-
1
-
-
33745373606
-
Primate segmental duplications: crucibles of evolution, diversity and disease
-
COI: 1:CAS:528:DC%2BD28XlvVGltL8%3D, PID: 16770338
-
Bailey JA, Eichler EE (2006) Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet 7(7):552–564
-
(2006)
Nat Rev Genet
, vol.7
, Issue.7
, pp. 552-564
-
-
Bailey, J.A.1
Eichler, E.E.2
-
2
-
-
84867332476
-
The mammalian gene function resource: the International Knockout Mouse Consortium
-
PID: 22968824
-
Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Burger A, Bult CJ et al (2012) The mammalian gene function resource: the International Knockout Mouse Consortium. Mamm Genome 23(9–10):580–586
-
(2012)
Mamm Genome
, vol.23
, Issue.9-10
, pp. 580-586
-
-
Bradley, A.1
Anastassiadis, K.2
Ayadi, A.3
Battey, J.F.4
Bell, C.5
Birling, M.C.6
Bottomley, J.7
Brown, S.D.8
Burger, A.9
Bult, C.J.10
-
3
-
-
79955555530
-
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
-
COI: 1:CAS:528:DC%2BC3MXmtV2qsbo%3D, PID: 21460061
-
Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS et al (2011) Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome. Genome Res 21(5):756–767
-
(2011)
Genome Res
, vol.21
, Issue.5
, pp. 756-767
-
-
Brosch, M.1
Saunders, G.I.2
Frankish, A.3
Collins, M.O.4
Yu, L.5
Wright, J.6
Verstraten, R.7
Adams, D.J.8
Harrow, J.9
Choudhary, J.S.10
-
4
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
COI: 1:CAS:528:DC%2BD2MXpsFWju7o%3D, PID: 16141072
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C et al (2005) The transcriptional landscape of the mammalian genome. Science 309(5740):1559–1563
-
(2005)
Science
, vol.309
, Issue.5740
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
Maeda, N.6
Oyama, R.7
Ravasi, T.8
Lenhard, B.9
Wells, C.10
-
5
-
-
84917695871
-
Ecological and evolutionary implications of genomic structural variations
-
PID: 25278961
-
Chain FJ, Feulner PG (2014) Ecological and evolutionary implications of genomic structural variations. Front Genet 5:326
-
(2014)
Front Genet
, vol.5
, pp. 326
-
-
Chain, F.J.1
Feulner, P.G.2
-
6
-
-
79960925372
-
Modernizing reference genome assemblies
-
COI: 1:CAS:528:DC%2BC3MXpsVamtr4%3D, PID: 21750661
-
Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen HC, Agarwala R, McLaren WM, Ritchie GR et al (2011) Modernizing reference genome assemblies. PLoS Biol 9(7):e1001091
-
(2011)
PLoS Biol
, vol.9
, Issue.7
, pp. 1001091
-
-
Church, D.M.1
Schneider, V.A.2
Graves, T.3
Auger, K.4
Cunningham, F.5
Bouk, N.6
Chen, H.C.7
Agarwala, R.8
McLaren, W.M.9
Ritchie, G.R.10
-
7
-
-
84926524893
-
Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing
-
COI: 1:CAS:528:DC%2BC2MXjvFOnsL8%3D, PID: 25751143
-
Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY et al (2015) Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Nat Methods. 12(4):339–342
-
(2015)
Nat Methods
, vol.12
, Issue.4
, pp. 339-342
-
-
Clark, M.B.1
Mercer, T.R.2
Bussotti, G.3
Leonardi, T.4
Haynes, K.R.5
Crawford, J.6
Brunck, M.E.7
Cao, K.A.8
Thomas, G.P.9
Chen, W.Y.10
-
8
-
-
64449088698
-
Continuous base identification for single-molecule nanopore DNA sequencing
-
COI: 1:CAS:528:DC%2BD1MXktFWktLg%3D, PID: 19350039
-
Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4(4):265–270
-
(2009)
Nat Nanotechnol
, vol.4
, Issue.4
, pp. 265-270
-
-
Clarke, J.1
Wu, H.C.2
Jayasinghe, L.3
Patel, A.4
Reid, S.5
Bayley, H.6
-
9
-
-
84946037477
-
-
Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S et al (2015) Ensembl 2015. Nucleic Acids Res 43(Database issue):D662–669
-
(2015)
Ensembl 2015. Nucleic Acids Res
, vol.43
, Issue.Database issue
, pp. 662-669
-
-
Cunningham, F.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Billis, K.5
Brent, S.6
Carvalho-Silva, D.7
Clapham, P.8
Coates, G.9
Fitzgerald, S.10
-
10
-
-
84865727393
-
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
-
COI: 1:CAS:528:DC%2BC38XhtlentLvO, PID: 22955988
-
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775–1789
-
(2012)
Genome Res
, vol.22
, Issue.9
, pp. 1775-1789
-
-
Derrien, T.1
Johnson, R.2
Bussotti, G.3
Tanzer, A.4
Djebali, S.5
Tilgner, H.6
Guernec, G.7
Martin, D.8
Merkel, A.9
Knowles, D.G.10
-
11
-
-
84861903786
-
A quantitative atlas of polyadenylation in five mammals
-
COI: 1:CAS:528:DC%2BC38XoslSitrs%3D, PID: 22454233
-
Derti A, Garrett-Engele P, Macisaac KD, Stevens RC, Sriram S, Chen R, Rohl CA, Johnson JM, Babak T (2012) A quantitative atlas of polyadenylation in five mammals. Genome Res 22(6):1173–1183
-
(2012)
Genome Res
, vol.22
, Issue.6
, pp. 1173-1183
-
-
Derti, A.1
Garrett-Engele, P.2
Macisaac, K.D.3
Stevens, R.C.4
Sriram, S.5
Chen, R.6
Rohl, C.A.7
Johnson, J.M.8
Babak, T.9
-
12
-
-
84865757142
-
Landscape of transcription in human cells
-
COI: 1:CAS:528:DC%2BC38XhtlGnt73M, PID: 22955620
-
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F et al (2012) Landscape of transcription in human cells. Nature 489(7414):101–108
-
(2012)
Nature
, vol.489
, Issue.7414
, pp. 101-108
-
-
Djebali, S.1
Davis, C.A.2
Merkel, A.3
Dobin, A.4
Lassmann, T.5
Mortazavi, A.6
Tanzer, A.7
Lagarde, J.8
Lin, W.9
Schlesinger, F.10
-
13
-
-
79952588244
-
Dalliance: interactive genome viewing on the web
-
COI: 1:CAS:528:DC%2BC3MXjt1Sksb0%3D, PID: 21252075
-
Down TA, Piipari M, Hubbard TJ (2011) Dalliance: interactive genome viewing on the web. Bioinformatics 27(6):889–890
-
(2011)
Bioinformatics
, vol.27
, Issue.6
, pp. 889-890
-
-
Down, T.A.1
Piipari, M.2
Hubbard, T.J.3
-
14
-
-
2942607685
-
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
-
PID: 12095421
-
Eddy SR (2002) A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics 3:18
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 18
-
-
Eddy, S.R.1
-
15
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74
-
(2012)
Nature
, vol.489
, Issue.7414
, pp. 57-74
-
-
Bernstein, B.E.1
Birney, E.2
Dunham, I.3
Green, E.D.4
Gunter, C.5
Snyder, M.6
-
16
-
-
84888861753
-
Systematic evaluation of spliced alignment programs for RNA-seq data
-
PID: 24185836
-
Engstrom PG, Steijger T, Sipos B, Grant GR, Kahles A, Ratsch G, Goldman N, Hubbard TJ, Harrow J, Guigo R et al (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods 10(12):1185–1191
-
(2013)
Nat Methods
, vol.10
, Issue.12
, pp. 1185-1191
-
-
Engstrom, P.G.1
Steijger, T.2
Sipos, B.3
Grant, G.R.4
Kahles, A.5
Ratsch, G.6
Goldman, N.7
Hubbard, T.J.8
Harrow, J.9
Guigo, R.10
-
17
-
-
84905372152
-
Analyzing the first drafts of the human proteome
-
COI: 1:CAS:528:DC%2BC2cXhtFelurjF, PID: 25014353
-
Ezkurdia I, Vazquez J, Valencia A, Tress M (2014) Analyzing the first drafts of the human proteome. J Proteome Res 13(8):3854–3855
-
(2014)
J Proteome Res
, vol.13
, Issue.8
, pp. 3854-3855
-
-
Ezkurdia, I.1
Vazquez, J.2
Valencia, A.3
Tress, M.4
-
18
-
-
84926443748
-
Most highly expressed protein-coding genes have a single dominant isoform
-
COI: 1:CAS:528:DC%2BC2MXjsF2itbg%3D, PID: 25732134
-
Ezkurdia I, Rodriguez JM, Carrillo-de Santa Pau E, Vazquez J, Valencia A, Tress ML (2015) Most highly expressed protein-coding genes have a single dominant isoform. J Proteome Res. 14(4):1880–1887
-
(2015)
J Proteome Res
, vol.14
, Issue.4
, pp. 1880-1887
-
-
Ezkurdia, I.1
Rodriguez, J.M.2
Carrillo-de Santa Pau, E.3
Vazquez, J.4
Valencia, A.5
Tress, M.L.6
-
19
-
-
84891777450
-
Current status and new features of the Consensus Coding Sequence database
-
Farrell CM, O’Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B et al (2014) Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res 42(Database issue):D865–872
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.Database issue
, pp. 865-872
-
-
Farrell, C.M.1
O’Leary, N.A.2
Harte, R.A.3
Loveland, J.E.4
Wilming, L.G.5
Wallin, C.6
Diekhans, M.7
Barrell, D.8
Searle, S.M.9
Aken, B.10
-
20
-
-
84926686213
-
Proteogenomics: emergence and promise
-
COI: 1:CAS:528:DC%2BC2MXht1Oktrs%3D, PID: 25609363
-
Faulkner S, Dun MD, Hondermarck H (2015) Proteogenomics: emergence and promise. Cell Mol Life Sci. 72(5):953–957
-
(2015)
Cell Mol Life Sci
, vol.72
, Issue.5
, pp. 953-957
-
-
Faulkner, S.1
Dun, M.D.2
Hondermarck, H.3
-
21
-
-
84897406127
-
A promoter-level mammalian expression atlas
-
COI: 1:CAS:528:DC%2BC2cXkvV2mt7c%3D, PID: 24670764
-
Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassman T, Kulakovskiy IV, Lizio M, Itoh M et al (2014) A promoter-level mammalian expression atlas. Nature 507(7493):462–470
-
(2014)
Nature
, vol.507
, Issue.7493
, pp. 462-470
-
-
Forrest, A.R.1
Kawaji, H.2
Rehli, M.3
Baillie, J.K.4
de Hoon, M.J.5
Haberle, V.6
Lassman, T.7
Kulakovskiy, I.V.8
Lizio, M.9
Itoh, M.10
-
23
-
-
34250330777
-
What is a gene, post-ENCODE?. History and updated definition
-
COI: 1:CAS:528:DC%2BD2sXntVSjsrc%3D, PID: 17567988
-
Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M (2007) What is a gene, post-ENCODE?. History and updated definition. Genome Res 17(6):669–681
-
(2007)
Genome Res
, vol.17
, Issue.6
, pp. 669-681
-
-
Gerstein, M.B.1
Bruce, C.2
Rozowsky, J.S.3
Zheng, D.4
Du, J.5
Korbel, J.O.6
Emanuelsson, O.7
Zhang, Z.D.8
Weissman, S.9
Snyder, M.10
-
24
-
-
84879488128
-
Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene
-
PID: 23815980
-
Gonzalez-Porta M, Frankish A, Rung J, Harrow J, Brazma A (2013) Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. Genome Biol 14(7):R70
-
(2013)
Genome Biol
, vol.14
, Issue.7
, pp. 70
-
-
Gonzalez-Porta, M.1
Frankish, A.2
Rung, J.3
Harrow, J.4
Brazma, A.5
-
25
-
-
0037252684
-
Rfam: an RNA family database
-
COI: 1:CAS:528:DC%2BD3sXhvFSls7w%3D, PID: 12520045
-
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR (2003) Rfam: an RNA family database. Nucleic Acids Res 31(1):439–441
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.1
, pp. 439-441
-
-
Griffiths-Jones, S.1
Bateman, A.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
26
-
-
33644750115
-
-
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34(Database issue):D140–144
-
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34(Database issue):D140–144
-
-
-
-
27
-
-
33748641351
-
EGASP: the human ENCODE Genome Annotation Assessment Project
-
Guigo R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E et al. 2006. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol 7 Suppl 1:S2 1–31
-
(2006)
Genome Biol 7 Suppl 1:S2
, pp. 1-31
-
-
Guigo, R.1
Flicek, P.2
Abril, J.F.3
Reymond, A.4
Lagarde, J.5
Denoeud, F.6
Antonarakis, S.7
Ashburner, M.8
Bajic, V.B.9
Birney, E.10
-
28
-
-
84879671055
-
Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs
-
COI: 1:CAS:528:DC%2BC3sXhtFersLvL, PID: 23818866
-
Hangauer MJ, Vaughn IW, McManus MT (2013) Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet 9(6):e1003569
-
(2013)
PLoS Genet
, vol.9
, Issue.6
, pp. 1003569
-
-
Hangauer, M.J.1
Vaughn, I.W.2
McManus, M.T.3
-
29
-
-
84865760395
-
GENCODE: the reference human genome annotation for The ENCODE Project
-
COI: 1:CAS:528:DC%2BC38XhtlentLvN, PID: 22955987
-
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22(9):1760–1774
-
(2012)
Genome Res
, vol.22
, Issue.9
, pp. 1760-1774
-
-
Harrow, J.1
Frankish, A.2
Gonzalez, J.M.3
Tapanari, E.4
Diekhans, M.5
Kokocinski, F.6
Aken, B.L.7
Barrell, D.8
Zadissa, A.9
Searle, S.10
-
30
-
-
84891791841
-
The Vertebrate Genome Annotation browser 10 years on
-
Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S et al. 2014. The Vertebrate Genome Annotation browser 10 years on. Nucleic Acids Res 42(Database issue):D771–779
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.Database issue
, pp. 771-779
-
-
Harrow, J.L.1
Steward, C.A.2
Frankish, A.3
Gilbert, J.G.4
Gonzalez, J.M.5
Loveland, J.E.6
Mudge, J.7
Sheppard, D.8
Thomas, M.9
Trevanion, S.10
-
31
-
-
84865728918
-
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
-
COI: 1:CAS:528:DC%2BC38XhtlentLrK, PID: 22955982
-
Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T et al (2012) Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res 22(9):1698–1710
-
(2012)
Genome Res
, vol.22
, Issue.9
, pp. 1698-1710
-
-
Howald, C.1
Tanzer, A.2
Chrast, J.3
Kokocinski, F.4
Derrien, T.5
Walters, N.6
Gonzalez, J.M.7
Frankish, A.8
Aken, B.L.9
Hourlier, T.10
-
32
-
-
84894318608
-
Ribosome profiling: new views of translation, from single codons to genome scale
-
COI: 1:CAS:528:DC%2BC2cXhtlequ7w%3D, PID: 24468696
-
Ingolia NT (2014) Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15(3):205–213
-
(2014)
Nat Rev Genet
, vol.15
, Issue.3
, pp. 205-213
-
-
Ingolia, N.T.1
-
33
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
COI: 1:CAS:528:DC%2BD1MXktFals7c%3D, PID: 19213877
-
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218–223
-
(2009)
Science
, vol.324
, Issue.5924
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Newman, J.R.3
Weissman, J.S.4
-
34
-
-
81055155799
-
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
-
COI: 1:CAS:528:DC%2BC3MXhsVKgsLnJ, PID: 22056041
-
Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147(4):789–802
-
(2011)
Cell
, vol.147
, Issue.4
, pp. 789-802
-
-
Ingolia, N.T.1
Lareau, L.F.2
Weissman, J.S.3
-
35
-
-
84865070369
-
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
-
COI: 1:CAS:528:DC%2BC38XhtFOqsb3L, PID: 22745249
-
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821
-
(2012)
Science
, vol.337
, Issue.6096
, pp. 816-821
-
-
Jinek, M.1
Chylinski, K.2
Fonfara, I.3
Hauer, M.4
Doudna, J.A.5
Charpentier, E.6
-
36
-
-
84906252981
-
Identification of structural variation in mouse genomes
-
PID: 25071822
-
Keane TM, Wong K, Adams DJ, Flint J, Reymond A, Yalcin B (2014) Identification of structural variation in mouse genomes. Front Genet 5:192
-
(2014)
Front Genet
, vol.5
, pp. 192
-
-
Keane, T.M.1
Wong, K.2
Adams, D.J.3
Flint, J.4
Reymond, A.5
Yalcin, B.6
-
37
-
-
84901599553
-
A draft map of the human proteome
-
COI: 1:CAS:528:DC%2BC2cXoslCrtrc%3D, PID: 24870542
-
Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S et al (2014) A draft map of the human proteome. Nature 509(7502):575–581
-
(2014)
Nature
, vol.509
, Issue.7502
, pp. 575-581
-
-
Kim, M.S.1
Pinto, S.M.2
Getnet, D.3
Nirujogi, R.S.4
Manda, S.S.5
Chaerkady, R.6
Madugundu, A.K.7
Kelkar, D.S.8
Isserlin, R.9
Jain, S.10
-
38
-
-
77957256775
-
AnnoTrack—a tracking system for genome annotation
-
Kokocinski F, Harrow J, Hubbard T (2010) AnnoTrack—a tracking system for genome annotation. BMC Genom 11:538
-
(2010)
BMC Genom
, vol.11
, pp. 538
-
-
Kokocinski, F.1
Harrow, J.2
Hubbard, T.3
-
39
-
-
84866267681
-
Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution
-
COI: 1:CAS:528:DC%2BC38XhsVCnu7vF, PID: 22927429
-
Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB (2012) Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc Natl Acad Sci USA 109(37):E2424–E2432
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.37
, pp. 2424-2432
-
-
Lee, S.1
Liu, B.2
Lee, S.3
Huang, S.X.4
Shen, B.5
Qian, S.B.6
-
40
-
-
84914125316
-
Comparison of the transcriptional landscapes between human and mouse tissues
-
COI: 1:CAS:528:DC%2BC2cXhvFKmu7vF, PID: 25413365
-
Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC et al (2014) Comparison of the transcriptional landscapes between human and mouse tissues. Proc Natl Acad Sci USA 111(48):17224–17229
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, Issue.48
, pp. 17224-17229
-
-
Lin, S.1
Lin, Y.2
Nery, J.R.3
Urich, M.A.4
Breschi, A.5
Davis, C.A.6
Dobin, A.7
Zaleski, C.8
Beer, M.A.9
Chapman, W.C.10
-
41
-
-
84884856342
-
Cas9 as a versatile tool for engineering biology
-
COI: 1:CAS:528:DC%2BC3sXhsFaks7rO, PID: 24076990
-
Mali P, Esvelt KM, Church GM (2013) Cas9 as a versatile tool for engineering biology. Nat Methods 10(10):957–963
-
(2013)
Nat Methods
, vol.10
, Issue.10
, pp. 957-963
-
-
Mali, P.1
Esvelt, K.M.2
Church, G.M.3
-
42
-
-
84901020092
-
Intergenic lncRNAs and the evolution of gene expression
-
COI: 1:CAS:528:DC%2BC2cXht1Oit7zP, PID: 24852186
-
Marques AC, Ponting CP (2014) Intergenic lncRNAs and the evolution of gene expression. Curr Opin Genet Dev 27:48–53
-
(2014)
Curr Opin Genet Dev
, vol.27
, pp. 48-53
-
-
Marques, A.C.1
Ponting, C.P.2
-
43
-
-
6944256813
-
Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise
-
COI: 1:CAS:528:DC%2BD2cXnvFamtLk%3D, PID: 15448691
-
Mendell JT, Sharifi NA, Meyers JL, Martinez-Murillo F, Dietz HC (2004) Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet 36(10):1073–1078
-
(2004)
Nat Genet
, vol.36
, Issue.10
, pp. 1073-1078
-
-
Mendell, J.T.1
Sharifi, N.A.2
Meyers, J.L.3
Martinez-Murillo, F.4
Dietz, H.C.5
-
44
-
-
84855539848
-
Targeted RNA sequencing reveals the deep complexity of the human transcriptome
-
COI: 1:CAS:528:DC%2BC3MXhsVKjsbrP
-
Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL (2012) Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol 30(1):99–104
-
(2012)
Nat Biotechnol
, vol.30
, Issue.1
, pp. 99-104
-
-
Mercer, T.R.1
Gerhardt, D.J.2
Dinger, M.E.3
Crawford, J.4
Trapnell, C.5
Jeddeloh, J.A.6
Mattick, J.S.7
Rinn, J.L.8
-
45
-
-
84901004299
-
The rise of regulatory RNA
-
COI: 1:CAS:528:DC%2BC2cXmvFSjtLo%3D, PID: 24776770
-
Morris KV, Mattick JS (2014) The rise of regulatory RNA. Nat Rev Genet 15(6):423–437
-
(2014)
Nat Rev Genet
, vol.15
, Issue.6
, pp. 423-437
-
-
Morris, K.V.1
Mattick, J.S.2
-
46
-
-
47149101500
-
Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice
-
PID: 18507838
-
Mudge JM, Armstrong SD, McLaren K, Beynon RJ, Hurst JL, Nicholson C, Robertson DH, Wilming LG, Harrow JL (2008) Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice. Genome Biol 9(5):R91
-
(2008)
Genome Biol
, vol.9
, Issue.5
, pp. 91
-
-
Mudge, J.M.1
Armstrong, S.D.2
McLaren, K.3
Beynon, R.J.4
Hurst, J.L.5
Nicholson, C.6
Robertson, D.H.7
Wilming, L.G.8
Harrow, J.L.9
-
47
-
-
84890449615
-
Functional transcriptomics in the post-ENCODE era
-
COI: 1:CAS:528:DC%2BC3sXhvFCisLrL, PID: 24172201
-
Mudge JM, Frankish A, Harrow J (2013) Functional transcriptomics in the post-ENCODE era. Genome Res 23(12):1961–1973
-
(2013)
Genome Res
, vol.23
, Issue.12
, pp. 1961-1973
-
-
Mudge, J.M.1
Frankish, A.2
Harrow, J.3
-
48
-
-
84908540871
-
Proteogenomics: concepts, applications and computational strategies
-
COI: 1:CAS:528:DC%2BC2cXhvVCnu7fI, PID: 25357241
-
Nesvizhskii AI (2014) Proteogenomics: concepts, applications and computational strategies. Nat Methods 11(11):1114–1125
-
(2014)
Nat Methods
, vol.11
, Issue.11
, pp. 1114-1125
-
-
Nesvizhskii, A.I.1
-
49
-
-
14744284678
-
Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice
-
COI: 1:CAS:528:DC%2BD2MXitV2htbg%3D, PID: 15716120
-
Niimura Y, Nei M (2005) Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Gene 346:13–21
-
(2005)
Gene
, vol.346
, pp. 13-21
-
-
Niimura, Y.1
Nei, M.2
-
50
-
-
65649126066
-
Transcript length bias in RNA-seq data confounds systems biology
-
PID: 19371405
-
Oshlack A, Wakefield MJ (2009) Transcript length bias in RNA-seq data confounds systems biology. Biology Direct 4:14
-
(2009)
Biology Direct
, vol.4
, pp. 14
-
-
Oshlack, A.1
Wakefield, M.J.2
-
51
-
-
84865726286
-
The GENCODE pseudogene resource
-
COI: 1:CAS:528:DC%2BC38Xhtl2msb3I, PID: 22951037
-
Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M et al (2012) The GENCODE pseudogene resource. Genome Biol 13(9):R51
-
(2012)
Genome Biol
, vol.13
, Issue.9
, pp. 51
-
-
Pei, B.1
Sisu, C.2
Frankish, A.3
Howald, C.4
Habegger, L.5
Mu, X.J.6
Harte, R.7
Balasubramanian, S.8
Tanzer, A.9
Diekhans, M.10
-
52
-
-
84920070787
-
Making proteomics data accessible and reusable: current state of proteomics databases and repositories
-
Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaino JA (2014) Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics 15(5–6):930–949
-
(2014)
Proteomics
, vol.15
, Issue.5-6
, pp. 930-949
-
-
Perez-Riverol, Y.1
Alpi, E.2
Wang, R.3
Hermjakob, H.4
Vizcaino, J.A.5
-
53
-
-
84891677425
-
Full-length RNA-seq from single cells using Smart-seq2
-
COI: 1:CAS:528:DC%2BC2cXls1ejtrc%3D, PID: 24385147
-
Picelli S, Faridani OR, Bjorklund AK, Winberg G, Sagasser S, Sandberg R (2014) Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9(1):171–181
-
(2014)
Nat Protoc
, vol.9
, Issue.1
, pp. 171-181
-
-
Picelli, S.1
Faridani, O.R.2
Bjorklund, A.K.3
Winberg, G.4
Sagasser, S.5
Sandberg, R.6
-
54
-
-
84891767394
-
RefSeq: an update on mammalian reference sequences
-
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al (2014) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res 42(Database issue):D756–763
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.Database issue
, pp. 756-763
-
-
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
-
55
-
-
84874687019
-
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
-
COI: 1:CAS:528:DC%2BC3sXjsFChs7s%3D, PID: 23452860
-
Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152(5):1173–1183
-
(2013)
Cell
, vol.152
, Issue.5
, pp. 1173-1183
-
-
Qi, L.S.1
Larson, M.H.2
Gilbert, L.A.3
Doudna, J.A.4
Weissman, J.S.5
Arkin, A.P.6
Lim, W.A.7
-
56
-
-
78049346632
-
De novo assembly and analysis of RNA-seq data
-
COI: 1:CAS:528:DC%2BC3cXht1KmsL%2FJ, PID: 20935650
-
Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ et al (2010) De novo assembly and analysis of RNA-seq data. Nat Methods 7(11):909–912
-
(2010)
Nat Methods
, vol.7
, Issue.11
, pp. 909-912
-
-
Robertson, G.1
Schein, J.2
Chiu, R.3
Corbett, R.4
Field, M.5
Jackman, S.D.6
Mungall, K.7
Lee, S.8
Okada, H.M.9
Qian, J.Q.10
-
57
-
-
84876513019
-
APPRIS: annotation of principal and alternative splice isoforms
-
Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML (2013) APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res 41(Database issue):D110–117
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.Database issue
, pp. 110-117
-
-
Rodriguez, J.M.1
Maietta, P.2
Ezkurdia, I.3
Pietrelli, A.4
Wesselink, J.J.5
Lopez, G.6
Valencia, A.7
Tress, M.L.8
-
58
-
-
84946100079
-
The UCSC Genome Browser database: 2015 update
-
Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M et al (2015) The UCSC Genome Browser database: 2015 update. Nucleic Acids Res 43(Database issue):D670–681
-
(2015)
Nucleic Acids Res
, vol.43
, Issue.Database issue
, pp. 670-681
-
-
Rosenbloom, K.R.1
Armstrong, J.2
Barber, G.P.3
Casper, J.4
Clawson, H.5
Diekhans, M.6
Dreszer, T.R.7
Fujita, P.A.8
Guruvadoo, L.9
Haeussler, M.10
-
59
-
-
84887412533
-
A single-molecule long-read survey of the human transcriptome
-
COI: 1:CAS:528:DC%2BC3sXhsFymsrzK, PID: 24108091
-
Sharon D, Tilgner H, Grubert F, Snyder M (2013) A single-molecule long-read survey of the human transcriptome. Nat Biotechnol 31(11):1009–1014
-
(2013)
Nat Biotechnol
, vol.31
, Issue.11
, pp. 1009-1014
-
-
Sharon, D.1
Tilgner, H.2
Grubert, F.3
Snyder, M.4
-
60
-
-
9144233601
-
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
-
COI: 1:CAS:528:DC%2BD2cXhtVCmsQ%3D%3D, PID: 14663149
-
Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T et al (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci USA 100(26):15776–15781
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.26
, pp. 15776-15781
-
-
Shiraki, T.1
Kondo, S.2
Katayama, S.3
Waki, K.4
Kasukawa, T.5
Kawaji, H.6
Kodzius, R.7
Watahiki, A.8
Nakamura, M.9
Arakawa, T.10
-
61
-
-
84888871954
-
Assessment of transcript reconstruction methods for RNA-seq
-
COI: 1:CAS:528:DC%2BC3sXhslWisrnE, PID: 24185837
-
Steijger T, Abril JF, Engstrom PG, Kokocinski F, Hubbard TJ, Guigo R, Harrow J, Bertone P (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 10(12):1177–1184
-
(2013)
Nat Methods
, vol.10
, Issue.12
, pp. 1177-1184
-
-
Steijger, T.1
Abril, J.F.2
Engstrom, P.G.3
Kokocinski, F.4
Hubbard, T.J.5
Guigo, R.6
Harrow, J.7
Bertone, P.8
-
62
-
-
84885940703
-
The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes
-
Steward CA, Gonzalez JM, Trevanion S, Sheppard D, Kerry G, Gilbert JG, Wicker LS, Rogers J, Harrow JL (2013) The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes. Database (Oxford) 2013:bat032
-
(2013)
Database (Oxford)
, vol.2013
, pp. 32
-
-
Steward, C.A.1
Gonzalez, J.M.2
Trevanion, S.3
Sheppard, D.4
Kerry, G.5
Gilbert, J.G.6
Wicker, L.S.7
Rogers, J.8
Harrow, J.L.9
-
63
-
-
80555139654
-
CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks
-
COI: 1:CAS:528:DC%2BC38Xht1Ogur%2FL, PID: 21938627
-
Takahashi H, Kato S, Murata M, Carninci P (2012) CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks. Methods Mol Biol 786:181–200
-
(2012)
Methods Mol Biol
, vol.786
, pp. 181-200
-
-
Takahashi, H.1
Kato, S.2
Murata, M.3
Carninci, P.4
-
64
-
-
84904735424
-
Transcriptional regulatory functions of nuclear long noncoding RNAs
-
COI: 1:CAS:528:DC%2BC2cXhtVKhurfI, PID: 24974018
-
Vance KW, Ponting CP (2014) Transcriptional regulatory functions of nuclear long noncoding RNAs. Trends Genet 30(8):348–355
-
(2014)
Trends Genet
, vol.30
, Issue.8
, pp. 348-355
-
-
Vance, K.W.1
Ponting, C.P.2
-
65
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
COI: 1:CAS:528:DC%2BD1cXhsVegtbfL, PID: 18978772
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456(7221):470–476
-
(2008)
Nature
, vol.456
, Issue.7221
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
Mayr, C.6
Kingsmore, S.F.7
Schroth, G.P.8
Burge, C.B.9
-
66
-
-
57749195712
-
RNA-Seq: a revolutionary tool for transcriptomics
-
COI: 1:CAS:528:DC%2BD1cXhsFWis7bL, PID: 19015660
-
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63
-
(2009)
Nat Rev Genet
, vol.10
, Issue.1
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
67
-
-
84877707375
-
One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering
-
COI: 1:CAS:528:DC%2BC3sXmvF2nt7w%3D, PID: 23643243
-
Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R (2013) One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153(4):910–918
-
(2013)
Cell
, vol.153
, Issue.4
, pp. 910-918
-
-
Wang, H.1
Yang, H.2
Shivalila, C.S.3
Dawlaty, M.M.4
Cheng, A.W.5
Zhang, F.6
Jaenisch, R.7
-
68
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
COI: 1:CAS:528:DC%2BD38Xpt1WhsLw%3D, PID: 12466850
-
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915):520–562
-
(2002)
Nature
, vol.420
, Issue.6915
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
Rogers, J.4
Abril, J.F.5
Agarwal, P.6
Agarwala, R.7
Ainscough, R.8
Alexandersson, M.9
An, P.10
-
69
-
-
84901611036
-
Mass-spectrometry-based draft of the human proteome
-
COI: 1:CAS:528:DC%2BC2cXoslCrt7k%3D, PID: 24870543
-
Wilhelm M, Schlegl J, Hahne H, Moghaddas Gholami A, Lieberenz M, Savitski MM, Ziegler E, Butzmann L, Gessulat S, Marx H et al (2014) Mass-spectrometry-based draft of the human proteome. Nature 509(7502):582–587
-
(2014)
Nature
, vol.509
, Issue.7502
, pp. 582-587
-
-
Wilhelm, M.1
Schlegl, J.2
Hahne, H.3
Moghaddas Gholami, A.4
Lieberenz, M.5
Savitski, M.M.6
Ziegler, E.7
Butzmann, L.8
Gessulat, S.9
Marx, H.10
-
70
-
-
80052851948
-
Sequence-based characterization of structural variation in the mouse genome
-
COI: 1:CAS:528:DC%2BC3MXhtFOls7%2FP, PID: 21921916
-
Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, Nellaker C, Goodstadt L, Nicod J, Bhomra A et al (2011) Sequence-based characterization of structural variation in the mouse genome. Nature 477(7364):326–329
-
(2011)
Nature
, vol.477
, Issue.7364
, pp. 326-329
-
-
Yalcin, B.1
Wong, K.2
Agam, A.3
Goodson, M.4
Keane, T.M.5
Gan, X.6
Nellaker, C.7
Goodstadt, L.8
Nicod, J.9
Bhomra, A.10
-
71
-
-
84867337106
-
Next-generation sequencing of experimental mouse strains
-
COI: 1:CAS:528:DC%2BC38XhsVKrtrfO, PID: 22772437
-
Yalcin B, Adams DJ, Flint J, Keane TM (2012) Next-generation sequencing of experimental mouse strains. Mamm Genome 23(9–10):490–498
-
(2012)
Mamm Genome
, vol.23
, Issue.9-10
, pp. 490-498
-
-
Yalcin, B.1
Adams, D.J.2
Flint, J.3
Keane, T.M.4
-
72
-
-
84873387934
-
The revolution and evolution of shotgun proteomics for large-scale proteome analysis
-
COI: 1:CAS:528:DC%2BC3sXktFWhtQ%3D%3D, PID: 23294060
-
Yates JR 3rd (2013) The revolution and evolution of shotgun proteomics for large-scale proteome analysis. J Am Chem Soc 135(5):1629–1640
-
(2013)
J Am Chem Soc
, vol.135
, Issue.5
, pp. 1629-1640
-
-
Yates, J.R.1
-
73
-
-
33745614319
-
PseudoPipe: an automated pseudogene identification pipeline
-
COI: 1:CAS:528:DC%2BD28XmsVensLs%3D, PID: 16574694
-
Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M (2006) PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics 22(12):1437–1439
-
(2006)
Bioinformatics
, vol.22
, Issue.12
, pp. 1437-1439
-
-
Zhang, Z.1
Carriero, N.2
Zheng, D.3
Karro, J.4
Harrison, P.M.5
Gerstein, M.6
|