-
1
-
-
85019212038
-
Autism and Development Disabilities Monitoring Network Surveillance Year 2008 Principal Investigators (2012). Prevalence of autism spectrum disorders-autism and developmental disabilities monitoring network
-
14 sites, United States
-
Autism and Development Disabilities Monitoring Network Surveillance Year 2008 Principal Investigators (2012). Prevalence of autism spectrum disorders-autism and developmental disabilities monitoring network, 14 sites, United States, 2008. Morbid. Mortal. Weekly Report Surveillance Summaries 61, 1-19.
-
(2008)
Morbid. Mortal. Weekly Report Surveillance Summaries
, vol.61
, pp. 1-19
-
-
-
2
-
-
62549134411
-
Mechanisms for human genomic rearrangements
-
W. Gu, F. Zhang, and J.R. Lupski Mechanisms for human genomic rearrangements Pathogenetics 1 2008 4
-
(2008)
Pathogenetics
, vol.1
, pp. 4
-
-
Gu, W.1
Zhang, F.2
Lupski, J.R.3
-
3
-
-
81955168032
-
The consequences of structural genomic alterations in humans: Genomic disorders, genomic instability and cancer
-
R. Colnaghi, G. Carpenter, M. Volker, and M. O'Driscoll The consequences of structural genomic alterations in humans: genomic disorders, genomic instability and cancer Semin. Cell Dev. Biol. 22 2011 875 885
-
(2011)
Semin. Cell Dev. Biol.
, vol.22
, pp. 875-885
-
-
Colnaghi, R.1
Carpenter, G.2
Volker, M.3
O'Driscoll, M.4
-
4
-
-
84860780495
-
De novo mutations revealed by whole-exome sequencing are strongly associated with autism
-
S.J. Sanders, M.T. Murtha, A.R. Gupta, J.D. Murdoch, M.J. Raubeson, A.J. Willsey, A.G. Ercan-Sencicek, N.M. DiLullo, N.N. Parikshak, and J.L. Stein et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism Nature 485 2012 237 241
-
(2012)
Nature
, vol.485
, pp. 237-241
-
-
Sanders, S.J.1
Murtha, M.T.2
Gupta, A.R.3
Murdoch, J.D.4
Raubeson, M.J.5
Willsey, A.J.6
Ercan-Sencicek, A.G.7
Dilullo, N.M.8
Parikshak, N.N.9
Stein, J.L.10
-
5
-
-
40749089626
-
Structural variation of chromosomes in autism spectrum disorder
-
C.R. Marshall, A. Noor, J.B. Vincent, A.C. Lionel, L. Feuk, J. Skaug, M. Shago, R. Moessner, D. Pinto, and Y. Ren et al. Structural variation of chromosomes in autism spectrum disorder Am. J. Hum. Genet. 82 2008 477 488
-
(2008)
Am. J. Hum. Genet.
, vol.82
, pp. 477-488
-
-
Marshall, C.R.1
Noor, A.2
Vincent, J.B.3
Lionel, A.C.4
Feuk, L.5
Skaug, J.6
Shago, M.7
Moessner, R.8
Pinto, D.9
Ren, Y.10
-
6
-
-
77954657070
-
Functional impact of global rare copy number variation in autism spectrum disorders
-
D. Pinto, A.T. Pagnamenta, L. Klei, R. Anney, D. Merico, R. Regan, J. Conroy, T.R. Magalhaes, C. Correia, and B.S. Abrahams et al. Functional impact of global rare copy number variation in autism spectrum disorders Nature 466 2010 368 372
-
(2010)
Nature
, vol.466
, pp. 368-372
-
-
Pinto, D.1
Pagnamenta, A.T.2
Klei, L.3
Anney, R.4
Merico, D.5
Regan, R.6
Conroy, J.7
Magalhaes, T.R.8
Correia, C.9
Abrahams, B.S.10
-
7
-
-
79958074870
-
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism
-
S.J. Sanders, A.G. Ercan-Sencicek, V. Hus, R. Luo, M.T. Murtha, D. Moreno-De-Luca, S.H. Chu, M.P. Moreau, A.R. Gupta, and S.A. Thomson et al. Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism Neuron 70 2011 863 885
-
(2011)
Neuron
, vol.70
, pp. 863-885
-
-
Sanders, S.J.1
Ercan-Sencicek, A.G.2
Hus, V.3
Luo, R.4
Murtha, M.T.5
Moreno-De-Luca, D.6
Chu, S.H.7
Moreau, M.P.8
Gupta, A.R.9
Thomson, S.A.10
-
8
-
-
84894590822
-
Disruption of MBD5 contributes to a spectrum of psychopathology and neurodevelopmental abnormalities
-
J.C. Hodge, E. Mitchell, V. Pillalamarri, T.L. Toler, F. Bartel, H.M. Kearney, Y.S. Zou, W.H. Tan, C. Hanscom, and S. Kirmani et al. Disruption of MBD5 contributes to a spectrum of psychopathology and neurodevelopmental abnormalities Mol. Psychiatry 19 2014 368 379
-
(2014)
Mol. Psychiatry
, vol.19
, pp. 368-379
-
-
Hodge, J.C.1
Mitchell, E.2
Pillalamarri, V.3
Toler, T.L.4
Bartel, F.5
Kearney, H.M.6
Zou, Y.S.7
Tan, W.H.8
Hanscom, C.9
Kirmani, S.10
-
9
-
-
80053931230
-
Assessment of 2q23.1 microdeletion syndrome implicates MBD5 as a single causal locus of intellectual disability, epilepsy, and autism spectrum disorder
-
M.E. Talkowski, S.V. Mullegama, J.A. Rosenfeld, B.W.M. van Bon, Y. Shen, E.A. Repnikova, J. Gastier-Foster, D.L. Thrush, S. Kathiresan, and D.M. Ruderfer et al. Assessment of 2q23.1 microdeletion syndrome implicates MBD5 as a single causal locus of intellectual disability, epilepsy, and autism spectrum disorder Am. J. Hum. Genet. 89 2011 551 563
-
(2011)
Am. J. Hum. Genet.
, vol.89
, pp. 551-563
-
-
Talkowski, M.E.1
Mullegama, S.V.2
Rosenfeld, J.A.3
Van Bon, B.W.M.4
Shen, Y.5
Repnikova, E.A.6
Gastier-Foster, J.7
Thrush, D.L.8
Kathiresan, S.9
Ruderfer, D.M.10
-
10
-
-
84860347597
-
Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries
-
M.E. Talkowski, J.A. Rosenfeld, I. Blumenthal, V. Pillalamarri, C. Chiang, A. Heilbut, C. Ernst, C. Hanscom, E. Rossin, and A.M. Lindgren et al. Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries Cell 149 2012 525 537
-
(2012)
Cell
, vol.149
, pp. 525-537
-
-
Talkowski, M.E.1
Rosenfeld, J.A.2
Blumenthal, I.3
Pillalamarri, V.4
Chiang, C.5
Heilbut, A.6
Ernst, C.7
Hanscom, C.8
Rossin, E.9
Lindgren, A.M.10
-
11
-
-
77949652528
-
Haploinsufficiency of MBD5 associated with a syndrome involving microcephaly, intellectual disabilities, severe speech impairment, and seizures
-
S.R. Williams, S.V. Mullegama, J.A. Rosenfeld, A.I. Dagli, E. Hatchwell, W.P. Allen, C.A. Williams, and S.H. Elsea Haploinsufficiency of MBD5 associated with a syndrome involving microcephaly, intellectual disabilities, severe speech impairment, and seizures Eur. J. Hum. Genet. 18 2010 436 441
-
(2010)
Eur. J. Hum. Genet.
, vol.18
, pp. 436-441
-
-
Williams, S.R.1
Mullegama, S.V.2
Rosenfeld, J.A.3
Dagli, A.I.4
Hatchwell, E.5
Allen, W.P.6
Williams, C.A.7
Elsea, S.H.8
-
12
-
-
33746563985
-
Loss-of-function mutations in euchromatin histone methyl transferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome
-
T. Kleefstra, H.G. Brunner, J. Amiel, A.R. Oudakker, W.M. Nillesen, A. Magee, D. Geneviève, V. Cormier-Daire, H. van Esch, and J.-P. Fryns et al. Loss-of-function mutations in euchromatin histone methyl transferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome Am. J. Hum. Genet. 79 2006 370 377
-
(2006)
Am. J. Hum. Genet.
, vol.79
, pp. 370-377
-
-
Kleefstra, T.1
Brunner, H.G.2
Amiel, J.3
Oudakker, A.R.4
Nillesen, W.M.5
Magee, A.6
Geneviève, D.7
Cormier-Daire, V.8
Van Esch, H.9
Fryns, J.-P.10
-
13
-
-
84863984610
-
Disruption of an EHMT1-associated chromatin-modification module causes intellectual disability
-
T. Kleefstra, J.M. Kramer, K. Neveling, M.H. Willemsen, T.S. Koemans, L.E.L.M. Vissers, W. Wissink-Lindhout, M. Fenckova, W.M.R. van den Akker, and N.N. Kasri et al. Disruption of an EHMT1-associated chromatin-modification module causes intellectual disability Am. J. Hum. Genet. 91 2012 73 82
-
(2012)
Am. J. Hum. Genet.
, vol.91
, pp. 73-82
-
-
Kleefstra, T.1
Kramer, J.M.2
Neveling, K.3
Willemsen, M.H.4
Koemans, T.S.5
Vissers, L.E.L.M.6
Wissink-Lindhout, W.7
Fenckova, M.8
Van Den Akker, W.M.R.9
Kasri, N.N.10
-
14
-
-
84879964832
-
Global increases in both common and rare copy number load associated with autism
-
S. Girirajan, R.L. Johnson, F. Tassone, J. Balciuniene, N. Katiyar, K. Fox, C. Baker, A. Srikanth, K.H. Yeoh, and S.J. Khoo et al. Global increases in both common and rare copy number load associated with autism Hum. Mol. Genet. 22 2013 2870 2880
-
(2013)
Hum. Mol. Genet.
, vol.22
, pp. 2870-2880
-
-
Girirajan, S.1
Johnson, R.L.2
Tassone, F.3
Balciuniene, J.4
Katiyar, N.5
Fox, K.6
Baker, C.7
Srikanth, A.8
Yeoh, K.H.9
Khoo, S.J.10
-
15
-
-
80052260252
-
A copy number variation morbidity map of developmental delay
-
G.M. Cooper, B.P. Coe, S. Girirajan, J.A. Rosenfeld, T.H. Vu, C. Baker, C. Williams, H. Stalker, R. Hamid, and V. Hannig et al. A copy number variation morbidity map of developmental delay Nat. Genet. 43 2011 838 846
-
(2011)
Nat. Genet.
, vol.43
, pp. 838-846
-
-
Cooper, G.M.1
Coe, B.P.2
Girirajan, S.3
Rosenfeld, J.A.4
Vu, T.H.5
Baker, C.6
Williams, C.7
Stalker, H.8
Hamid, R.9
Hannig, V.10
-
16
-
-
84860297457
-
De novo gene disruptions in children on the autistic spectrum
-
I. Iossifov, M. Ronemus, D. Levy, Z. Wang, I. Hakker, J. Rosenbaum, B. Yamrom, Y.H. Lee, G. Narzisi, and A. Leotta et al. De novo gene disruptions in children on the autistic spectrum Neuron 74 2012 285 299
-
(2012)
Neuron
, vol.74
, pp. 285-299
-
-
Iossifov, I.1
Ronemus, M.2
Levy, D.3
Wang, Z.4
Hakker, I.5
Rosenbaum, J.6
Yamrom, B.7
Lee, Y.H.8
Narzisi, G.9
Leotta, A.10
-
17
-
-
84860712363
-
Patterns and rates of exonic de novo mutations in autism spectrum disorders
-
B.M. Neale, Y. Kou, L. Liu, A. Ma'ayan, K.E. Samocha, A. Sabo, C.-F. Lin, C. Stevens, L.-S. Wang, and V. Makarov et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders Nature 485 2012 242 245
-
(2012)
Nature
, vol.485
, pp. 242-245
-
-
Neale, B.M.1
Kou, Y.2
Liu, L.3
Ma'Ayan, A.4
Samocha, K.E.5
Sabo, A.6
Lin, C.-F.7
Stevens, C.8
Wang, L.-S.9
Makarov, V.10
-
18
-
-
84860741138
-
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
-
B.J. O'Roak, L. Vives, S. Girirajan, E. Karakoc, N. Krumm, B.P. Coe, R. Levy, A. Ko, C. Lee, and J.D. Smith et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations Nature 485 2012 246 250
-
(2012)
Nature
, vol.485
, pp. 246-250
-
-
O'Roak, B.J.1
Vives, L.2
Girirajan, S.3
Karakoc, E.4
Krumm, N.5
Coe, B.P.6
Levy, R.7
Ko, A.8
Lee, C.9
Smith, J.D.10
-
19
-
-
54049144653
-
Copy-number variations associated with neuropsychiatric conditions
-
E.H. Cook Jr., and S.W. Scherer Copy-number variations associated with neuropsychiatric conditions Nature 455 2008 919 923
-
(2008)
Nature
, vol.455
, pp. 919-923
-
-
Cook, Jr.E.H.1
Scherer, S.W.2
-
20
-
-
84876686460
-
From neural development to cognition: Unexpected roles for chromatin
-
J.L. Ronan, W. Wu, and G.R. Crabtree From neural development to cognition: unexpected roles for chromatin Nat. Rev. Genet. 14 2013 347 359
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 347-359
-
-
Ronan, J.L.1
Wu, W.2
Crabtree, G.R.3
-
21
-
-
81955163096
-
Genome-wide expression studies in autism spectrum disorder, Rett syndrome, and Down syndrome
-
C. Lintas, R. Sacco, and A.M. Persico Genome-wide expression studies in autism spectrum disorder, Rett syndrome, and Down syndrome Neurobiol. Dis. 45 2012 57 68
-
(2012)
Neurobiol. Dis.
, vol.45
, pp. 57-68
-
-
Lintas, C.1
Sacco, R.2
Persico, A.M.3
-
22
-
-
81555207759
-
Gene expression studies in autism: Moving from the genome to the transcriptome and beyond
-
I. Voineagu Gene expression studies in autism: moving from the genome to the transcriptome and beyond Neurobiol. Dis. 45 2012 69 75
-
(2012)
Neurobiol. Dis.
, vol.45
, pp. 69-75
-
-
Voineagu, I.1
-
23
-
-
79959262465
-
Transcriptomic analysis of autistic brain reveals convergent molecular pathology
-
I. Voineagu, X. Wang, P. Johnston, J.K. Lowe, Y. Tian, S. Horvath, J. Mill, R.M. Cantor, B.J. Blencowe, and D.H. Geschwind Transcriptomic analysis of autistic brain reveals convergent molecular pathology Nature 474 2011 380 384
-
(2011)
Nature
, vol.474
, pp. 380-384
-
-
Voineagu, I.1
Wang, X.2
Johnston, P.3
Lowe, J.K.4
Tian, Y.5
Horvath, S.6
Mill, J.7
Cantor, R.M.8
Blencowe, B.J.9
Geschwind, D.H.10
-
24
-
-
84890801954
-
Reciprocal deletion and duplication at 2q23.1 indicates a role for MBD5 in autism spectrum disorder
-
S.V. Mullegama, J.A. Rosenfeld, C. Orellana, B.W.M. van Bon, S. Halbach, E.A. Repnikova, L. Brick, C. Li, L. Dupuis, and M. Rosello et al. Reciprocal deletion and duplication at 2q23.1 indicates a role for MBD5 in autism spectrum disorder Eur. J. Hum. Genet. 22 2014 57 63
-
(2014)
Eur. J. Hum. Genet.
, vol.22
, pp. 57-63
-
-
Mullegama, S.V.1
Rosenfeld, J.A.2
Orellana, C.3
Van Bon, B.W.M.4
Halbach, S.5
Repnikova, E.A.6
Brick, L.7
Li, C.8
Dupuis, L.9
Rosello, M.10
-
25
-
-
39049163023
-
Association between microdeletion and microduplication at 16p11.2 and autism
-
Autism Consortium
-
L.A. Weiss, Y. Shen, J.M. Korn, D.E. Arking, D.T. Miller, R. Fossdal, E. Saemundsen, H. Stefansson, M.A.R. Ferreira, T. Green Autism Consortium Association between microdeletion and microduplication at 16p11.2 and autism N. Engl. J. Med. 358 2008 667 675
-
(2008)
N. Engl. J. Med.
, vol.358
, pp. 667-675
-
-
Weiss, L.A.1
Shen, Y.2
Korn, J.M.3
Arking, D.E.4
Miller, D.T.5
Fossdal, R.6
Saemundsen, E.7
Stefansson, H.8
Ferreira, M.A.R.9
Green, T.10
-
26
-
-
80053920983
-
Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus
-
S. Jacquemont, A. Reymond, F. Zufferey, L. Harewood, R.G. Walters, Z. Kutalik, D. Martinet, Y. Shen, A. Valsesia, and N.D. Beckmann et al. Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus Nature 478 2011 97 102
-
(2011)
Nature
, vol.478
, pp. 97-102
-
-
Jacquemont, S.1
Reymond, A.2
Zufferey, F.3
Harewood, L.4
Walters, R.G.5
Kutalik, Z.6
Martinet, D.7
Shen, Y.8
Valsesia, A.9
Beckmann, N.D.10
-
27
-
-
84878873338
-
Estimates of penetrance for recurrent pathogenic copy-number variations
-
J.A. Rosenfeld, B.P. Coe, E.E. Eichler, H. Cuckle, and L.G. Shaffer Estimates of penetrance for recurrent pathogenic copy-number variations Genet. Med. 15 2013 478 481
-
(2013)
Genet. Med.
, vol.15
, pp. 478-481
-
-
Rosenfeld, J.A.1
Coe, B.P.2
Eichler, E.E.3
Cuckle, H.4
Shaffer, L.G.5
-
28
-
-
84861075586
-
KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant
-
C. Golzio, J. Willer, M.E. Talkowski, E.C. Oh, Y. Taniguchi, S. Jacquemont, A. Reymond, M. Sun, A. Sawa, and J.F. Gusella et al. KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant Nature 485 2012 363 367
-
(2012)
Nature
, vol.485
, pp. 363-367
-
-
Golzio, C.1
Willer, J.2
Talkowski, M.E.3
Oh, E.C.4
Taniguchi, Y.5
Jacquemont, S.6
Reymond, A.7
Sun, M.8
Sawa, A.9
Gusella, J.F.10
-
29
-
-
84870002860
-
Zebrafish homologs of genes within 16p11.2, a genomic region associated with brain disorders, are active during brain development, and include two deletion dosage sensor genes
-
A. Blaker-Lee, S. Gupta, J.M. McCammon, G. De Rienzo, and H. Sive Zebrafish homologs of genes within 16p11.2, a genomic region associated with brain disorders, are active during brain development, and include two deletion dosage sensor genes Dis. Model. Mech. 5 2012 834 851
-
(2012)
Dis. Model. Mech.
, vol.5
, pp. 834-851
-
-
Blaker-Lee, A.1
Gupta, S.2
McCammon, J.M.3
De Rienzo, G.4
Sive, H.5
-
30
-
-
80054754473
-
Dosage-dependent phenotypes in models of 16p11.2 lesions found in autism
-
G. Horev, J. Ellegood, J.P. Lerch, Y.E. Son, L. Muthuswamy, H. Vogel, A.M. Krieger, A. Buja, R.M. Henkelman, M. Wigler, and A.A. Mills Dosage-dependent phenotypes in models of 16p11.2 lesions found in autism Proc. Natl. Acad. Sci. USA 108 2011 17076 17081
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 17076-17081
-
-
Horev, G.1
Ellegood, J.2
Lerch, J.P.3
Son, Y.E.4
Muthuswamy, L.5
Vogel, H.6
Krieger, A.M.7
Buja, A.8
Henkelman, R.M.9
Wigler, M.10
Mills, A.A.11
-
31
-
-
77956340995
-
Comprehensive comparative analysis of strand-specific RNA sequencing methods
-
J.Z. Levin, M. Yassour, X. Adiconis, C. Nusbaum, D.A. Thompson, N. Friedman, A. Gnirke, and A. Regev Comprehensive comparative analysis of strand-specific RNA sequencing methods Nat. Methods 7 2010 709 715
-
(2010)
Nat. Methods
, vol.7
, pp. 709-715
-
-
Levin, J.Z.1
Yassour, M.2
Adiconis, X.3
Nusbaum, C.4
Thompson, D.A.5
Friedman, N.6
Gnirke, A.7
Regev, A.8
-
32
-
-
70350653808
-
Transcriptome analysis by strand-specific sequencing of complementary DNA
-
e123-e123
-
D. Parkhomchuk, T. Borodina, V. Amstislavskiy, M. Banaru, L. Hallen, S. Krobitsch, H. Lehrach, and A. Soldatov Transcriptome analysis by strand-specific sequencing of complementary DNA Nucleic Acids Res. 37 2009 e123-e123
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Parkhomchuk, D.1
Borodina, T.2
Amstislavskiy, V.3
Banaru, M.4
Hallen, L.5
Krobitsch, S.6
Lehrach, H.7
Soldatov, A.8
-
33
-
-
79961230772
-
High-throughput illumina strand-specific RNA sequencing library preparation
-
S. Zhong, J.-G. Joung, Y. Zheng, Y.R. Chen, B. Liu, Y. Shao, J.Z. Xiang, Z. Fei, and J.J. Giovannoni High-throughput illumina strand-specific RNA sequencing library preparation Cold Spring Harb. Protoc. 2011 2011 940 949
-
(2011)
Cold Spring Harb. Protoc.
, vol.2011
, pp. 940-949
-
-
Zhong, S.1
Joung, J.-G.2
Zheng, Y.3
Chen, Y.R.4
Liu, B.5
Shao, Y.6
Xiang, J.Z.7
Fei, Z.8
Giovannoni, J.J.9
-
34
-
-
84902154062
-
Standards, Guidelines and Best Practices for RNA-Seq
-
(2011). Standards, Guidelines and Best Practices for RNA-Seq. The ENCODE Consortium,http://encodeproject.org/ENCODE/protocols/dataStandards/ ENCODE-RNAseq-Standards-V1.0.pdf.
-
(2011)
The ENCODE Consortium
-
-
-
35
-
-
80052521697
-
Synthetic spike-in standards for RNA-seq experiments
-
L. Jiang, F. Schlesinger, C.A. Davis, Y. Zhang, R. Li, M. Salit, T.R. Gingeras, and B. Oliver Synthetic spike-in standards for RNA-seq experiments Genome Res. 21 2011 1543 1551
-
(2011)
Genome Res.
, vol.21
, pp. 1543-1551
-
-
Jiang, L.1
Schlesinger, F.2
Davis, C.A.3
Zhang, Y.4
Li, R.5
Salit, M.6
Gingeras, T.R.7
Oliver, B.8
-
37
-
-
84861743958
-
RNA-SeQC: RNA-seq metrics for quality control and process optimization
-
D.S. DeLuca, J.Z. Levin, A. Sivachenko, T. Fennell, M.-D. Nazaire, C. Williams, M. Reich, W. Winckler, and G. Getz RNA-SeQC: RNA-seq metrics for quality control and process optimization Bioinformatics 28 2012 1530 1532
-
(2012)
Bioinformatics
, vol.28
, pp. 1530-1532
-
-
Deluca, D.S.1
Levin, J.Z.2
Sivachenko, A.3
Fennell, T.4
Nazaire, M.-D.5
Williams, C.6
Reich, M.7
Winckler, W.8
Getz, G.9
-
38
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
A.R. Quinlan, and I.M. Hall BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
39
-
-
84879198972
-
Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates
-
S.P. Lund, D. Nettleton, D.J. McCarthy, and G.K. Smyth Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates Stat. Appl. Genet. Mol. Biol. 11 2012 11
-
(2012)
Stat. Appl. Genet. Mol. Biol.
, vol.11
, pp. 11
-
-
Lund, S.P.1
Nettleton, D.2
McCarthy, D.J.3
Smyth, G.K.4
-
40
-
-
84874677498
-
A comparison of methods for differential expression analysis of RNA-seq data
-
C. Soneson, and M. Delorenzi A comparison of methods for differential expression analysis of RNA-seq data BMC Bioinformatics 14 2013 91
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 91
-
-
Soneson, C.1
Delorenzi, M.2
-
42
-
-
75949102155
-
Technical note: An R package for fitting generalized linear mixed models in animal breeding
-
A.I. Vazquez, D.M. Bates, G.J.M. Rosa, D. Gianola, and K.A. Weigel Technical note: an R package for fitting generalized linear mixed models in animal breeding J. Anim. Sci. 88 2010 497 504
-
(2010)
J. Anim. Sci.
, vol.88
, pp. 497-504
-
-
Vazquez, A.I.1
Bates, D.M.2
Rosa, G.J.M.3
Gianola, D.4
Weigel, K.A.5
-
43
-
-
60549111634
-
WGCNA: An R package for weighted correlation network analysis
-
P. Langfelder, and S. Horvath WGCNA: an R package for weighted correlation network analysis BMC Bioinformatics 9 2008 559
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 559
-
-
Langfelder, P.1
Horvath, S.2
-
44
-
-
84859326067
-
Fast R Functions for Robust Correlations and Hierarchical Clustering
-
P. Langfelder, and S. Horvath Fast R Functions for Robust Correlations and Hierarchical Clustering J. Stat. Softw. 46 2012 46
-
(2012)
J. Stat. Softw.
, vol.46
, pp. 46
-
-
Langfelder, P.1
Horvath, S.2
-
45
-
-
79851502150
-
Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology
-
International Inflammatory Bowel Disease Genetics Constortium
-
E.J. Rossin, K. Lage, S. Raychaudhuri, R.J. Xavier, D. Tatar, Y. Benita, C. Cotsapas, M.J. Daly International Inflammatory Bowel Disease Genetics Constortium Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology PLoS Genet. 7 2011 e1001273
-
(2011)
PLoS Genet.
, vol.7
, pp. 1001273
-
-
Rossin, E.J.1
Lage, K.2
Raychaudhuri, S.3
Xavier, R.J.4
Tatar, D.5
Benita, Y.6
Cotsapas, C.7
Daly, M.J.8
-
46
-
-
0033982936
-
KEGG: Kyoto encyclopedia of genes and genomes
-
M. Kanehisa, and S. Goto KEGG: kyoto encyclopedia of genes and genomes Nucleic Acids Res. 28 2000 27 30
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
47
-
-
84858983547
-
KEGG for integration and interpretation of large-scale molecular data sets
-
DATABASE ISSUE
-
M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, and M. Tanabe KEGG for integration and interpretation of large-scale molecular data sets Nucleic Acids Res. 40 Database issue 2012 D109 D114
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Furumichi, M.4
Tanabe, M.5
-
48
-
-
13444312083
-
The PANTHER database of protein families, subfamilies, functions and pathways
-
DATABASE ISSUE
-
H. Mi, B. Lazareva-Ulitsky, R. Loo, A. Kejariwal, J. Vandergriff, S. Rabkin, N. Guo, A. Muruganujan, O. Doremieux, and M.J. Campbell et al. The PANTHER database of protein families, subfamilies, functions and pathways Nucleic Acids Res. 33 Database issue 2005 D284 D288
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Mi, H.1
Lazareva-Ulitsky, B.2
Loo, R.3
Kejariwal, A.4
Vandergriff, J.5
Rabkin, S.6
Guo, N.7
Muruganujan, A.8
Doremieux, O.9
Campbell, M.J.10
-
49
-
-
58149177166
-
Reactome knowledgebase of human biological pathways and processes
-
DATABASE ISSUE
-
L. Matthews, G. Gopinath, M. Gillespie, M. Caudy, D. Croft, B. de Bono, P. Garapati, J. Hemish, H. Hermjakob, and B. Jassal et al. Reactome knowledgebase of human biological pathways and processes Nucleic Acids Res. 37 Database issue 2009 D619 D622
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Matthews, L.1
Gopinath, G.2
Gillespie, M.3
Caudy, M.4
Croft, D.5
De Bono, B.6
Garapati, P.7
Hemish, J.8
Hermjakob, H.9
Jassal, B.10
-
50
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
W. Huang, B.T. Sherman, and R.A. Lempicki Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat. Protoc. 4 2009 44 57
-
(2009)
Nat. Protoc.
, vol.4
, pp. 44-57
-
-
Huang, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
51
-
-
79960610118
-
REVIGO summarizes and visualizes long lists of gene ontology terms
-
F. Supek, M. Bošnjak, N. Škunca, and T. Šmuc REVIGO summarizes and visualizes long lists of gene ontology terms PLoS ONE 6 2011 e21800
-
(2011)
PLoS ONE
, vol.6
, pp. 21800
-
-
Supek, F.1
Bošnjak, M.2
Škunca, N.3
Šmuc, T.4
-
52
-
-
84876100615
-
Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool
-
E.Y. Chen, C.M. Tan, Y. Kou, Q. Duan, Z. Wang, G.V. Meirelles, N.R. Clark, and A. Ma'ayan Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool BMC Bioinformatics 14 2013 128
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 128
-
-
Chen, E.Y.1
Tan, C.M.2
Kou, Y.3
Duan, Q.4
Wang, Z.5
Meirelles, G.V.6
Clark, N.R.7
Ma'Ayan, A.8
-
53
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
A. Subramanian, P. Tamayo, V.K. Mootha, S. Mukherjee, B.L. Ebert, M.A. Gillette, A. Paulovich, S.L. Pomeroy, T.R. Golub, E.S. Lander, and J.P. Mesirov Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles Proc. Natl. Acad. Sci. USA 102 2005 15545 15550
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
54
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
P. Shannon, A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 13 2003 2498 2504
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
55
-
-
84884929362
-
SFARI Gene 2.0: A community-driven knowledgebase for the autism spectrum disorders (ASDs)
-
B.S. Abrahams, D.E. Arking, D.B. Campbell, H.C. Mefford, E.M. Morrow, L.A. Weiss, I. Menashe, T. Wadkins, S. Banerjee-Basu, and A. Packer SFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs) Mol. Autism 4 2013 36
-
(2013)
Mol. Autism
, vol.4
, pp. 36
-
-
Abrahams, B.S.1
Arking, D.E.2
Campbell, D.B.3
Mefford, H.C.4
Morrow, E.M.5
Weiss, L.A.6
Menashe, I.7
Wadkins, T.8
Banerjee-Basu, S.9
Packer, A.10
-
56
-
-
84862224852
-
AutismKB: An evidence-based knowledgebase of autism genetics
-
DATABASE ISSUE
-
L.M. Xu, J.R. Li, Y. Huang, M. Zhao, X. Tang, and L. Wei AutismKB: an evidence-based knowledgebase of autism genetics Nucleic Acids Res. 40 Database issue 2012 D1016 D1022
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Xu, L.M.1
Li, J.R.2
Huang, Y.3
Zhao, M.4
Tang, X.5
Wei, L.6
-
57
-
-
84863988574
-
Genome-wide transcriptome profiling reveals the functional impact of rare de novo and recurrent CNVs in autism spectrum disorders
-
R. Luo, S.J. Sanders, Y. Tian, I. Voineagu, N. Huang, S.H. Chu, L. Klei, C. Cai, J. Ou, and J.K. Lowe et al. Genome-wide transcriptome profiling reveals the functional impact of rare de novo and recurrent CNVs in autism spectrum disorders Am. J. Hum. Genet. 91 2012 38 55
-
(2012)
Am. J. Hum. Genet.
, vol.91
, pp. 38-55
-
-
Luo, R.1
Sanders, S.J.2
Tian, Y.3
Voineagu, I.4
Huang, N.5
Chu, S.H.6
Klei, L.7
Cai, C.8
Ou, J.9
Lowe, J.K.10
-
58
-
-
79955019148
-
The atypical 16p11.2 deletion: A not so atypical microdeletion syndrome?
-
D.Q. Barge-Schaapveld, S.M. Maas, A. Polstra, L.C. Knegt, and R.C. Hennekam The atypical 16p11.2 deletion: a not so atypical microdeletion syndrome? Am. J. Med. Genet. A. 155A 2011 1066 1072
-
(2011)
Am. J. Med. Genet. A.
, vol.155 A
, pp. 1066-1072
-
-
Barge-Schaapveld, D.Q.1
Maas, S.M.2
Polstra, A.3
Knegt, L.C.4
Hennekam, R.C.5
-
59
-
-
77951860836
-
The effect of translocation-induced nuclear reorganization on gene expression
-
L. Harewood, F. Schütz, S. Boyle, P. Perry, M. Delorenzi, W.A. Bickmore, and A. Reymond The effect of translocation-induced nuclear reorganization on gene expression Genome Res. 20 2010 554 564
-
(2010)
Genome Res.
, vol.20
, pp. 554-564
-
-
Harewood, L.1
Schütz, F.2
Boyle, S.3
Perry, P.4
Delorenzi, M.5
Bickmore, W.A.6
Reymond, A.7
-
60
-
-
84902130550
-
Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome
-
M.J. Zeitz, P.P. Lerner, F. Ay, E. Van Nostrand, J.D. Heidmann, W.S. Noble, and A.R. Hoffman Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome Nucleus 4 2013 487 493
-
(2013)
Nucleus
, vol.4
, pp. 487-493
-
-
Zeitz, M.J.1
Lerner, P.P.2
Ay, F.3
Van Nostrand, E.4
Heidmann, J.D.5
Noble, W.S.6
Hoffman, A.R.7
-
61
-
-
79551615055
-
Esrrg functions in early branch generation of the ureteric bud and is essential for normal development of the renal papilla
-
R. Berry, L. Harewood, L. Pei, M. Fisher, D. Brownstein, A. Ross, W.A. Alaynick, J. Moss, N.D. Hastie, and P. Hohenstein et al. Esrrg functions in early branch generation of the ureteric bud and is essential for normal development of the renal papilla Hum. Mol. Genet. 20 2011 917 926
-
(2011)
Hum. Mol. Genet.
, vol.20
, pp. 917-926
-
-
Berry, R.1
Harewood, L.2
Pei, L.3
Fisher, M.4
Brownstein, D.5
Ross, A.6
Alaynick, W.A.7
Moss, J.8
Hastie, N.D.9
Hohenstein, P.10
-
62
-
-
84889583293
-
Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism
-
A.J. Willsey, S.J. Sanders, M. Li, S. Dong, A.T. Tebbenkamp, R.A. Muhle, S.K. Reilly, L. Lin, S. Fertuzinhos, and J.A. Miller et al. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism Cell 155 2013 997 1007
-
(2013)
Cell
, vol.155
, pp. 997-1007
-
-
Willsey, A.J.1
Sanders, S.J.2
Li, M.3
Dong, S.4
Tebbenkamp, A.T.5
Muhle, R.A.6
Reilly, S.K.7
Lin, L.8
Fertuzinhos, S.9
Miller, J.A.10
-
63
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
E. Lieberman-Aiden, N.L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B.R. Lajoie, P.J. Sabo, and M.O. Dorschner et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 2009 289 293
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
Van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
Amit, I.7
Lajoie, B.R.8
Sabo, P.J.9
Dorschner, M.O.10
-
64
-
-
84887141165
-
Differential expression for RNA sequencing (RNA-seq) data: Mapping, summarization, statistical analysis, and experimental design
-
M.H.N. Rodríguez-Ezpeleta, A.M. Aransay, Springer New York New York
-
M. Young, D. McCarthy, M. Wakefield, G. Smyth, A. Oshlack, and M. Robinson Differential expression for RNA sequencing (RNA-seq) data: mapping, summarization, statistical analysis, and experimental design M.H.N. Rodríguez-Ezpeleta, A.M. Aransay, Bioinformatics for High Throughput Sequencing 2012 Springer New York New York 169 190
-
(2012)
Bioinformatics for High Throughput Sequencing
, pp. 169-190
-
-
Young, M.1
McCarthy, D.2
Wakefield, M.3
Smyth, G.4
Oshlack, A.5
Robinson, M.6
-
65
-
-
84891767394
-
RefSeq: An update on mammalian reference sequences
-
DATABASE ISSUE
-
K.D. Pruitt, G.R. Brown, S.M. Hiatt, F. Thibaud-Nissen, A. Astashyn, O. Ermolaeva, C.M. Farrell, J. Hart, M.J. Landrum, and K.M. McGarvey et al. RefSeq: an update on mammalian reference sequences Nucleic Acids Res. 42 Database issue 2014 D756 D763
-
(2014)
Nucleic Acids Res.
, vol.42
-
-
Pruitt, K.D.1
Brown, G.R.2
Hiatt, S.M.3
Thibaud-Nissen, F.4
Astashyn, A.5
Ermolaeva, O.6
Farrell, C.M.7
Hart, J.8
Landrum, M.J.9
McGarvey, K.M.10
-
68
-
-
79958117254
-
The NBP negative binomial model for assessing differential gene expression from RNA-seq
-
Y. Di, D.W. Schafer, J.S. Cumbie, and J.H. Chang The NBP negative binomial model for assessing differential gene expression from RNA-seq Stat. Appl. Genet. Mol. Biol. 10 2011 1 28
-
(2011)
Stat. Appl. Genet. Mol. Biol.
, vol.10
, pp. 1-28
-
-
Di, Y.1
Schafer, D.W.2
Cumbie, J.S.3
Chang, J.H.4
-
69
-
-
77958471357
-
Differential expression analysis for sequence count data
-
S. Anders, and W. Huber Differential expression analysis for sequence count data Genome Biol. 11 2010 R106
-
(2010)
Genome Biol.
, vol.11
, pp. 106
-
-
Anders, S.1
Huber, W.2
-
70
-
-
84879417655
-
A tutorial on count regression and zero-altered count models for longitudinal substance use data
-
D.C. Atkins, S.A. Baldwin, C. Zheng, R.J. Gallop, and C. Neighbors A tutorial on count regression and zero-altered count models for longitudinal substance use data Psychol. Addict. Behav. 27 2013 166 177
-
(2013)
Psychol. Addict. Behav.
, vol.27
, pp. 166-177
-
-
Atkins, D.C.1
Baldwin, S.A.2
Zheng, C.3
Gallop, R.J.4
Neighbors, C.5
|