HistCite - The sequence of the human genome (Venter)

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#	Date / Author / Journal	LCS	GCS	LCR	CR
101	289 Das M, Burge CB, Park E, Colinas J, Pelletier J Assessment of the total number of human transcription units GENOMICS. 2001 SEP; 77 (1-2): 71-78	17	38	2	28
102	404 Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF Genomic and genetic definition of a functional human centromere SCIENCE. 2001 OCT 5; 294 (5540): 109-115	17	192	2	43
103	876 Ma B, Tromp J, Li M PatternHunter: faster and more sensitive homology search BIOINFORMATICS. 2002 MAR; 18 (3): 440-445	17	231	2	16
104	1915 Pawson T, Nash P Assembly of cell regulatory systems through protein interaction domains SCIENCE. 2003 APR 18; 300 (5618): 445-452	17	453	3	148
105	87 Chasman D, Adams RM Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation JOURNAL OF MOLECULAR BIOLOGY. 2001 MAR 23; 307 (2): 683-706	16	144	2	53
106	193 Stein L Genome annotation: From sequence to biology NATURE REVIEWS GENETICS. 2001 JUL; 2 (7): 493-503	16	74	4	72
107	1908 Snyder M, Gerstein M Genomics - Defining genes in the genomics era SCIENCE. 2003 APR 11; 300 (5617): 258-260	16	54	8	29
108	2006 Kiyosawa H, Yamanaka I, Osato N, Kondo S, Hayashizaki Y, et al. Antisense transcripts with FANTOM2 clone set and their implications for gene regulation GENOME RESEARCH. 2003 JUN; 13 (6B): 1324-1334	16	143	5	113
109	69 Roos DS Computational biology - Bioinformatics - Trying to swim in a sea of data SCIENCE. 2001 FEB 16; 291 (5507): 1260-+	15	33	1	20
110	91 Kuehl P, Zhang J, Lin Y, Lamba J, Assem M, et al. Sequence diversity in CYP3A promoters and characterization of the genetic basis of polymorphic CYP3A5 expression NATURE GENETICS. 2001 APR; 27 (4): 383-391	15	721	2	44
#	Date / Author / Journal	LCS	GCS	LCR	CR
111	421 Altmuller J, Palmer LJ, Fischer G, Scherb H, Wjst M Genomewide scans of complex human diseases: True linkage is hard to find AMERICAN JOURNAL OF HUMAN GENETICS. 2001 NOV; 69 (5): 936-950	15	273	1	135
112	1504 Betran E, Thornton K, Long M Retroposed new genes out of the X in Drosophila GENOME RESEARCH. 2002 DEC; 12 (12): 1854-1859	15	135	3	42
113	1835 Patterson SD, Aebersold RH Proteomics: the first decade and beyond NATURE GENETICS. 2003 MAR; 33: 311-323	15	247	3	198
114	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
115	2344 Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, et al. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios SCIENCE. 2003 DEC 12; 302 (5652): 1960-1963	15	289	5	23
116	2981 Narezkina A, Taganov KD, Litwin S, Stoyanova R, Hayashi J, et al. Genome-wide analyses of avian sarcoma virus integration sites JOURNAL OF VIROLOGY. 2004 NOV; 78 (21): 11656-11663	15	72	3	43
117	61 Bork P, Copley R The draft sequences - Filling in the gaps NATURE. 2001 FEB 15; 409 (6822): 818-820	14	30	2	15
118	161 Salzberg SL, White O, Peterson J, Eisen JA Microbial genes in the human genome: Lateral transfer or gene loss? SCIENCE. 2001 JUN 8; 292 (5523): 1903-1906	14	119	2	23
119	1279 Kirk BW, Feinsod M, Favis R, Kliman RM, Barany F Single nucleotide polymorphism seeking long term association with complex disease NUCLEIC ACIDS RESEARCH. 2002 AUG 1; 30 (15): 3295-3311	14	107	3	162
120	1378 Zhang ZL, Harrison P, Gerstein M Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome GENOME RESEARCH. 2002 OCT; 12 (10): 1466-1482	14	73	7	65
#	Date / Author / Journal	LCS	GCS	LCR	CR
121	1503 Kan ZY, States D, Gish W Selecting for functional alternative splices in ESTs GENOME RESEARCH. 2002 DEC; 12 (12): 1837-1845	14	120	4	31
122	1891 Muller M, Kersten S Nutrigenomics: goals and strategies NATURE REVIEWS GENETICS. 2003 APR; 4 (4): 315-322	14	171	6	100
123	2192 Knight ZA, Schilling B, Row RH, Kenski DM, Gibson BW, et al. Phosphospecific proteolysis for mapping sites of protein phosphorylation NATURE BIOTECHNOLOGY. 2003 SEP; 21 (9): 1047-1054	14	143	2	38
124	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
125	118 Costello JF, Plass C Methylation matters JOURNAL OF MEDICAL GENETICS. 2001 MAY; 38 (5): 285-303	13	196	1	330
126	772 Kerlavage A, Bonazzi V, di Tommaso M, Lawrence C, Li P, et al. The Celera Discovery System (TM) NUCLEIC ACIDS RESEARCH. 2002 JAN 1; 30 (1): 129-136	13	41	1	7
127	793 Markstein M, Markstein P, Markstein V, Levine MS Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2002 JAN 22; 99 (2): 763-768	13	198	2	37
128	971 Cristea PD Conversion of nucleotides sequences into genomic signals JOURNAL OF CELLULAR AND MOLECULAR MEDICINE. 2002 APR-JUN; 6 (2): 279-303	13	32	2	13
129	1083 Harrison PM, Gerstein M Studying Genomes through the aeons: Protein families, pseudogenes and proteome evolution JOURNAL OF MOLECULAR BIOLOGY. 2002 MAY 17; 318 (5): 1155-1174	13	92	6	108
130	1324 Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, et al. Human genome sequence variation and the influence of gene history, mutation and recombination NATURE GENETICS. 2002 SEP; 32 (1): 135-142	13	143	3	46
#	Date / Author / Journal	LCS	GCS	LCR	CR
131	1624 Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, et al. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence GENOME BIOLOGY. 2003; 4 (4): Art. No. R25	13	77	7	26
132	1697 Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, et al. Strategies and tools for whole-genome alignments GENOME RESEARCH. 2003 JAN; 13 (1): 73-80	13	113	10	36
133	2005 Panopoulou G, Hennig S, Groth D, Krause A, Poustka AJ, et al. New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes GENOME RESEARCH. 2003 JUN; 13 (6): 1056-1066	13	97	6	40
134	2327 Torrents D, Suyama M, Zdobnov E, Bork P A genome-wide survey of human pseudogenes GENOME RESEARCH. 2003 DEC; 13 (12): 2559-2567	13	99	7	32
135	3159 Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W, et al. Evolution and functional classification of vertebrate gene deserts GENOME RESEARCH. 2005 JAN; 15 (1): 137-145	13	78	8	34
136	36 Gut IG Automation in genotyping of single nucleotide polymorphisms HUMAN MUTATION. 2001; 17 (6): 475-492	12	108	2	82
137	318 Nachman MW Single nucleotide polymorphisms and recombination rate in humans TRENDS IN GENETICS. 2001 SEP; 17 (9): 481-485	12	103	3	43
138	344 Levy S, Hannenhalli S, Workman C Enrichment of regulatory signals in conserved non-coding genomic sequence BIOINFORMATICS. 2001 OCT; 17 (10): 871-877	12	73	1	23
139	450 Friedman R, Hughes AL Pattern and timing of gene duplication in animal genomes GENOME RESEARCH. 2001 NOV; 11 (11): 1842-1847	12	77	3	29
140	490 King HC, Sinha AA Gene expression profile analysis by DNA microarrays - Promise and pitfalls JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION. 2001 NOV 14; 286 (18): 2280-2288	12	108	1	70
#	Date / Author / Journal	LCS	GCS	LCR	CR
141	777 Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, et al. Recent improvements to the SMART domain-based sequence annotation resource NUCLEIC ACIDS RESEARCH. 2002 JAN 1; 30 (1): 242-244	12	463	3	18
142	831 Beerli RR, Barbas CF Engineering polydactyl zinc-finger transcription factors NATURE BIOTECHNOLOGY. 2002 FEB; 20 (2): 135-141	12	140	3	60
143	1111 Roberts GC, Smith CWJ Alternative splicing: combinatorial output from the genome CURRENT OPINION IN CHEMICAL BIOLOGY. 2002 JUN; 6 (3): 375-383	12	73	7	62
144	1283 Jessani N, Liu YS, Humphrey M, Cravatt BF Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2002 AUG 6; 99 (16): 10335-10340	12	127	2	33
145	1448 Rockman MV, Wray GA Abundant raw material for cis-regulatory evolution in humans MOLECULAR BIOLOGY AND EVOLUTION. 2002 NOV; 19 (11): 1991-2004	12	168	2	91
146	1858 Waterston RH, Lander ES, Sulston JE More on the sequencing of the human genome PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2003 MAR 18; 100 (6): 3022-3024	12	16	8	9
147	2086 Puente XS, Sanchez LM, Overall CM, Lopez-Otin C Human and mouse proteases: A comparative genomic approach NATURE REVIEWS GENETICS. 2003 JUL; 4 (7): 544-558	12	232	9	143
148	2191 Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, et al. The evolution of transcriptional regulation in eukaryotes MOLECULAR BIOLOGY AND EVOLUTION. 2003 SEP; 20 (9): 1377-1419	12	341	4	432
149	2954 Nobrega MA, Zhu YW, Plajzer-Frick I, Afzal V, Rubin EM Megabase deletions of gene deserts result in viable mice NATURE. 2004 OCT 21; 431 (7011): 988-993	12	65	6	28
150	3505 Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, et al. Genome wide analysis of retroviral DNA integration NATURE REVIEWS MICROBIOLOGY. 2005 NOV; 3 (11): 848-858	12	104	7	92
#	Date / Author / Journal	LCS	GCS	LCR	CR
151	4241 Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences NATURE. 2007 MAY 10; 447 (7141): 167-U1	12	148	8	109
152	65 Paabo S Genomics and society - The human genome and our view of ourselves SCIENCE. 2001 FEB 16; 291 (5507): 1219-+	11	46	2	6
153	224 Caron PR, Mullican MD, Mashal RD, Wilson KP, Su MS, et al. Chemogenomic approaches to drug discovery - Commentary CURRENT OPINION IN CHEMICAL BIOLOGY. 2001 AUG; 5 (4): 464-470	11	77	2	38
154	383 Grabowski PJ, Black DL Alternative RNA splicing in the nervous system PROGRESS IN NEUROBIOLOGY. 2001 OCT; 65 (3): 289-308	11	167	2	182
155	398 Bernardi G Misunderstandings about isochores. Part 1 GENE. 2001 OCT 3; 276 (1-2): 3-13	11	61	3	73
156	452 Cutler DJ, Zwick ME, Carrasquillo MM, Yohn CT, Tobin KP, et al. High-throughput variation detection and genotyping using microarrays GENOME RESEARCH. 2001 NOV; 11 (11): 1913-1925	11	148	2	40
157	783 Fujiyama A, Watanabe H, Toyoda A, Taylor TD, Itoh T, et al. Construction and analysis of a human-chimpanzee comparative clone map SCIENCE. 2002 JAN 4; 295 (5552): 131-134	11	122	3	14
158	802 Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA Score tests for association between traits and haplotypes when linkage phase is ambiguous AMERICAN JOURNAL OF HUMAN GENETICS. 2002 FEB; 70 (2): 425-434	11	903	2	40
159	1043 Wang J, Wong GKS, Ni PX, Han YJ, Huang XG, et al. RePS: A sequence assembler that masks exact repeats identified from the shotgun data GENOME RESEARCH. 2002 MAY; 12 (5): 824-831	11	33	4	25
160	2234 Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, et al. Development of human protein reference database as an initial platform for approaching systems biology in humans GENOME RESEARCH. 2003 OCT; 13 (10): 2363-2371	11	352	6	39
#	Date / Author / Journal	LCS	GCS	LCR	CR
161	2369 de Hoog CL, Mann M Proteomics ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2004; 5: 267-293	11	99	10	122
162	2656 Mattick JS RNA regulation: a new genetics? NATURE REVIEWS GENETICS. 2004 APR; 5 (4): 316-323	11	215	14	80
163	2673 Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, et al. The DNA sequence and biology of human chromosome 19 NATURE. 2004 APR 1; 428 (6982): 529-535	11	60	7	48
164	2726 Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, et al. The diploid genome sequence of Candida albicans PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2004 MAY 11; 101 (19): 7329-7334	11	230	2	24
165	2928 Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, et al. The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC) GENOME RESEARCH. 2004 OCT; 14 (10B): 2121-2127	11	137	8	33
166	3385 Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, et al. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps SCIENCE. 2005 JUL 22; 309 (5734): 613-617	11	201	8	31
167	4577 Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, et al. Single-molecule DNA sequencing of a viral genome SCIENCE. 2008 APR 4; 320 (5872): 106-109	11	77	4	14
168	142 Hastings ML, Krainer AR Pre-mRNA splicing in the new millennium CURRENT OPINION IN CELL BIOLOGY. 2001 JUN; 13 (3): 302-309	10	261	2	54
169	194 Eyre-Walker A, Hurst LD The evolution of isochores NATURE REVIEWS GENETICS. 2001 JUL; 2 (7): 549-555	10	164	2	63
170	245 Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO Beyond the "recognition code": Structures of two Cys(2)His(2) zinc finger/TATA box complexes STRUCTURE. 2001 AUG; 9 (8): 717-723	10	53	2	27
#	Date / Author / Journal	LCS	GCS	LCR	CR
171	328 Dong XZ, Han SK, Zylka MJ, Simon MI, Anderson DJ A diverse family of GPCRs expressed in specific subsets of nociceptive sensory neurons CELL. 2001 SEP 7; 106 (5): 619-632	10	125	2	72
172	399 Oliver JL, Bernaola-Galvan P, Carpena P, Roman-Roldan R Isochore chromosome maps of eukaryotic genomes GENE. 2001 OCT 3; 276 (1-2): 47-56	10	52	2	46
173	475 Taylor JG, Choi EH, Foster CB, Chanock SJ Using genetic variation to study human disease TRENDS IN MOLECULAR MEDICINE. 2001 NOV; 7 (11): 507-512	10	64	4	33
174	691 Haga H, Yamada R, Ohnishi Y, Nakamura Y, Tanaka T Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190562 genetic variations in the human genome JOURNAL OF HUMAN GENETICS. 2002; 47 (11): 605-610	10	176	2	21
175	855 Hoffman SL, Subramanian GM, Collins FH, Venter JC Plasmodium, human and Anopheles genomics and malaria NATURE. 2002 FEB 7; 415 (6872): 702-709	10	81	3	85
176	870 Finta C, Zaphiropoulos PG Intergenic mRNA molecules resulting from trans-splicing JOURNAL OF BIOLOGICAL CHEMISTRY. 2002 FEB 22; 277 (8): 5882-5890	10	57	2	47
177	901 Graves PR, Haystead TAJ Molecular biologist's guide to proteomics MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS. 2002 MAR; 66 (1): 39-+	10	144	2	180
178	980 Yeakley JM, Fan JB, Doucet D, Luo L, Wickham E, et al. Profiling alternative splicing on fiber-optic arrays NATURE BIOTECHNOLOGY. 2002 APR; 20 (4): 353-358	10	131	2	33
179	1020 Furlong RF, Holland PWH Were vertebrates octoploid? PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 2002 APR 29; 357 (1420): 531-544	10	98	2	118
180	1074 Daly MJ Estimating the human gene count CELL. 2002 MAY 3; 109 (3): 283-284	10	15	3	5
#	Date / Author / Journal	LCS	GCS	LCR	CR
181	1126 Reymond A, Camargo AA, Deutsch S, Stevenson BJ, Parmigiani RB, et al. Nineteen additional unpredicted transcripts from human chromosome 21 GENOMICS. 2002 JUN; 79 (6): 824-832	10	34	5	49
182	1356 Chen JJ, Sun M, Lee SG, Zhou GL, Rowley JD, et al. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2002 SEP 17; 99 (19): 12257-12262	10	100	4	34
183	1405 Chumakov I, Blumenfeld M, Guerassimenko O, Cavarec L, Palicio M, et al. Genetic and physiological data implicating the new human gene G72 and the gene for D-amino acid oxidase in schizophrenia PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2002 OCT 15; 99 (21): 13675-13680	10	372	2	49
184	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
185	2119 Antequera F Structure, function and evolution of CpG island promoters CELLULAR AND MOLECULAR LIFE SCIENCES. 2003 AUG; 60 (8): 1647-1658	10	112	8	127
186	2179 Thomas PD, Campbell MJ, Kejariwal A, Mi HY, Karlak B, et al. PANTHER: A library of protein families and subfamilies indexed by function GENOME RESEARCH. 2003 SEP; 13 (9): 2129-2141	10	228	5	44
187	2252 Stuart JM, Segal E, Koller D, Kim SK A gene-coexpression network for global discovery of conserved genetic modules SCIENCE. 2003 OCT 10; 302 (5643): 249-255	10	399	3	30
188	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
189	2565 Maquat LE Nonsense-mediated mRNA decay: Splicing, translation and mRNP dynamics NATURE REVIEWS MOLECULAR CELL BIOLOGY. 2004 FEB; 5 (2): 89-99	10	451	3	162
190	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
#	Date / Author / Journal	LCS	GCS	LCR	CR
191	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
192	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
193	4595 Zerbino DR, Birney E Velvet: Algorithms for de novo short read assembly using de Bruijn graphs GENOME RESEARCH. 2008 MAY; 18 (5): 821-829	10	76	9	28
194	155 Polyak K, Riggins GJ Gene discovery using the serial analysis of gene expression technique: Implications for cancer research JOURNAL OF CLINICAL ONCOLOGY. 2001 JUN 1; 19 (11): 2948-2958	9	73	1	74
195	367 Zhao SY, Shatsman S, Ayodeji B, Geer K, Tsegaye G, et al. Mouse BAC ends quality assessment and sequence analyses GENOME RESEARCH. 2001 OCT; 11 (10): 1736-1745	9	37	3	38
196	495 Clarke PA, Poele RT, Wooster R, Workman P Gene expression microarray analysis in cancer biology, pharmacology, and drug development: progress and potential BIOCHEMICAL PHARMACOLOGY. 2001 NOV 15; 62 (10): 1311-1336	9	106	2	95
197	520 Segal DJ, Barbas CF Custom DNA-binding proteins come of age: polydactyl zinc-finger proteins CURRENT OPINION IN BIOTECHNOLOGY. 2001 DEC; 12 (6): 632-637	9	43	3	43
198	536 Wong GKS, Passey DA, Yu J Most of the human genome is transcribed GENOME RESEARCH. 2001 DEC; 11 (12): 1975-1977	9	27	3	14
199	774 Hirakawa M, Tanaka T, Hashimoto Y, Kuroda M, Takagi T, et al. JSNP: a database of common gene variations in the Japanese population NUCLEIC ACIDS RESEARCH. 2002 JAN 1; 30 (1): 158-162	9	149	2	19
200	887 Liu RX, States DJ Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling GENOME RESEARCH. 2002 MAR; 12 (3): 462-469	9	24	2	22

Date / Author / Journal

LCS

GCS

LCR

101

289 Das M, Burge CB, Park E, Colinas J, Pelletier J

Assessment of the total number of human transcription units

GENOMICS. 2001 SEP; 77 (1-2): 71-78

102

404 Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF

Genomic and genetic definition of a functional human centromere

SCIENCE. 2001 OCT 5; 294 (5540): 109-115

192

103

876 Ma B, Tromp J, Li M

PatternHunter: faster and more sensitive homology search

BIOINFORMATICS. 2002 MAR; 18 (3): 440-445

231

104

1915 Pawson T, Nash P

Assembly of cell regulatory systems through protein interaction domains

SCIENCE. 2003 APR 18; 300 (5618): 445-452

453

148

105

87 Chasman D, Adams RM

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation

JOURNAL OF MOLECULAR BIOLOGY. 2001 MAR 23; 307 (2): 683-706

144

106

193 Stein L

Genome annotation: From sequence to biology

NATURE REVIEWS GENETICS. 2001 JUL; 2 (7): 493-503

107

1908 Snyder M, Gerstein M

Genomics - Defining genes in the genomics era

SCIENCE. 2003 APR 11; 300 (5617): 258-260

108

2006 Kiyosawa H, Yamanaka I, Osato N, Kondo S, Hayashizaki Y, et al.

Antisense transcripts with FANTOM2 clone set and their implications for gene regulation

GENOME RESEARCH. 2003 JUN; 13 (6B): 1324-1334

143

113

109

69 Roos DS

Computational biology - Bioinformatics - Trying to swim in a sea of data

SCIENCE. 2001 FEB 16; 291 (5507): 1260-+

110

91 Kuehl P, Zhang J, Lin Y, Lamba J, Assem M, et al.

Sequence diversity in CYP3A promoters and characterization of the genetic basis of polymorphic CYP3A5 expression

NATURE GENETICS. 2001 APR; 27 (4): 383-391

721

Date / Author / Journal

LCS

GCS

LCR

111

421 Altmuller J, Palmer LJ, Fischer G, Scherb H, Wjst M

Genomewide scans of complex human diseases: True linkage is hard to find

AMERICAN JOURNAL OF HUMAN GENETICS. 2001 NOV; 69 (5): 936-950

273

135

112

1504 Betran E, Thornton K, Long M

Retroposed new genes out of the X in Drosophila

GENOME RESEARCH. 2002 DEC; 12 (12): 1854-1859

135

113

1835 Patterson SD, Aebersold RH

Proteomics: the first decade and beyond

NATURE GENETICS. 2003 MAR; 33: 311-323

247

198

114

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

115

2344 Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, et al.

Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios

SCIENCE. 2003 DEC 12; 302 (5652): 1960-1963

289

116

2981 Narezkina A, Taganov KD, Litwin S, Stoyanova R, Hayashi J, et al.

Genome-wide analyses of avian sarcoma virus integration sites

JOURNAL OF VIROLOGY. 2004 NOV; 78 (21): 11656-11663

117

61 Bork P, Copley R

The draft sequences - Filling in the gaps

NATURE. 2001 FEB 15; 409 (6822): 818-820

118

161 Salzberg SL, White O, Peterson J, Eisen JA

Microbial genes in the human genome: Lateral transfer or gene loss?

SCIENCE. 2001 JUN 8; 292 (5523): 1903-1906

119

1279 Kirk BW, Feinsod M, Favis R, Kliman RM, Barany F

Single nucleotide polymorphism seeking long term association with complex disease

NUCLEIC ACIDS RESEARCH. 2002 AUG 1; 30 (15): 3295-3311

107

162

120

1378 Zhang ZL, Harrison P, Gerstein M

Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome

GENOME RESEARCH. 2002 OCT; 12 (10): 1466-1482

Date / Author / Journal

LCS

GCS

LCR

121

1503 Kan ZY, States D, Gish W

Selecting for functional alternative splices in ESTs

GENOME RESEARCH. 2002 DEC; 12 (12): 1837-1845

120

122

1891 Muller M, Kersten S

Nutrigenomics: goals and strategies

NATURE REVIEWS GENETICS. 2003 APR; 4 (4): 315-322

171

100

123

2192 Knight ZA, Schilling B, Row RH, Kenski DM, Gibson BW, et al.

Phosphospecific proteolysis for mapping sites of protein phosphorylation

NATURE BIOTECHNOLOGY. 2003 SEP; 21 (9): 1047-1054

143

124

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

125

118 Costello JF, Plass C

Methylation matters

JOURNAL OF MEDICAL GENETICS. 2001 MAY; 38 (5): 285-303

196

330

126

772 Kerlavage A, Bonazzi V, di Tommaso M, Lawrence C, Li P, et al.

The Celera Discovery System (TM)

NUCLEIC ACIDS RESEARCH. 2002 JAN 1; 30 (1): 129-136

127

793 Markstein M, Markstein P, Markstein V, Levine MS

Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2002 JAN 22; 99 (2): 763-768

198

128

971 Cristea PD

Conversion of nucleotides sequences into genomic signals

JOURNAL OF CELLULAR AND MOLECULAR MEDICINE. 2002 APR-JUN; 6 (2): 279-303

129

1083 Harrison PM, Gerstein M

Studying Genomes through the aeons: Protein families, pseudogenes and proteome evolution

JOURNAL OF MOLECULAR BIOLOGY. 2002 MAY 17; 318 (5): 1155-1174

108

130

1324 Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, et al.

Human genome sequence variation and the influence of gene history, mutation and recombination

NATURE GENETICS. 2002 SEP; 32 (1): 135-142

143

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131

1624 Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, et al.

Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence

GENOME BIOLOGY. 2003; 4 (4): Art. No. R25

132

1697 Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, et al.

Strategies and tools for whole-genome alignments

GENOME RESEARCH. 2003 JAN; 13 (1): 73-80

113

133

2005 Panopoulou G, Hennig S, Groth D, Krause A, Poustka AJ, et al.

New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes

GENOME RESEARCH. 2003 JUN; 13 (6): 1056-1066

134

2327 Torrents D, Suyama M, Zdobnov E, Bork P

A genome-wide survey of human pseudogenes

GENOME RESEARCH. 2003 DEC; 13 (12): 2559-2567

135

3159 Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W, et al.

Evolution and functional classification of vertebrate gene deserts

GENOME RESEARCH. 2005 JAN; 15 (1): 137-145

136

36 Gut IG

Automation in genotyping of single nucleotide polymorphisms

HUMAN MUTATION. 2001; 17 (6): 475-492

108

137

318 Nachman MW

Single nucleotide polymorphisms and recombination rate in humans

TRENDS IN GENETICS. 2001 SEP; 17 (9): 481-485

103

138

344 Levy S, Hannenhalli S, Workman C

Enrichment of regulatory signals in conserved non-coding genomic sequence

BIOINFORMATICS. 2001 OCT; 17 (10): 871-877

139

450 Friedman R, Hughes AL

Pattern and timing of gene duplication in animal genomes

GENOME RESEARCH. 2001 NOV; 11 (11): 1842-1847

140

490 King HC, Sinha AA

Gene expression profile analysis by DNA microarrays - Promise and pitfalls

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION. 2001 NOV 14; 286 (18): 2280-2288

108

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GCS

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141

777 Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, et al.

Recent improvements to the SMART domain-based sequence annotation resource

NUCLEIC ACIDS RESEARCH. 2002 JAN 1; 30 (1): 242-244

463

142

831 Beerli RR, Barbas CF

Engineering polydactyl zinc-finger transcription factors

NATURE BIOTECHNOLOGY. 2002 FEB; 20 (2): 135-141

140

143

1111 Roberts GC, Smith CWJ

Alternative splicing: combinatorial output from the genome

CURRENT OPINION IN CHEMICAL BIOLOGY. 2002 JUN; 6 (3): 375-383

144

1283 Jessani N, Liu YS, Humphrey M, Cravatt BF

Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2002 AUG 6; 99 (16): 10335-10340

127

145

1448 Rockman MV, Wray GA

Abundant raw material for cis-regulatory evolution in humans

MOLECULAR BIOLOGY AND EVOLUTION. 2002 NOV; 19 (11): 1991-2004

168

146

1858 Waterston RH, Lander ES, Sulston JE

More on the sequencing of the human genome

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2003 MAR 18; 100 (6): 3022-3024

147

2086 Puente XS, Sanchez LM, Overall CM, Lopez-Otin C

Human and mouse proteases: A comparative genomic approach

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

232

143

148

2191 Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, et al.

The evolution of transcriptional regulation in eukaryotes

MOLECULAR BIOLOGY AND EVOLUTION. 2003 SEP; 20 (9): 1377-1419

341

432

149

2954 Nobrega MA, Zhu YW, Plajzer-Frick I, Afzal V, Rubin EM

Megabase deletions of gene deserts result in viable mice

NATURE. 2004 OCT 21; 431 (7011): 988-993

150

3505 Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, et al.

Genome wide analysis of retroviral DNA integration

NATURE REVIEWS MICROBIOLOGY. 2005 NOV; 3 (11): 848-858

104

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151

4241 Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, et al.

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

NATURE. 2007 MAY 10; 447 (7141): 167-U1

148

109

152

65 Paabo S

Genomics and society - The human genome and our view of ourselves

SCIENCE. 2001 FEB 16; 291 (5507): 1219-+

153

224 Caron PR, Mullican MD, Mashal RD, Wilson KP, Su MS, et al.

Chemogenomic approaches to drug discovery - Commentary

CURRENT OPINION IN CHEMICAL BIOLOGY. 2001 AUG; 5 (4): 464-470

154

383 Grabowski PJ, Black DL

Alternative RNA splicing in the nervous system

PROGRESS IN NEUROBIOLOGY. 2001 OCT; 65 (3): 289-308

167

182

155

398 Bernardi G

Misunderstandings about isochores. Part 1

GENE. 2001 OCT 3; 276 (1-2): 3-13

156

452 Cutler DJ, Zwick ME, Carrasquillo MM, Yohn CT, Tobin KP, et al.

High-throughput variation detection and genotyping using microarrays

GENOME RESEARCH. 2001 NOV; 11 (11): 1913-1925

148

157

783 Fujiyama A, Watanabe H, Toyoda A, Taylor TD, Itoh T, et al.

Construction and analysis of a human-chimpanzee comparative clone map

SCIENCE. 2002 JAN 4; 295 (5552): 131-134

122

158

802 Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA

Score tests for association between traits and haplotypes when linkage phase is ambiguous

AMERICAN JOURNAL OF HUMAN GENETICS. 2002 FEB; 70 (2): 425-434

903

159

1043 Wang J, Wong GKS, Ni PX, Han YJ, Huang XG, et al.

RePS: A sequence assembler that masks exact repeats identified from the shotgun data

GENOME RESEARCH. 2002 MAY; 12 (5): 824-831

160

2234 Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, et al.

Development of human protein reference database as an initial platform for approaching systems biology in humans

GENOME RESEARCH. 2003 OCT; 13 (10): 2363-2371

352

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LCS

GCS

LCR

161

2369 de Hoog CL, Mann M

Proteomics

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 2004; 5: 267-293

122

162

2656 Mattick JS

RNA regulation: a new genetics?

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

215

163

2673 Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, et al.

The DNA sequence and biology of human chromosome 19

NATURE. 2004 APR 1; 428 (6982): 529-535

164

2726 Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, et al.

The diploid genome sequence of Candida albicans

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2004 MAY 11; 101 (19): 7329-7334

230

165

2928 Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, et al.

The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC)

GENOME RESEARCH. 2004 OCT; 14 (10B): 2121-2127

137

166

3385 Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, et al.

Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps

SCIENCE. 2005 JUL 22; 309 (5734): 613-617

201

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4577 Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, et al.

Single-molecule DNA sequencing of a viral genome

SCIENCE. 2008 APR 4; 320 (5872): 106-109

168

142 Hastings ML, Krainer AR

Pre-mRNA splicing in the new millennium

CURRENT OPINION IN CELL BIOLOGY. 2001 JUN; 13 (3): 302-309

261

169

194 Eyre-Walker A, Hurst LD

The evolution of isochores

NATURE REVIEWS GENETICS. 2001 JUL; 2 (7): 549-555

164

170

245 Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO

Beyond the "recognition code": Structures of two Cys(2)His(2) zinc finger/TATA box complexes

STRUCTURE. 2001 AUG; 9 (8): 717-723

Date / Author / Journal

LCS

GCS

LCR

171

328 Dong XZ, Han SK, Zylka MJ, Simon MI, Anderson DJ

A diverse family of GPCRs expressed in specific subsets of nociceptive sensory neurons

CELL. 2001 SEP 7; 106 (5): 619-632

125

172

399 Oliver JL, Bernaola-Galvan P, Carpena P, Roman-Roldan R

Isochore chromosome maps of eukaryotic genomes

GENE. 2001 OCT 3; 276 (1-2): 47-56

173

475 Taylor JG, Choi EH, Foster CB, Chanock SJ

Using genetic variation to study human disease

TRENDS IN MOLECULAR MEDICINE. 2001 NOV; 7 (11): 507-512

174

691 Haga H, Yamada R, Ohnishi Y, Nakamura Y, Tanaka T

Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190562 genetic variations in the human genome

JOURNAL OF HUMAN GENETICS. 2002; 47 (11): 605-610

176

175

855 Hoffman SL, Subramanian GM, Collins FH, Venter JC

Plasmodium, human and Anopheles genomics and malaria

NATURE. 2002 FEB 7; 415 (6872): 702-709

176

870 Finta C, Zaphiropoulos PG

Intergenic mRNA molecules resulting from trans-splicing

JOURNAL OF BIOLOGICAL CHEMISTRY. 2002 FEB 22; 277 (8): 5882-5890

177

901 Graves PR, Haystead TAJ

Molecular biologist's guide to proteomics

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS. 2002 MAR; 66 (1): 39-+

144

180

178

980 Yeakley JM, Fan JB, Doucet D, Luo L, Wickham E, et al.

Profiling alternative splicing on fiber-optic arrays

NATURE BIOTECHNOLOGY. 2002 APR; 20 (4): 353-358

131

179

1020 Furlong RF, Holland PWH

Were vertebrates octoploid?

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 2002 APR 29; 357 (1420): 531-544

118

180

1074 Daly MJ

Estimating the human gene count

CELL. 2002 MAY 3; 109 (3): 283-284

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181

1126 Reymond A, Camargo AA, Deutsch S, Stevenson BJ, Parmigiani RB, et al.

Nineteen additional unpredicted transcripts from human chromosome 21

GENOMICS. 2002 JUN; 79 (6): 824-832

182

1356 Chen JJ, Sun M, Lee SG, Zhou GL, Rowley JD, et al.

Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2002 SEP 17; 99 (19): 12257-12262

100

183

1405 Chumakov I, Blumenfeld M, Guerassimenko O, Cavarec L, Palicio M, et al.

Genetic and physiological data implicating the new human gene G72 and the gene for D-amino acid oxidase in schizophrenia

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2002 OCT 15; 99 (21): 13675-13680

372

184

1577 Ashurst JL, Collins JE

Gene annotation: Prediction and testing

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

101

185

2119 Antequera F

Structure, function and evolution of CpG island promoters

CELLULAR AND MOLECULAR LIFE SCIENCES. 2003 AUG; 60 (8): 1647-1658

112

127

186

2179 Thomas PD, Campbell MJ, Kejariwal A, Mi HY, Karlak B, et al.

PANTHER: A library of protein families and subfamilies indexed by function

GENOME RESEARCH. 2003 SEP; 13 (9): 2129-2141

228

187

2252 Stuart JM, Segal E, Koller D, Kim SK

A gene-coexpression network for global discovery of conserved genetic modules

SCIENCE. 2003 OCT 10; 302 (5643): 249-255

399

188

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

Comparative genomics

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

193

189

2565 Maquat LE

Nonsense-mediated mRNA decay: Splicing, translation and mRNP dynamics

NATURE REVIEWS MOLECULAR CELL BIOLOGY. 2004 FEB; 5 (2): 89-99

451

162

190

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

Date / Author / Journal

LCS

GCS

LCR

191

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

192

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

193

4595 Zerbino DR, Birney E

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

GENOME RESEARCH. 2008 MAY; 18 (5): 821-829

194

155 Polyak K, Riggins GJ

Gene discovery using the serial analysis of gene expression technique: Implications for cancer research

JOURNAL OF CLINICAL ONCOLOGY. 2001 JUN 1; 19 (11): 2948-2958

195

367 Zhao SY, Shatsman S, Ayodeji B, Geer K, Tsegaye G, et al.

Mouse BAC ends quality assessment and sequence analyses

GENOME RESEARCH. 2001 OCT; 11 (10): 1736-1745

196

495 Clarke PA, Poele RT, Wooster R, Workman P

Gene expression microarray analysis in cancer biology, pharmacology, and drug development: progress and potential

BIOCHEMICAL PHARMACOLOGY. 2001 NOV 15; 62 (10): 1311-1336

106

197

520 Segal DJ, Barbas CF

Custom DNA-binding proteins come of age: polydactyl zinc-finger proteins

CURRENT OPINION IN BIOTECHNOLOGY. 2001 DEC; 12 (6): 632-637

198

536 Wong GKS, Passey DA, Yu J

Most of the human genome is transcribed

GENOME RESEARCH. 2001 DEC; 11 (12): 1975-1977

199

774 Hirakawa M, Tanaka T, Hashimoto Y, Kuroda M, Takagi T, et al.

JSNP: a database of common gene variations in the Japanese population

NUCLEIC ACIDS RESEARCH. 2002 JAN 1; 30 (1): 158-162

149

200

887 Liu RX, States DJ

Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling

GENOME RESEARCH. 2002 MAR; 12 (3): 462-469

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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