HistCite - The sequence of the human genome (Venter)

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#	Date / Author / Journal	LCS	GCS	LCR	CR
1	3090 Brosius J Echoes from the past - are we still in an RNP world? CYTOGENETIC AND GENOME RESEARCH. 2005; 110 (1-4): 8-24	0	17	46	302
2	2672 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	118	752	32	226
3	1544 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	462	2474	29	331
4	4262 Gingeras TR Origin of phenotypes: Genes and transcripts GENOME RESEARCH. 2007 JUN; 17 (6): 682-690	5	49	28	105
5	3518 Salzano FM Evolutionary change - patterns and processes ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS. 2005 DEC; 77 (4): 627-650	0	1	27	145
6	4359 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	6	15	27	106
7	4374 Kleparnik K, Bocek P DNA diagnostics by capillary electrophoresis CHEMICAL REVIEWS. 2007 NOV; 107 (11): 5279-5317	0	12	27	748
8	2773 Southan C Has the yo-yo stopped? - An assessment of human protein-coding gene number PROTEOMICS. 2004 JUN; 4 (6): 1712-1726	9	41	26	78
9	4301 Tang H Genome assembly, rearrangement, and repeats CHEMICAL REVIEWS. 2007 AUG; 107 (8): 3391-3406	1	1	26	154
10	4302 Artamonova II, Gelfand MS Comparative genomics and evolution of alternative splicing: The pessimists' science CHEMICAL REVIEWS. 2007 AUG; 107 (8): 3407-3430	1	12	26	384
#	Date / Author / Journal	LCS	GCS	LCR	CR
11	4274 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	39	671	25	128
12	4169 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	0	28	24	131
13	4938 Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, et al. Sequence assembly COMPUTATIONAL BIOLOGY AND CHEMISTRY. 2009 APR; 33 (2): 121-136	0	2	23	186
14	1577 Ashurst JL, Collins JE Gene annotation: Prediction and testing ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2003; 4: 69-88	10	34	21	101
15	3554 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	36	470	21	119
16	2833 Suzuki M, Hayashizaki Y Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs BIOESSAYS. 2004 AUG; 26 (8): 833-843	2	27	20	115
17	3935 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	1	25	20	209
18	2320 Copley RR, Goodstadt L, Ponting C Eukaryotic domain evolution inferred from genome comparisons CURRENT OPINION IN GENETICS & DEVELOPMENT. 2003 DEC; 13 (6): 623-628	1	18	19	47
19	2362 Pop M Shotgun sequence assembly ADVANCES IN COMPUTERS, VOL. 60. 2004; 60: 193-248	1	2	19	135
20	1888 Ureta-Vidal A, Ettwiller L, Birney E Comparative genomics: Genome-wide analysis in metazoan eukaryotes NATURE REVIEWS GENETICS. 2003 APR; 4 (4): 251-262	18	117	18	100
#	Date / Author / Journal	LCS	GCS	LCR	CR
21	2953 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	167	901	18	71
22	3062 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	18	117
23	3313 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	3	34	18	46
24	3881 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	18	64
25	2371 Borevitz JO, Ecker JR Plant genomics: The third wave ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2004; 5: 443-477	1	28	17	173
26	2818 Wendl MC, Yang SP Gap statistics for whole genome shotgun DNA sequencing projects BIOINFORMATICS. 2004 JUL 1; 20 (10): 1527-1534	1	5	17	44
27	3007 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	17	81
28	3061 Crawford DC, Akey DT, Nickerson DA The patterns of natural variation in human genes ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2005; 6: 287-312	4	49	17	118
29	3204 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	10	121	17	48
30	4436 Phillippy AM, Schatz MC, Pop M Genome assembly forensics: finding the elusive mis-assembly GENOME BIOLOGY. 2008; 9 (3): Art. No. R55	2	10	17	42
#	Date / Author / Journal	LCS	GCS	LCR	CR
31	4698 Vagena E, Fakis G, Boukouvala S Arylamine N-acetyltransferases in prokaryotic and eukaryotic genomes: A survey of public databases CURRENT DRUG METABOLISM. 2008 SEP; 9 (7): 628-660	0	0	17	230
32	2224 Mattick JS Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms BIOESSAYS. 2003 OCT; 25 (10): 930-939	15	191	16	104
33	2368 Miller W, Makova KD, Nekrutenko A, Hardison RC Comparative genomics ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2004; 5: 15-56	10	77	16	193
34	3530 Little PFR Structure and function of the human genome GENOME RESEARCH. 2005 DEC; 15 (12): 1759-1766	2	9	16	54
35	3531 Brent MR Genome annotation past, present, and future: How to define an ORF at each locus GENOME RESEARCH. 2005 DEC; 15 (12): 1777-1786	1	42	16	70
36	3771 Singh R, Robida MD, Karimpour S Building biological complexity with limited genes CURRENT GENOMICS. 2006 APR; 7 (2): 97-114	1	3	16	195
37	4261 Gerstein MB, Bruce C, Rozowsky JS, Zheng DY, Du J, et al. What is a gene, post-ENCODE? History and updated definition GENOME RESEARCH. 2007 JUN; 17 (6): 669-681	10	78	16	103
38	4381 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	1	47	16	102
39	4586 Oberacher H On the use of different mass spectrometric techniques for characterization of sequence variability in genomic DNA ANALYTICAL AND BIOANALYTICAL CHEMISTRY. 2008 MAY; 391 (1): 135-149	0	2	16	222
40	4707 Ponting CP The functional repertoires of metazoan genomes NATURE REVIEWS GENETICS. 2008 SEP; 9 (9): 689-698	0	8	16	94
#	Date / Author / Journal	LCS	GCS	LCR	CR
41	4778 Ciuffi A Mechanisms Governing Lentivirus Integration Site Selection CURRENT GENE THERAPY. 2008 DEC; 8 (6): 419-429	0	3	16	177
42	4781 Hert DG, Fredlake CP, Barron AE Advantages and limitations of next-generation sequencing technologies: A comparison of electrophoresis and non-electrophoresis methods ELECTROPHORESIS. 2008 DEC; 29 (23): 4618-4626	0	4	16	92
43	4848 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	16	229
44	2642 Havlak P, Chen R, Durbin KJ, Egan A, Ren YR, et al. The atlas genome assembly system GENOME RESEARCH. 2004 APR; 14 (4): 721-732	10	46	15	39
45	2923 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	4	42	15	62
46	2972 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	8	34	15	50
47	3644 Wendl MC Occupancy modeling of coverage distribution for whole genome shotgun DNA sequencing BULLETIN OF MATHEMATICAL BIOLOGY. 2006 JAN; 68 (1): 179-196	1	5	15	54
48	3815 Millan MJ Multi-target strategies for the improved treatment of depressive states: Conceptual foundations and neuronal substrates, drug discovery and therapeutic application PHARMACOLOGY & THERAPEUTICS. 2006 MAY; 110 (2): 135-370	0	86	15	3729
49	3925 Yu J, Ni PX, Wong GKS Comparing the whole-genome-shotgun and map-based sequences of the rice genome TRENDS IN PLANT SCIENCE. 2006 AUG; 11 (8): 387-391	0	3	15	34
50	5023 Singh R, Knight R Systems Biology: Understanding Function from Genes to Networks CURRENT PROTEOMICS. 2009 JUL; 6 (2): 93-103	0	0	15	165
#	Date / Author / Journal	LCS	GCS	LCR	CR
51	2193 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	14	39
52	2289 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	9	202	14	122
53	2656 Mattick JS RNA regulation: a new genetics? NATURE REVIEWS GENETICS. 2004 APR; 5 (4): 316-323	11	215	14	80
54	2803 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	1	10	14	66
55	3200 Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation NATURE METHODS. 2005 FEB; 2 (2): 105-111	7	93	14	30
56	3201 Hirschhorn JN, Daly MJ Genome-wide association studies for common diseases and complex traits NATURE REVIEWS GENETICS. 2005 FEB; 6 (2): 95-108	22	399	14	138
57	3574 Maston GA, Evans SK, Green MR Transcriptional regulatory elements in the human genome ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2006; 7: 29-59	8	51	14	196
58	3743 Durand D, Hoberman R Diagnosing duplications - can it be done? TRENDS IN GENETICS. 2006 MAR; 22 (3): 156-164	3	18	14	79
59	3867 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	0	8	14	59
60	3910 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	0	2	14	105
#	Date / Author / Journal	LCS	GCS	LCR	CR
61	4062 Small KS, Brudno M, Hill MM, Sidow A A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome GENOME BIOLOGY. 2007; 8 (3): Art. No. R41	0	9	14	39
62	4362 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	14	322
63	4581 Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, et al. Consensus generation and variant detection by Celera Assembler BIOINFORMATICS. 2008 APR 15; 24 (8): 1035-1040	1	3	14	41
64	4700 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	14	144
65	4978 Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, et al. Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse PLOS BIOLOGY. 2009 MAY; 7 (5): Art. No. e1000112	0	8	14	83
66	1453 Dunham I Human genome sequences: enigmatic variations MUTAGENESIS. 2002 NOV; 17 (6): 457-461	0	0	13	49
67	1856 Barr MM Super models PHYSIOLOGICAL GENOMICS. 2003 MAR 18; 13 (1): 15-24	0	34	13	107
68	2693 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	8	52	13	51
69	2898 Haubold B, Wiehe T Comparative genomics: methods and applications NATURWISSENSCHAFTEN. 2004 SEP; 91 (9): 405-421	1	8	13	133
70	2971 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	4	56	13	82
#	Date / Author / Journal	LCS	GCS	LCR	CR
71	3251 Zheng XH, Lu F, Wang ZY, Hoover J, Mural R Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs BIOINFORMATICS. 2005 MAR 15; 21 (6): 703-710	1	16	13	36
72	3311 Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution SCIENCE. 2005 MAY 20; 308 (5725): 1149-1154	30	346	13	35
73	3480 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	13	51
74	3616 Huang YH, Barouch-Bentov R, Herman A, Walker J, Sauer K Integrating traditional and postgenomic approaches to investigate lymphocyte development and function LYMPHOCYTE SIGNAL TRANSDUCTION. 2006; 584: 245-276	0	2	13	143
75	3768 Vij S, Gupta V, Kumar D, Vydianathan R, Raghuvanshi S, et al. Decoding the rice genome BIOESSAYS. 2006 APR; 28 (4): 421-432	0	14	13	101
76	4019 Khaja R, Zhang JJ, MacDonald JR, He YS, Joseph-George AM, et al. Genome assembly comparison identifies structural variants in the human genome NATURE GENETICS. 2006 DEC; 38 (12): 1413-1418	8	73	13	30
77	4228 Song N, Sedgewick RD, Durand D Domain architecture comparison for multidomain homology identification JOURNAL OF COMPUTATIONAL BIOLOGY. 2007 MAY; 14 (4): 496-516	0	6	13	103
78	4300 Rabinowicz PD Plant genomic sequencing using gene-enriched libraries CHEMICAL REVIEWS. 2007 AUG; 107 (8): 3377-3390	0	0	13	158
79	4320 Yu Z, Morais D, Ivanga M, Harrison PM Analysis of the role of retrotransposition in gene evolution in vertebrates BMC BIOINFORMATICS. 2007 AUG 24; 8: Art. No. 308	1	8	13	35
80	4584 Copley RR The animal in the genome: comparative genomics and evolution PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 2008 APR 27; 363 (1496): 1453-1461	2	5	13	88
#	Date / Author / Journal	LCS	GCS	LCR	CR
81	5020 Pop M Genome assembly reborn: recent computational challenges BRIEFINGS IN BIOINFORMATICS. 2009 JUL; 10 (4): 354-366	1	2	13	73
82	1113 Stankiewicz P, Lupski JR Molecular-evolutionary mechanisms for genomic disorders CURRENT OPINION IN GENETICS & DEVELOPMENT. 2002 JUN; 12 (3): 312-319	9	81	12	78
83	1216 Yao T Bioinformatics for the genomic sciences and towards systems biology. Japanese activities in the post-genome era PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY. 2002 JUL-AUG; 80 (1-2): 23-42	2	10	12	93
84	1228 Maniatis T, Tasic B Alternative pre-mRNA splicing and proteome expansion in metazoans NATURE. 2002 JUL 11; 418 (6894): 236-243	20	349	12	96
85	1545 Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs NATURE. 2002 DEC 5; 420 (6915): 563-573	75	619	12	52
86	1594 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	12	78
87	1696 Thomas JW, Schueler MG, Summers TJ, Blakesley RW, McDowell JC, et al. Pericentromeric duplications in the laboratory mouse GENOME RESEARCH. 2003 JAN; 13 (1): 55-63	4	26	12	43
88	1715 Boright AP, Kere J, Scherer SW Genomics and pediatric research PEDIATRIC RESEARCH. 2003 JAN; 53 (1): 4-9	0	0	12	60
89	2321 Seoighe C Turning the clock back on ancient genome duplication CURRENT OPINION IN GENETICS & DEVELOPMENT. 2003 DEC; 13 (6): 636-643	2	16	12	62
90	2326 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	14	132	12	96
#	Date / Author / Journal	LCS	GCS	LCR	CR
91	2414 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	8	58	12	48
92	2634 de Magalhaes JP, Toussaint O How bioinformatics can help reverse engineer human aging AGEING RESEARCH REVIEWS. 2004 APR; 3 (2): 125-141	0	10	12	101
93	2734 Bentley DR Genomes for medicine NATURE. 2004 MAY 27; 429 (6990): 440-445	6	27	12	60
94	2769 Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones PLOS BIOLOGY. 2004 JUN; 2 (6): Art. No. e162	0	168	12	116
95	3088 Ryder OA Conservation genomics: applying whole genome studies to species conservation efforts CYTOGENETIC AND GENOME RESEARCH. 2005; 108 (1-3): 6-15	1	9	12	90
96	3128 Harrison PM, Zheng DY, Zhang ZL, Carriero N, Gerstein M Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability NUCLEIC ACIDS RESEARCH. 2005; 33 (8): 2374-2383	5	53	12	54
97	3243 Reis EM, Louro R, Nakaya HI, Verjovski-Almeida S As antisense RNA gets intronic OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY. 2005 MAR; 9 (1): 2-12	2	18	12	60
98	3577 Cheok MH, Lugthart S, Evans WE Pharmacogenomics of acute leukemia ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY. 2006; 46: 317-353	1	15	12	210
99	3602 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	12	73
100	3611 Oh DY, Kim K, Kwon HB, Seong JY Cellular and molecular biology of orphan G protein-coupled receptors INTERNATIONAL REVIEW OF CYTOLOGY - A SURVEY OF CELL BIOLOGY, VOL 252. 2006; 252: 163-218	0	5	12	295

Date / Author / Journal

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

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

302

2672 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

118

752

226

1544 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

462

2474

331

4262 Gingeras TR

Origin of phenotypes: Genes and transcripts

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

105

3518 Salzano FM

Evolutionary change - patterns and processes

ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS. 2005 DEC; 77 (4): 627-650

145

4359 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

4374 Kleparnik K, Bocek P

DNA diagnostics by capillary electrophoresis

CHEMICAL REVIEWS. 2007 NOV; 107 (11): 5279-5317

748

2773 Southan C

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

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

4301 Tang H

Genome assembly, rearrangement, and repeats

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

154

4302 Artamonova II, Gelfand MS

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

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

384

Date / Author / Journal

LCS

GCS

LCR

4274 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

4169 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

4938 Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, et al.

Sequence assembly

COMPUTATIONAL BIOLOGY AND CHEMISTRY. 2009 APR; 33 (2): 121-136

186

1577 Ashurst JL, Collins JE

Gene annotation: Prediction and testing

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

101

3554 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

470

119

2833 Suzuki M, Hayashizaki Y

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

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

115

3935 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

2320 Copley RR, Goodstadt L, Ponting C

Eukaryotic domain evolution inferred from genome comparisons

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

2362 Pop M

Shotgun sequence assembly

ADVANCES IN COMPUTERS, VOL. 60. 2004; 60: 193-248

135

1888 Ureta-Vidal A, Ettwiller L, Birney E

Comparative genomics: Genome-wide analysis in metazoan eukaryotes

NATURE REVIEWS GENETICS. 2003 APR; 4 (4): 251-262

117

100

Date / Author / Journal

LCS

GCS

LCR

2953 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

167

901

3062 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

3313 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

3881 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

2371 Borevitz JO, Ecker JR

Plant genomics: The third wave

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

173

2818 Wendl MC, Yang SP

Gap statistics for whole genome shotgun DNA sequencing projects

BIOINFORMATICS. 2004 JUL 1; 20 (10): 1527-1534

3007 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

3061 Crawford DC, Akey DT, Nickerson DA

The patterns of natural variation in human genes

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2005; 6: 287-312

118

3204 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

4436 Phillippy AM, Schatz MC, Pop M

Genome assembly forensics: finding the elusive mis-assembly

GENOME BIOLOGY. 2008; 9 (3): Art. No. R55

Date / Author / Journal

LCS

GCS

LCR

4698 Vagena E, Fakis G, Boukouvala S

Arylamine N-acetyltransferases in prokaryotic and eukaryotic genomes: A survey of public databases

CURRENT DRUG METABOLISM. 2008 SEP; 9 (7): 628-660

230

2224 Mattick JS

Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms

BIOESSAYS. 2003 OCT; 25 (10): 930-939

191

104

2368 Miller W, Makova KD, Nekrutenko A, Hardison RC

Comparative genomics

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

193

3530 Little PFR

Structure and function of the human genome

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

3531 Brent MR

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

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

3771 Singh R, Robida MD, Karimpour S

Building biological complexity with limited genes

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

195

4261 Gerstein MB, Bruce C, Rozowsky JS, Zheng DY, Du J, et al.

What is a gene, post-ENCODE? History and updated definition

GENOME RESEARCH. 2007 JUN; 17 (6): 669-681

103

4381 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

4586 Oberacher H

On the use of different mass spectrometric techniques for characterization of sequence variability in genomic DNA

ANALYTICAL AND BIOANALYTICAL CHEMISTRY. 2008 MAY; 391 (1): 135-149

222

4707 Ponting CP

The functional repertoires of metazoan genomes

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

Date / Author / Journal

Mechanisms Governing Lentivirus Integration Site Selection

CURRENT GENE THERAPY. 2008 DEC; 8 (6): 419-429

177

4781 Hert DG, Fredlake CP, Barron AE

Advantages and limitations of next-generation sequencing technologies: A comparison of electrophoresis and non-electrophoresis methods

ELECTROPHORESIS. 2008 DEC; 29 (23): 4618-4626

4848 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

2642 Havlak P, Chen R, Durbin KJ, Egan A, Ren YR, et al.

The atlas genome assembly system

GENOME RESEARCH. 2004 APR; 14 (4): 721-732

2923 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

2972 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

3644 Wendl MC

Occupancy modeling of coverage distribution for whole genome shotgun DNA sequencing

BULLETIN OF MATHEMATICAL BIOLOGY. 2006 JAN; 68 (1): 179-196

3815 Millan MJ

Multi-target strategies for the improved treatment of depressive states: Conceptual foundations and neuronal substrates, drug discovery and therapeutic application

PHARMACOLOGY & THERAPEUTICS. 2006 MAY; 110 (2): 135-370

3729

3925 Yu J, Ni PX, Wong GKS

Comparing the whole-genome-shotgun and map-based sequences of the rice genome

TRENDS IN PLANT SCIENCE. 2006 AUG; 11 (8): 387-391

5023 Singh R, Knight R

Systems Biology: Understanding Function from Genes to Networks

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

165

Date / Author / Journal

LCS

GCS

LCR

2193 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

2289 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

2656 Mattick JS

RNA regulation: a new genetics?

NATURE REVIEWS GENETICS. 2004 APR; 5 (4): 316-323

215

2803 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

3200 Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, et al.

Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation

NATURE METHODS. 2005 FEB; 2 (2): 105-111

3201 Hirschhorn JN, Daly MJ

Genome-wide association studies for common diseases and complex traits

NATURE REVIEWS GENETICS. 2005 FEB; 6 (2): 95-108

399

138

3574 Maston GA, Evans SK, Green MR

Transcriptional regulatory elements in the human genome

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2006; 7: 29-59

196

3743 Durand D, Hoberman R

Diagnosing duplications - can it be done?

TRENDS IN GENETICS. 2006 MAR; 22 (3): 156-164

3867 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

3910 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

Date / Author / Journal

LCS

GCS

LCR

4062 Small KS, Brudno M, Hill MM, Sidow A

A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome

GENOME BIOLOGY. 2007; 8 (3): Art. No. R41

4362 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

4581 Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, et al.

Consensus generation and variant detection by Celera Assembler

BIOINFORMATICS. 2008 APR 15; 24 (8): 1035-1040

4700 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

4978 Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, et al.

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

PLOS BIOLOGY. 2009 MAY; 7 (5): Art. No. e1000112

1453 Dunham I

Human genome sequences: enigmatic variations

MUTAGENESIS. 2002 NOV; 17 (6): 457-461

1856 Barr MM

Super models

PHYSIOLOGICAL GENOMICS. 2003 MAR 18; 13 (1): 15-24

107

2693 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

2898 Haubold B, Wiehe T

Comparative genomics: methods and applications

NATURWISSENSCHAFTEN. 2004 SEP; 91 (9): 405-421

133

2971 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

Date / Author / Journal

LCS

GCS

LCR

3251 Zheng XH, Lu F, Wang ZY, Hoover J, Mural R

Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs

BIOINFORMATICS. 2005 MAR 15; 21 (6): 703-710

3311 Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, et al.

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution

SCIENCE. 2005 MAY 20; 308 (5725): 1149-1154

346

3480 Dehal P, Boore JL

Two rounds of whole genome duplication in the ancestral vertebrate

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

218

3616 Huang YH, Barouch-Bentov R, Herman A, Walker J, Sauer K

Integrating traditional and postgenomic approaches to investigate lymphocyte development and function

LYMPHOCYTE SIGNAL TRANSDUCTION. 2006; 584: 245-276

143

3768 Vij S, Gupta V, Kumar D, Vydianathan R, Raghuvanshi S, et al.

Decoding the rice genome

BIOESSAYS. 2006 APR; 28 (4): 421-432

101

4019 Khaja R, Zhang JJ, MacDonald JR, He YS, Joseph-George AM, et al.

Genome assembly comparison identifies structural variants in the human genome

NATURE GENETICS. 2006 DEC; 38 (12): 1413-1418

4228 Song N, Sedgewick RD, Durand D

Domain architecture comparison for multidomain homology identification

JOURNAL OF COMPUTATIONAL BIOLOGY. 2007 MAY; 14 (4): 496-516

103

4300 Rabinowicz PD

Plant genomic sequencing using gene-enriched libraries

CHEMICAL REVIEWS. 2007 AUG; 107 (8): 3377-3390

158

4320 Yu Z, Morais D, Ivanga M, Harrison PM

Analysis of the role of retrotransposition in gene evolution in vertebrates

BMC BIOINFORMATICS. 2007 AUG 24; 8: Art. No. 308

4584 Copley RR

The animal in the genome: comparative genomics and evolution

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 2008 APR 27; 363 (1496): 1453-1461

Date / Author / Journal

Genome assembly reborn: recent computational challenges

BRIEFINGS IN BIOINFORMATICS. 2009 JUL; 10 (4): 354-366

1113 Stankiewicz P, Lupski JR

Molecular-evolutionary mechanisms for genomic disorders

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

1216 Yao T

Bioinformatics for the genomic sciences and towards systems biology. Japanese activities in the post-genome era

PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY. 2002 JUL-AUG; 80 (1-2): 23-42

1228 Maniatis T, Tasic B

Alternative pre-mRNA splicing and proteome expansion in metazoans

NATURE. 2002 JUL 11; 418 (6894): 236-243

349

1545 Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, et al.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

NATURE. 2002 DEC 5; 420 (6915): 563-573

619

1594 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

1696 Thomas JW, Schueler MG, Summers TJ, Blakesley RW, McDowell JC, et al.

Pericentromeric duplications in the laboratory mouse

GENOME RESEARCH. 2003 JAN; 13 (1): 55-63

1715 Boright AP, Kere J, Scherer SW

Genomics and pediatric research

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

2321 Seoighe C

Turning the clock back on ancient genome duplication

CURRENT OPINION IN GENETICS & DEVELOPMENT. 2003 DEC; 13 (6): 636-643

2326 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

Date / Author / Journal

LCS

GCS

LCR

2414 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

2634 de Magalhaes JP, Toussaint O

How bioinformatics can help reverse engineer human aging

AGEING RESEARCH REVIEWS. 2004 APR; 3 (2): 125-141

101

2734 Bentley DR

Genomes for medicine

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

2769 Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, et al.

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

PLOS BIOLOGY. 2004 JUN; 2 (6): Art. No. e162

168

116

3088 Ryder OA

Conservation genomics: applying whole genome studies to species conservation efforts

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

3128 Harrison PM, Zheng DY, Zhang ZL, Carriero N, Gerstein M

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability

NUCLEIC ACIDS RESEARCH. 2005; 33 (8): 2374-2383

3243 Reis EM, Louro R, Nakaya HI, Verjovski-Almeida S

As antisense RNA gets intronic

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY. 2005 MAR; 9 (1): 2-12

3577 Cheok MH, Lugthart S, Evans WE

Pharmacogenomics of acute leukemia

ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY. 2006; 46: 317-353

210

3602 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

100

3611 Oh DY, Kim K, Kwon HB, Seong JY

Cellular and molecular biology of orphan G protein-coupled receptors

INTERNATIONAL REVIEW OF CYTOLOGY - A SURVEY OF CELL BIOLOGY, VOL 252. 2006; 252: 163-218

295

The sequence of the human genome (Venter) The papers citing Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. "The sequence of the human genome." SCIENCE. 2001 FEB 16; 291 (5507): 1304	Historiographs	Glossary HistCite Guide About Grand Totals: LCS 18020, GCS 180410, CR 319862 Collection span: 2000 - 2010
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