• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4835299)   Today's Articles (33)
For: Li H. Toward better understanding of artifacts in variant calling from high-coverage samples. ACTA ACUST UNITED AC 2014;30:2843-51. [PMID: 24974202 DOI: 10.1093/bioinformatics/btu356] [Citation(s) in RCA: 576] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Number Cited by Other Article(s)
151
Vrbová E, Noda AA, Grillová L, Rodríguez I, Forsyth A, Oppelt J, Šmajs D. Whole genome sequences of Treponema pallidum subsp. endemicum isolated from Cuban patients: The non-clonal character of isolates suggests a persistent human infection rather than a single outbreak. PLoS Negl Trop Dis 2022;16:e0009900. [PMID: 35687593 PMCID: PMC9223347 DOI: 10.1371/journal.pntd.0009900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/23/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022]  Open
152
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics. Nat Methods 2022;19:635-638. [PMID: 35689027 DOI: 10.1038/s41592-022-01512-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
153
Dong W, Wong KHY, Liu Y, Levy-Sakin M, Hung WC, Li M, Li B, Jin SC, Choi J, Lopez-Giraldez F, Vaka D, Poon A, Chu C, Lao R, Balamir M, Movsesyan I, Malloy MJ, Zhao H, Kwok PY, Kane JP, Lifton RP, Pullinger CR. Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia. J Lipid Res 2022;63:100209. [PMID: 35460704 PMCID: PMC9126845 DOI: 10.1016/j.jlr.2022.100209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/02/2022]  Open
154
Feng YCA, Stanaway IB, Connolly JJ, Denny JC, Luo Y, Weng C, Wei WQ, Weiss ST, Karlson EW, Smoller JW. Psychiatric manifestations of rare variation in medically actionable genes: a PheWAS approach. BMC Genomics 2022;23:385. [PMID: 35590255 PMCID: PMC9121574 DOI: 10.1186/s12864-022-08600-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 04/22/2022] [Indexed: 11/10/2022]  Open
155
Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability. Nat Commun 2022;13:2532. [PMID: 35534486 PMCID: PMC9085767 DOI: 10.1038/s41467-022-30208-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 04/21/2022] [Indexed: 12/03/2022]  Open
156
Computational analysis of cancer genome sequencing data. Nat Rev Genet 2022;23:298-314. [PMID: 34880424 DOI: 10.1038/s41576-021-00431-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 02/07/2023]
157
Estimating bonobo (Pan paniscus) and chimpanzee (Pan troglodytes) evolutionary history from nucleotide site patterns. Proc Natl Acad Sci U S A 2022;119:e2200858119. [PMID: 35452306 PMCID: PMC9170072 DOI: 10.1073/pnas.2200858119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
158
Ng AWT, Contino G, Killcoyne S, Devonshire G, Hsu R, Abbas S, Su J, Redmond AM, Weaver JMJ, Eldridge MD, Tavaré S, Edwards PAW, Fitzgerald RC. Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas. Commun Biol 2022;5:335. [PMID: 35396535 PMCID: PMC8993906 DOI: 10.1038/s42003-022-03238-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/25/2022] [Indexed: 11/26/2022]  Open
159
Jiang Y, Hu X, Yuan Y, Guo X, Chase MW, Ge S, Li J, Fu J, Li K, Hao M, Wang Y, Jiao Y, Jiang W, Jin X. The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions. BMC PLANT BIOLOGY 2022;22:179. [PMID: 35392808 PMCID: PMC8988336 DOI: 10.1186/s12870-022-03573-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/01/2022] [Indexed: 06/01/2023]
160
Noyes MD, Harvey WT, Porubsky D, Sulovari A, Li R, Rose NR, Audano PA, Munson KM, Lewis AP, Hoekzema K, Mantere T, Graves-Lindsay TA, Sanders AD, Goodwin S, Kramer M, Mokrab Y, Zody MC, Hoischen A, Korbel JO, McCombie WR, Eichler EE. Familial long-read sequencing increases yield of de novo mutations. Am J Hum Genet 2022;109:631-646. [PMID: 35290762 PMCID: PMC9069071 DOI: 10.1016/j.ajhg.2022.02.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/16/2022] [Indexed: 12/11/2022]  Open
161
An Amish founder population reveals rare-population genetic determinants of the human lipidome. Commun Biol 2022;5:334. [PMID: 35393526 PMCID: PMC8989972 DOI: 10.1038/s42003-022-03291-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 03/17/2022] [Indexed: 12/02/2022]  Open
162
Yi X, Liu J, Chen S, Wu H, Liu M, Xu Q, Lei L, Lee S, Zhang B, Kudrna D, Fan W, Wing RA, Wang X, Zhang M, Zhang J, Yang C, Chen N. Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics. G3 (BETHESDA, MD.) 2022;12:jkac017. [PMID: 35188189 PMCID: PMC8982393 DOI: 10.1093/g3journal/jkac017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/11/2022] [Indexed: 12/30/2022]
163
Ozerov M, Noreikiene K, Kahar S, Huss M, Huusko A, Kõiv T, Sepp M, López M, Gårdmark A, Gross R, Vasemägi A. Whole-genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch. Mol Ecol 2022;31:2367-2383. [PMID: 35202502 PMCID: PMC9314028 DOI: 10.1111/mec.16409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/10/2022] [Accepted: 02/17/2022] [Indexed: 11/30/2022]
164
Marin M, Vargas R, Harris M, Jeffrey B, Epperson LE, Durbin D, Strong M, Salfinger M, Iqbal Z, Akhundova I, Vashakidze S, Crudu V, Rosenthal A, Farhat MR. Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome. Bioinformatics 2022;38:1781-1787. [PMID: 35020793 PMCID: PMC8963317 DOI: 10.1093/bioinformatics/btac023] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 02/04/2023]  Open
165
Giacopuzzi E, Popitsch N, Taylor JC. GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data. Nucleic Acids Res 2022;50:2522-2535. [PMID: 35234913 PMCID: PMC8934622 DOI: 10.1093/nar/gkac130] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 11/25/2022]  Open
166
Niu Y, Teng X, Zhou H, Shi Y, Li Y, Tang Y, Zhang P, Luo H, Kang Q, Xu T, He S. Characterizing mobile element insertions in 5675 genomes. Nucleic Acids Res 2022;50:2493-2508. [PMID: 35212372 PMCID: PMC8934628 DOI: 10.1093/nar/gkac128] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/07/2022] [Accepted: 02/11/2022] [Indexed: 12/30/2022]  Open
167
Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations. BMC Genomics 2022;23:193. [PMID: 35264116 PMCID: PMC8908679 DOI: 10.1186/s12864-022-08418-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/24/2022] [Indexed: 12/29/2022]  Open
168
Futas J, Oppelt J, Vychodilova L, Burger P, Horin P. The deadly face of felid killer cells: the cytotoxic proteins and their genes. HLA 2022;100:37-51. [PMID: 35263044 DOI: 10.1111/tan.14595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/08/2022] [Accepted: 03/03/2022] [Indexed: 11/29/2022]
169
Sandoval-Castillo J, Beheregaray LB, Wellenreuther M. Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus). G3 (BETHESDA, MD.) 2022;12:jkac015. [PMID: 35100370 PMCID: PMC8896003 DOI: 10.1093/g3journal/jkac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
170
Genome-wide scan for selection signatures and genes related to heat tolerance in domestic chickens in the tropical and temperate regions in Asia. Poult Sci 2022;101:101821. [PMID: 35537342 PMCID: PMC9118144 DOI: 10.1016/j.psj.2022.101821] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 11/24/2022]  Open
171
Couvin D, Dereeper A, Meyer DF, Noroy C, Gaete S, Bhakkan B, Poullet N, Gaspard S, Bezault E, Marcelino I, Pruneau L, Segretier W, Stattner E, Cazenave D, Garnier M, Pot M, Tressières B, Deloumeaux J, Breurec S, Ferdinand S, Gonzalez-Rizzo S, Reynaud Y. KaruBioNet: a network and discussion group for a better collaboration and structuring of bioinformatics in Guadeloupe (French West Indies). BIOINFORMATICS ADVANCES 2022;2:vbac010. [PMID: 36699379 PMCID: PMC9710593 DOI: 10.1093/bioadv/vbac010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 01/28/2023]
172
Yamaguchi M, Nakaoka H, Suda K, Yoshihara K, Ishiguro T, Yachida N, Saito K, Ueda H, Sugino K, Mori Y, Yamawaki K, Tamura R, Revathidevi S, Motoyama T, Tainaka K, Verhaak RGW, Inoue I, Enomoto T. Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium. Nat Commun 2022;13:943. [PMID: 35177608 PMCID: PMC8854701 DOI: 10.1038/s41467-022-28568-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 02/02/2022] [Indexed: 12/15/2022]  Open
173
Handayani ND, Lestari P, van As W, Holterman M, van den Elsen S, Dikin A, Bert W, Helder J, Van Steenbrugge JJM. Genomic Reconstruction of the Introduction and Diversification of Golden Potato Cyst Nematode Populations in Indonesia. PHYTOPATHOLOGY 2022;112:396-403. [PMID: 34129357 DOI: 10.1094/phyto-04-21-0150-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
174
Uranga C, Nelson KE, Edlund A, Baker JL. Tetramic Acids Mutanocyclin and Reutericyclin A, Produced by Streptococcus mutans Strain B04Sm5 Modulate the Ecology of an in vitro Oral Biofilm. FRONTIERS IN ORAL HEALTH 2022;2:796140. [PMID: 35048077 PMCID: PMC8757879 DOI: 10.3389/froh.2021.796140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/29/2021] [Indexed: 01/04/2023]  Open
175
De Angelis F, Romboni M, Veltre V, Catalano P, Martínez-Labarga C, Gazzaniga V, Rickards O. First Glimpse into the Genomic Characterization of People from the Imperial Roman Community of Casal Bertone (Rome, First–Third Centuries AD). Genes (Basel) 2022;13:genes13010136. [PMID: 35052476 PMCID: PMC8774527 DOI: 10.3390/genes13010136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 02/01/2023]  Open
176
Bergeron LA, Besenbacher S, Turner T, Versoza CJ, Wang RJ, Price AL, Armstrong E, Riera M, Carlson J, Chen HY, Hahn MW, Harris K, Kleppe AS, López-Nandam EH, Moorjani P, Pfeifer SP, Tiley GP, Yoder AD, Zhang G, Schierup MH. The mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates. eLife 2022;11:73577. [PMID: 35018888 PMCID: PMC8830884 DOI: 10.7554/elife.73577] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022]  Open
177
Adams PE, Crist AB, Young EM, Willis JH, Phillips PC, Fierst JL. Slow Recovery from Inbreeding Depression Generated by the Complex Genetic Architecture of Segregating Deleterious Mutations. Mol Biol Evol 2022;39:msab330. [PMID: 34791426 PMCID: PMC8789292 DOI: 10.1093/molbev/msab330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
178
Pan B, Ren L, Onuchic V, Guan M, Kusko R, Bruinsma S, Trigg L, Scherer A, Ning B, Zhang C, Glidewell-Kenney C, Xiao C, Donaldson E, Sedlazeck FJ, Schroth G, Yavas G, Grunenwald H, Chen H, Meinholz H, Meehan J, Wang J, Yang J, Foox J, Shang J, Miclaus K, Dong L, Shi L, Mohiyuddin M, Pirooznia M, Gong P, Golshani R, Wolfinger R, Lababidi S, Sahraeian SME, Sherry S, Han T, Chen T, Shi T, Hou W, Ge W, Zou W, Guo W, Bao W, Xiao W, Fan X, Gondo Y, Yu Y, Zhao Y, Su Z, Liu Z, Tong W, Xiao W, Zook JM, Zheng Y, Hong H. Assessing reproducibility of inherited variants detected with short-read whole genome sequencing. Genome Biol 2022;23:2. [PMID: 34980216 PMCID: PMC8722114 DOI: 10.1186/s13059-021-02569-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/06/2021] [Indexed: 12/15/2022]  Open
179
Chang TC, Xu K, Cheng Z, Wu G. Somatic and Germline Variant Calling from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022;1361:37-54. [DOI: 10.1007/978-3-030-91836-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
180
Wang MS, Thakur M, Jhala Y, Wang S, Srinivas Y, Dai SS, Liu ZX, Chen HM, Green RE, Koepfli KP, Shapiro B. OUP accepted manuscript. Genome Biol Evol 2022;14:6524629. [PMID: 35137061 PMCID: PMC8841465 DOI: 10.1093/gbe/evac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2022] [Indexed: 11/14/2022]  Open
181
Host Lung Environment Limits Aspergillus fumigatus Germination through an SskA-Dependent Signaling Response. mSphere 2021;6:e0092221. [PMID: 34878292 PMCID: PMC8653827 DOI: 10.1128/msphere.00922-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
182
Çelik G, Tuncalı T. ROHMM-A flexible hidden Markov model framework to detect runs of homozygosity from genotyping data. Hum Mutat 2021;43:158-168. [PMID: 34923717 DOI: 10.1002/humu.24316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/29/2021] [Accepted: 12/15/2021] [Indexed: 11/05/2022]
183
Lin LH, Chou CH, Cheng HW, Chang KW, Liu CJ. Precise Identification of Recurrent Somatic Mutations in Oral Cancer Through Whole-Exome Sequencing Using Multiple Mutation Calling Pipelines. Front Oncol 2021;11:741626. [PMID: 34912705 PMCID: PMC8666431 DOI: 10.3389/fonc.2021.741626] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/11/2021] [Indexed: 01/18/2023]  Open
184
Zhao YW, Pan HX, Liu Z, Wang Y, Zeng Q, Fang ZH, Luo TF, Xu K, Wang Z, Zhou X, He R, Li B, Zhao G, Xu Q, Sun QY, Yan XX, Tan JQ, Li JC, Guo JF, Tang BS. The Association Between Lysosomal Storage Disorder Genes and Parkinson's Disease: A Large Cohort Study in Chinese Mainland Population. Front Aging Neurosci 2021;13:749109. [PMID: 34867278 PMCID: PMC8634711 DOI: 10.3389/fnagi.2021.749109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/29/2021] [Indexed: 12/20/2022]  Open
185
Montasser ME, Van Hout CV, Miloscio L, Howard AD, Rosenberg A, Callaway M, Shen B, Li N, Locke AE, Verweij N, De T, Ferreira MA, Lotta LA, Baras A, Daly TJ, Hartford SA, Lin W, Mao Y, Ye B, White D, Gong G, Perry JA, Ryan KA, Fang Q, Tzoneva G, Pefanis E, Hunt C, Tang Y, Lee L, Sztalryd-Woodle C, Mitchell BD, Healy M, Streeten EA, Taylor SI, O'Connell JR, Economides AN, Della Gatta G, Shuldiner AR. Genetic and functional evidence links a missense variant in B4GALT1 to lower LDL and fibrinogen. Science 2021;374:1221-1227. [PMID: 34855475 DOI: 10.1126/science.abe0348] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
186
Zhang Z, Bai H, Blumenfeld J, Ramnauth AB, Barash I, Prince M, Tan AY, Michaeel A, Liu G, Chicos I, Rennert L, Giannakopoulos S, Larbi K, Hughes S, Salvatore SP, Robinson BD, Kapur S, Rennert H. Detection of PKD1 and PKD2 Somatic Variants in Autosomal Dominant Polycystic Kidney Cyst Epithelial Cells by Whole-Genome Sequencing. J Am Soc Nephrol 2021;32:3114-3129. [PMID: 34716216 PMCID: PMC8638386 DOI: 10.1681/asn.2021050690] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/03/2021] [Indexed: 02/04/2023]  Open
187
Tellaetxe-Abete M, Calvo B, Lawrie C. Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data. NAR Genom Bioinform 2021;3:lqab092. [PMID: 34729472 PMCID: PMC8557387 DOI: 10.1093/nargab/lqab092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 09/14/2021] [Accepted: 09/29/2021] [Indexed: 12/16/2022]  Open
188
Mercier A, Simon A, Lapalu N, Giraud T, Bardin M, Walker AS, Viaud M, Gladieux P. Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal Pathogen Botrytis cinerea in France. PHYTOPATHOLOGY 2021;111:2355-2366. [PMID: 33829853 DOI: 10.1094/phyto-07-20-0302-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
189
Kreiner JM, Caballero A, Wright SI, Stinchcombe JR. Selective ancestral sorting and de novo evolution in the agricultural invasion of Amaranthus tuberculatus. Evolution 2021;76:70-85. [PMID: 34806764 DOI: 10.1111/evo.14404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/12/2021] [Accepted: 10/24/2021] [Indexed: 12/16/2022]
190
Peng MS, Li JB, Cai ZF, Liu H, Tang X, Ying R, Zhang JN, Tao JJ, Yin TT, Zhang T, Hu JY, Wu RN, Zhou ZY, Zhang ZG, Yu L, Yao YG, Shi ZL, Lu XM, Lu J, Zhang YP. The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks. Zool Res 2021;42:834-844. [PMID: 34766482 PMCID: PMC8645874 DOI: 10.24272/j.issn.2095-8137.2021.334] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 11/07/2022]  Open
191
Yang Y, Li S, Xing Y, Zhang Z, Liu T, Ao W, Bao G, Zhan Z, Zhao R, Zhang T, Zhang D, Song Y, Bian C, Xu L, Kang T. The first high-quality chromosomal genome assembly of a medicinal and edible plant Arctium lappa. Mol Ecol Resour 2021;22:1493-1507. [PMID: 34758188 DOI: 10.1111/1755-0998.13547] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 08/11/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022]
192
Little P, Jo H, Hoyle A, Mazul A, Zhao X, Salazar AH, Farquhar D, Sheth S, Masood M, Hayward MC, Parker JS, Hoadley KA, Zevallos J, Hayes DN. UNMASC: tumor-only variant calling with unmatched normal controls. NAR Cancer 2021;3:zcab040. [PMID: 34632388 PMCID: PMC8494212 DOI: 10.1093/narcan/zcab040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/07/2021] [Accepted: 10/04/2021] [Indexed: 12/11/2022]  Open
193
Wang M, Lee-Kim VS, Atri DS, Elowe NH, Yu J, Garvie CW, Won HH, Hadaya JE, MacDonald BT, Trindade K, Melander O, Rader DJ, Natarajan P, Kathiresan S, Kaushik VK, Khera AV, Gupta RM. Rare, Damaging DNA Variants in CORIN and Risk of Coronary Artery Disease: Insights From Functional Genomics and Large-Scale Sequencing Analyses. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021;14:e003399. [PMID: 34592835 DOI: 10.1161/circgen.121.003399] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
194
Biswas P, Villanueva AL, Soto-Hermida A, Duncan JL, Matsui H, Borooah S, Kurmanov B, Richard G, Khan SY, Branham K, Huang B, Suk J, Bakall B, Goldberg JL, Gabriel L, Khan NW, Raghavendra PB, Zhou J, Devalaraja S, Huynh A, Alapati A, Zawaydeh Q, Weleber RG, Heckenlively JR, Hejtmancik JF, Riazuddin S, Sieving PA, Riazuddin SA, Frazer KA, Ayyagari R. Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis. PLoS Genet 2021;17:e1009848. [PMID: 34662339 PMCID: PMC8589175 DOI: 10.1371/journal.pgen.1009848] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 11/12/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022]  Open
195
Mahadevaiah C, Appunu C, Aitken K, Suresha GS, Vignesh P, Mahadeva Swamy HK, Valarmathi R, Hemaprabha G, Alagarasan G, Ram B. Genomic Selection in Sugarcane: Current Status and Future Prospects. FRONTIERS IN PLANT SCIENCE 2021;12:708233. [PMID: 34646284 PMCID: PMC8502939 DOI: 10.3389/fpls.2021.708233] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/24/2021] [Indexed: 05/18/2023]
196
Ferré Q, Chèneby J, Puthier D, Capponi C, Ballester B. Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders. BMC Bioinformatics 2021;22:460. [PMID: 34563116 PMCID: PMC8467021 DOI: 10.1186/s12859-021-04359-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 06/04/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022]  Open
197
Boso G, Lam O, Bamunusinghe D, Oler AJ, Wollenberg K, Liu Q, Shaffer E, Kozak CA. Patterns of Coevolutionary Adaptations across Time and Space in Mouse Gammaretroviruses and Three Restrictive Host Factors. Viruses 2021;13:v13091864. [PMID: 34578445 PMCID: PMC8472935 DOI: 10.3390/v13091864] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/04/2021] [Accepted: 09/15/2021] [Indexed: 10/26/2022]  Open
198
Liu S, Westbury MV, Dussex N, Mitchell KJ, Sinding MHS, Heintzman PD, Duchêne DA, Kapp JD, von Seth J, Heiniger H, Sánchez-Barreiro F, Margaryan A, André-Olsen R, De Cahsan B, Meng G, Yang C, Chen L, van der Valk T, Moodley Y, Rookmaaker K, Bruford MW, Ryder O, Steiner C, Bruins-van Sonsbeek LGR, Vartanyan S, Guo C, Cooper A, Kosintsev P, Kirillova I, Lister AM, Marques-Bonet T, Gopalakrishnan S, Dunn RR, Lorenzen ED, Shapiro B, Zhang G, Antoine PO, Dalén L, Gilbert MTP. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell 2021;184:4874-4885.e16. [PMID: 34433011 DOI: 10.1016/j.cell.2021.07.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/16/2021] [Accepted: 07/23/2021] [Indexed: 12/27/2022]
199
Taylor RS, Manseau M, Klütsch CFC, Polfus JL, Steedman A, Hervieux D, Kelly A, Larter NC, Gamberg M, Schwantje H, Wilson PJ. Population dynamics of caribou shaped by glacial cycles before the last glacial maximum. Mol Ecol 2021;30:6121-6143. [PMID: 34482596 PMCID: PMC9293238 DOI: 10.1111/mec.16166] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/04/2022]
200
Morales-Cruz A, Aguirre-Liguori JA, Zhou Y, Minio A, Riaz S, Walker AM, Cantu D, Gaut BS. Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation. Genome Biol 2021;22:254. [PMID: 34479604 PMCID: PMC8414701 DOI: 10.1186/s13059-021-02467-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/12/2021] [Indexed: 01/27/2023]  Open
PrevPage 4 of 12 123451112Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA