-
1
-
-
0001753628
-
An association between ulcerative colitis, regional enteritis, and ankylosing spondylitis
-
Acheson, E.D. (1960) An association between ulcerative colitis, regional enteritis, and ankylosing spondylitis. Q. J. Med., 29, 489-499.
-
(1960)
Q. J. Med.
, vol.29
, pp. 489-499
-
-
Acheson, E.D.1
-
2
-
-
84857980747
-
BLUEPRINT to decode the epigenetic signature written in blood
-
Adams, D. et al. (2012) BLUEPRINT to decode the epigenetic signature written in blood. Nat. Biotechnol., 30, 224-226.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 224-226
-
-
Adams, D.1
-
3
-
-
0034758045
-
Genomewide scans of complex human diseases: True linkage is hard to find
-
Altmuller, J. et al. (2001) Genomewide scans of complex human diseases: true linkage is hard to find. Am. J. Hum. Genet., 69, 936-950.
-
(2001)
Am. J. Hum. Genet.
, vol.69
, pp. 936-950
-
-
Altmuller, J.1
-
4
-
-
80055031911
-
A new methodology to associate SNPs with human diseases according to their pathway related context
-
Bakir-Gungor, B. and Sezerman, O.U. (2011) A new methodology to associate SNPs with human diseases according to their pathway related context. PLoS One, 6, e26277.
-
(2011)
PLoS One
, vol.6
, pp. e26277
-
-
Bakir-Gungor, B.1
Sezerman, O.U.2
-
5
-
-
84891685308
-
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
-
Battle, A. et al. (2014) Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res., 24, 14-24.
-
(2014)
Genome Res.
, vol.24
, pp. 14-24
-
-
Battle, A.1
-
6
-
-
77957940722
-
The NIH Roadmap Epigenomics Mapping Consortium
-
Bernstein, B.E. et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol., 28, 1045-1048.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 1045-1048
-
-
Bernstein, B.E.1
-
7
-
-
44349132708
-
Common and rare variants in multifactorial susceptibility to common diseases
-
Bodmer, W. and Bonilla, C. (2008) Common and rare variants in multifactorial susceptibility to common diseases. Nat. Genet., 40, 695-701.
-
(2008)
Nat. Genet.
, vol.40
, pp. 695-701
-
-
Bodmer, W.1
Bonilla, C.2
-
8
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci, P. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
-
9
-
-
68949211709
-
Genetics of human gene expression: Mapping DNA variants that influence gene expression
-
Cheung, V.G. and Spielman, R.S. (2009) Genetics of human gene expression: mapping DNA variants that influence gene expression. Nat. Rev. Genet., 10, 595-604.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 595-604
-
-
Cheung, V.G.1
Spielman, R.S.2
-
10
-
-
84891697734
-
Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
-
Corradin, O. et al. (2014) Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res., 24, 1-13.
-
(2014)
Genome Res.
, vol.24
, pp. 1-13
-
-
Corradin, O.1
-
11
-
-
84861527388
-
The genomic and transcriptomic architecture of 2, 000 breast tumours reveals novel subgroups
-
Curtis, C. et al. (2012) The genomic and transcriptomic architecture of 2, 000 breast tumours reveals novel subgroups. Nature, 486, 346-352.
-
(2012)
Nature
, vol.486
, pp. 346-352
-
-
Curtis, C.1
-
12
-
-
83355177243
-
Pybedtools: A flexible Python library for manipulating genomic datasets and annotations
-
Dale, R.K. et al.(2011) Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics, 27, 3423-3424.
-
(2011)
Bioinformatics
, vol.27
, pp. 3423-3424
-
-
Dale, R.K.1
-
13
-
-
84857111200
-
DNase i sensitivity QTLs are a major determinant of human expression variation
-
Degner, J.F. et al. (2012) DNase I sensitivity QTLs are a major determinant of human expression variation. Nature, 482, 390-394.
-
(2012)
Nature
, vol.482
, pp. 390-394
-
-
Degner, J.F.1
-
14
-
-
84943812884
-
Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes
-
Dozmorov, M.G. (2015) Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes. Epigenetics, 10, 484-495.
-
(2015)
Epigenetics
, vol.10
, pp. 484-495
-
-
Dozmorov, M.G.1
-
15
-
-
84856574579
-
GenomeRunner: Automating genome exploration
-
Dozmorov, M.G. et al. (2012) GenomeRunner: Automating genome exploration. Bioinformatics, 28, 2.
-
(2012)
Bioinformatics
, vol.28
, pp. 2
-
-
Dozmorov, M.G.1
-
16
-
-
84885215226
-
Systematic classification of non-coding RNAs by epigenomic similarity
-
In Press
-
Dozmorov, M.G. et al. (2013) Systematic classification of non-coding RNAs by epigenomic similarity. BMC Bioinformatics, In Press.
-
(2013)
BMC Bioinformatics
-
-
Dozmorov, M.G.1
-
17
-
-
84892589392
-
Epigenomic elements enriched in the promoters of autoimmunity susceptibility genes
-
Dozmorov, M.G. et al.(2014) Epigenomic elements enriched in the promoters of autoimmunity susceptibility genes. Epigenetics, 9, 276-285.
-
(2014)
Epigenetics
, vol.9
, pp. 276-285
-
-
Dozmorov, M.G.1
-
18
-
-
0345447463
-
Mutation rate variation in the mammalian genome
-
Ellegren, H. et al. (2003) Mutation rate variation in the mammalian genome. Curr. Opin. Genet. Develop., 13, 562-568.
-
(2003)
Curr. Opin. Genet. Develop.
, vol.13
, pp. 562-568
-
-
Ellegren, H.1
-
19
-
-
7444260846
-
The ENCODE (ENCyclopedia of DNA Elements) Project
-
ENCODE Project Consortium. (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306, 636-640.
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
20
-
-
84857707318
-
ChromHMM: Automating chromatin-state discovery and characterization
-
Ernst, J. and Kellis, M. (2012) ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods, 9, 215-216.
-
(2012)
Nat. Methods
, vol.9
, pp. 215-216
-
-
Ernst, J.1
Kellis, M.2
-
21
-
-
84926632357
-
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
-
Ernst, J. and Kellis, M. (2015) Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. Nat Biotechnol, 33, 364-376.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 364-376
-
-
Ernst, J.1
Kellis, M.2
-
22
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst, J. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-49.
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
-
23
-
-
84923326765
-
Genetic and epigenetic fine mapping of causal autoimmune disease variants
-
Farh, K.K. et al. (2014) Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature, 518, 337-343.
-
(2014)
Nature
, vol.518
, pp. 337-343
-
-
Farh, K.K.1
-
24
-
-
84947476425
-
Dendextend: An R package for visualizing, adjusting and comparing trees of hierarchical clustering
-
Galili, T. (2015) dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics, 31, 3718-3720.
-
(2015)
Bioinformatics
, vol.31
, pp. 3718-3720
-
-
Galili, T.1
-
25
-
-
84975795680
-
An integrated map of genetic variation from 1, 092 human genomes
-
[TQ2]
-
Genomes Project, C. et al. (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65. [TQ2]
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
Genomes Project, C.1
-
26
-
-
84943171338
-
A global reference for human genetic variation
-
Genomes Project, C. et al. (2015) A global reference for human genetic variation. Nature, 526, 68-74.
-
(2015)
Nature
, vol.526
, pp. 68-74
-
-
Genomes Project, C.1
-
27
-
-
80052306947
-
Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation
-
Gertz, J. et al. (2011) Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet., 7, e1002228.
-
(2011)
PLoS Genet.
, vol.7
, pp. e1002228
-
-
Gertz, J.1
-
28
-
-
84922273141
-
Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases
-
Gusev, A. et al. (2014) Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. Am. J. Hum. Genet., 95, 535-552.
-
(2014)
Am. J. Hum. Genet.
, vol.95
, pp. 535-552
-
-
Gusev, A.1
-
29
-
-
84885188208
-
Impacts of variation in the human genome on gene regulation
-
Haraksingh, R.R. and Snyder, M.P. (2013) Impacts of variation in the human genome on gene regulation. J. Mol. Biol., 425, 3970-3977.
-
(2013)
J. Mol. Biol.
, vol.425
, pp. 3970-3977
-
-
Haraksingh, R.R.1
Snyder, M.P.2
-
30
-
-
67249117049
-
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
-
Hindorff, L.A. et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA, 106, 9362-9367.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 9362-9367
-
-
Hindorff, L.A.1
-
31
-
-
84887084951
-
Network-based stratification of tumor mutations
-
Hofree, M. et al. (2013) Network-based stratification of tumor mutations. Nat. Methods, 10, 1108-1115.
-
(2013)
Nat. Methods
, vol.10
, pp. 1108-1115
-
-
Hofree, M.1
-
32
-
-
84878697229
-
Systematic functional regulatory assessment of disease-associated variants
-
Karczewski, K.J. et al. (2013) Systematic functional regulatory assessment of disease-associated variants. Proc. Natl. Acad. Sci. USA, 110, 9607-9612.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 9607-9612
-
-
Karczewski, K.J.1
-
33
-
-
77950833803
-
Variation in transcription factor binding among humans
-
Kasowski, M. et al. (2010) Variation in transcription factor binding among humans. Science, 328, 232-235.
-
(2010)
Science
, vol.328
, pp. 232-235
-
-
Kasowski, M.1
-
34
-
-
84887320760
-
Extensive variation in chromatin states across humans
-
Kasowski, M. et al. (2013) Extensive variation in chromatin states across humans. Science, 342, 750-752.
-
(2013)
Science
, vol.342
, pp. 750-752
-
-
Kasowski, M.1
-
35
-
-
84887320563
-
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription
-
Kilpinen, H. et al. (2013) Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science, 342, 744-747.
-
(2013)
Science
, vol.342
, pp. 744-747
-
-
Kilpinen, H.1
-
36
-
-
84875608234
-
The UCSC genome browser and associated tools
-
Kuhn, R.M. et al.(2013) The UCSC genome browser and associated tools. Brief. Bioinformatics, 14, 144-161.
-
(2013)
Brief. Bioinformatics
, vol.14
, pp. 144-161
-
-
Kuhn, R.M.1
-
37
-
-
79951993896
-
Tabix: Fast retrieval of sequence features from generic TAB-delimited files
-
Li, H. (2011) Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics, 27, 718-719.
-
(2011)
Bioinformatics
, vol.27
, pp. 718-719
-
-
Li, H.1
-
38
-
-
79959632257
-
DOSim: An R package for similarity between diseases based on Disease Ontology
-
Li, J. et al. (2011) DOSim: an R package for similarity between diseases based on Disease Ontology. BMC Bioinformatics, 12, 266.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 266
-
-
Li, J.1
-
39
-
-
80052022462
-
Cistrome: An integrative platform for transcriptional regulation studies
-
Liu, T. et al. (2011) Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol., 12, R83.
-
(2011)
Genome Biol.
, vol.12
, pp. R83
-
-
Liu, T.1
-
40
-
-
84949091882
-
Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo
-
Maurano, M.T. et al. (2015) Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo. Nat. Genet., 47, 1393-1401.
-
(2015)
Nat. Genet.
, vol.47
, pp. 1393-1401
-
-
Maurano, M.T.1
-
41
-
-
84865822182
-
Systematic localization of common disease-associated variation in regulatory DNA
-
Maurano, M.T. et al. (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science, 337, 1190-1195.
-
(2012)
Science
, vol.337
, pp. 1190-1195
-
-
Maurano, M.T.1
-
42
-
-
77950854479
-
Heritable individual-specific and allele-specific chromatin signatures in humans
-
McDaniell, R. et al. (2010) Heritable individual-specific and allele-specific chromatin signatures in humans. Science, 328, 235-239.
-
(2010)
Science
, vol.328
, pp. 235-239
-
-
McDaniell, R.1
-
43
-
-
84887322043
-
Identification of genetic variants that affect histone modifications in human cells
-
McVicker, G. et al. (2013) Identification of genetic variants that affect histone modifications in human cells. Science, 342, 747-749.
-
(2013)
Science
, vol.342
, pp. 747-749
-
-
McVicker, G.1
-
44
-
-
4043128071
-
Genetic analysis of genome-wide variation in human gene expression
-
Morley, M. et al. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature, 430, 743-747.
-
(2004)
Nature
, vol.430
, pp. 743-747
-
-
Morley, M.1
-
45
-
-
84919922134
-
Multiple sclerosis and susceptibility to celiac disease: An osteopontin gene haplotypes affair?
-
Mormile, R. (2015) Multiple sclerosis and susceptibility to celiac disease: an osteopontin gene haplotypes affair? Immunol. Lett., 163, 132-133.
-
(2015)
Immunol. Lett.
, vol.163
, pp. 132-133
-
-
Mormile, R.1
-
46
-
-
84923774308
-
DSysMap: Exploring the edgetic role of disease mutations
-
Mosca, R. et al. (2015) dSysMap: exploring the edgetic role of disease mutations. Nat. Methods, 12, 167-168.
-
(2015)
Nat. Methods
, vol.12
, pp. 167-168
-
-
Mosca, R.1
-
47
-
-
84863541347
-
An abundance of rare functional variants in 202 drug target genes sequenced in 14, 002 people
-
Nelson, M.R. et al. (2012) An abundance of rare functional variants in 202 drug target genes sequenced in 14, 002 people. Science, 337, 100-104.
-
(2012)
Science
, vol.337
, pp. 100-104
-
-
Nelson, M.R.1
-
48
-
-
84864147180
-
BEDOPS: High-performance genomic feature operations
-
Neph, S. et al. (2012) BEDOPS: high-performance genomic feature operations. Bioinformatics, 28, 1919-1920.
-
(2012)
Bioinformatics
, vol.28
, pp. 1919-1920
-
-
Neph, S.1
-
49
-
-
78149276744
-
Permutation P-values should never be zero: Calculating exact P-values when permutations are randomly drawn
-
Phipson, B. and Smyth, G.K. (2010) Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn. Stat. Appl. Genet. Mol. Biol., 9, Article39.
-
(2010)
Stat. Appl. Genet. Mol. Biol.
, vol.9
, pp. Article39
-
-
Phipson, B.1
Smyth, G.K.2
-
50
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
51
-
-
84859916280
-
Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
-
Reddy, T.E. et al. (2012) Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res, 22, 860-869.
-
(2012)
Genome Res
, vol.22
, pp. 860-869
-
-
Reddy, T.E.1
-
52
-
-
84937231465
-
Populational landscape of INDELs affecting transcription factor-binding sites inhumans
-
Ribeiro-Dos-Santos, A.M. et al. (2015) Populational landscape of INDELs affecting transcription factor-binding sites inhumans. BMC Genomics, 16, 536.
-
(2015)
BMC Genomics
, vol.16
, pp. 536
-
-
Ribeiro-Dos-Santos, A.M.1
-
53
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Roadmap Epigenomics, C. et al. (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518, 317-330.
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
Roadmap Epigenomics, C.1
-
54
-
-
84875945705
-
ENCODE data in the UCSC Genome Browser: Year 5 update
-
Rosenbloom, K.R. et al. (2013) ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res., 41, D56-D63.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D56-D63
-
-
Rosenbloom, K.R.1
-
55
-
-
84957426411
-
Epigenomic functional characterization of genetic susceptibility variants in systemic vasculitis
-
Sawalha, A.H. and Dozmorov, M.G. (2015) Epigenomic functional characterization of genetic susceptibility variants in systemic vasculitis. J. Autoimmun., 67, 76-81.
-
(2015)
J. Autoimmun.
, vol.67
, pp. 76-81
-
-
Sawalha, A.H.1
Dozmorov, M.G.2
-
56
-
-
84865777825
-
Linking disease associations with regulatory information in the human genome
-
Schaub, M.A. et al. (2012) Linking disease associations with regulatory information in the human genome. Genome Res., 22, 1748-1759.
-
(2012)
Genome Res.
, vol.22
, pp. 1748-1759
-
-
Schaub, M.A.1
-
57
-
-
0041333134
-
Type 2 diabetes, cardiovascular risk, and the link to insulin resistance
-
Stolar, M.W. and Chilton, R.J. (2003) Type 2 diabetes, cardiovascular risk, and the link to insulin resistance. Clin. Ther., 25(Suppl B), B4-31.
-
(2003)
Clin. Ther.
, vol.25
, pp. B4-B31
-
-
Stolar, M.W.1
Chilton, R.J.2
-
58
-
-
34548738566
-
Population genomics of human gene expression
-
Stranger, B.E. et al. (2007) Population genomics of human gene expression. Nat. Genet., 39, 1217-1224.
-
(2007)
Nat. Genet.
, vol.39
, pp. 1217-1224
-
-
Stranger, B.E.1
-
59
-
-
33745612095
-
Pvclust: An R package for assessing the uncertainty in hierarchical clustering
-
Suzuki, R. and Shimodaira, H. (2006) Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics, 22, 1540-1542.
-
(2006)
Bioinformatics
, vol.22
, pp. 1540-1542
-
-
Suzuki, R.1
Shimodaira, H.2
-
61
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
Thurman, R.E. et al. (2012) The accessible chromatin landscape of the human genome. Nature, 489, 75-82.
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
-
62
-
-
84904445867
-
Functional characterization of breast cancer using pathway profiles
-
Tian, F. et al. (2014) Functional characterization of breast cancer using pathway profiles. BMC Med. Genomics, 7, 45.
-
(2014)
BMC Med. Genomics
, vol.7
, pp. 45
-
-
Tian, F.1
-
63
-
-
84873086126
-
Chromatin marks identify critical cell types for fine mapping complex trait variants
-
Trynka, G. et al. (2013) Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat. Genet., 45, 124-130.
-
(2013)
Nat. Genet.
, vol.45
, pp. 124-130
-
-
Trynka, G.1
-
64
-
-
84937424402
-
Disentangling the effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex-trait loci
-
Trynka, G. et al. (2015) Disentangling the effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex-trait loci. Am. J. Hum. Genet., 97, 139-152.
-
(2015)
Am. J. Hum. Genet.
, vol.97
, pp. 139-152
-
-
Trynka, G.1
-
65
-
-
84895516704
-
Similarity network fusion for aggregating data types on a genomic scale
-
Wang, B. et al. (2014) Similarity network fusion for aggregating data types on a genomic scale. Nat. Methods, 11, 333-337.
-
(2014)
Nat. Methods
, vol.11
, pp. 333-337
-
-
Wang, B.1
-
66
-
-
84866775366
-
Evidence of abundant purifying selection in humans for recently acquired regulatory functions
-
Ward, L.D. and Kellis, M. (2012) Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science, 337, 1675-1678.
-
(2012)
Science
, vol.337
, pp. 1675-1678
-
-
Ward, L.D.1
Kellis, M.2
-
67
-
-
1342330525
-
Knowledge discovery by automated identification and ranking of implicit relationships
-
Wren, J.D. et al. (2004) Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics, 20, 389-398.
-
(2004)
Bioinformatics
, vol.20
, pp. 389-398
-
-
Wren, J.D.1
|