMC GENOMICS. 2006 AUG 1; 7: Art. No. 194

192

5542 Duret L, Eyre-Walker A, Galtier N

A new perspective on isochore evolution

GENE. 2006 DEC 30; 385: 71-74

193

5676 Ellegren H

Characteristics, causes and evolutionary consequences of male-biased mutation

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 2007 JAN 7; 274 (1606): 1-10

111

194

5820 Song MZ, Boissinot S

Selection against LINE-1 retrotransposons results principally from their ability to mediate ectopic recombination

GENE. 2007 APR 1; 390 (1-2): 206-213

195

5957 Giordano J, Ge YC, Gelfand Y, Abrusan G, Benson G, et al.

Evolutionary history of mammalian transposons determined by genome-wide defragmentation

PLOS COMPUTATIONAL BIOLOGY. 2007 JUL; 3 (7): Art. No. e137

196

6034 Ichiyanagi K, Nishihara H, Duvernell DD, Okada N

Acquisition of endonuclease specificity during evolution of L1 retrotransposon

MOLECULAR BIOLOGY AND EVOLUTION. 2007 SEP; 24 (9): 2009-2015

197

6161 Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, et al.

A unified classification system for eukaryotic transposable elements

NATURE REVIEWS GENETICS. 2007 DEC; 8 (12): 973-982

198

6212 McGuire AM, Pearson MD, Neafsey DE, Galagan JE

Cross-kingdom patterns of alternative splicing and splice recognition

GENOME BIOLOGY. 2008; 9 (3): Art. No. R50

199

6275 Abrusan G, Krambeck HJ, Junier T, Giordano J, Warburton PE

Biased distributions and decay of long interspersed nuclear elements in the chicken genome

GENETICS. 2008 JAN; 178 (1): 573-581

200

6342 Rodriguez J, Vives L, Jorda M, Morales C, Munoz M, et al.

Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells

NUCLEIC ACIDS RESEARCH. 2008 FEB; 36 (3): 770-784

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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