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For: Weber JL, Myers EW. Human whole-genome shotgun sequencing. Genome Res 1997;7:401-9. [PMID: 9149936 DOI: 10.1101/gr.7.5.401] [Citation(s) in RCA: 150] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Number Cited by Other Article(s)
1
Tanade C, Khan NS, Rakestraw E, Ladd WD, Draeger EW, Randles A. Establishing the longitudinal hemodynamic mapping framework for wearable-driven coronary digital twins. NPJ Digit Med 2024;7:236. [PMID: 39242829 PMCID: PMC11379815 DOI: 10.1038/s41746-024-01216-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 08/05/2024] [Indexed: 09/09/2024]  Open
2
Hadar N, Dolgin V, Oustinov K, Yogev Y, Poleg T, Safran A, Freund O, Agam N, Jean MM, Proskorovski-Ohayon R, Wormser O, Drabkin M, Halperin D, Eskin-Schwartz M, Narkis G, Sued-Hendrickson S, Aminov I, Gombosh M, Aharoni S, Birk OS. VARista: a free web platform for streamlined whole-genome variant analysis across T2T, hg38, and hg19. Hum Genet 2024;143:695-701. [PMID: 38607411 DOI: 10.1007/s00439-024-02671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/24/2024] [Indexed: 04/13/2024]
3
Morishita S. A whole-genome shotgun approach to human reference genome sequencing. Nat Rev Genet 2024;25:236. [PMID: 38307946 DOI: 10.1038/s41576-024-00703-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
4
Venkadesh S, Santarelli A, Boesen T, Dong HW, Ascoli GA. Combinatorial quantification of distinct neural projections from retrograde tracing. Nat Commun 2023;14:7271. [PMID: 37949860 PMCID: PMC10638408 DOI: 10.1038/s41467-023-43124-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]  Open
5
Tanade C, Rakestraw E, Ladd W, Draeger E, Randles A. Cloud Computing to Enable Wearable-Driven Longitudinal Hemodynamic Maps. INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS : [PROCEEDINGS]. SC (CONFERENCE : SUPERCOMPUTING) 2023;2023:82. [PMID: 38939612 PMCID: PMC11210499 DOI: 10.1145/3581784.3607101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
6
Han X, Guo S, Ji N, Li T, Liu J, Ye X, Wang Y, Yun Z, Xiong F, Rong J, Liu D, Ma H, Wang Y, Huang Y, Zhang P, Wu W, Ding L, Hawrylycz M, Lein E, Ascoli GA, Xie W, Liu L, Zhang L, Peng H. Whole human-brain mapping of single cortical neurons for profiling morphological diversity and stereotypy. SCIENCE ADVANCES 2023;9:eadf3771. [PMID: 37824619 PMCID: PMC10569712 DOI: 10.1126/sciadv.adf3771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/18/2023] [Indexed: 10/14/2023]
7
LeBlanc P, Ma L. Microbiome subcommunity learning with logistic-tree normal latent Dirichlet allocation. Biometrics 2023;79:2321-2332. [PMID: 36222326 PMCID: PMC10090221 DOI: 10.1111/biom.13772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 09/26/2022] [Indexed: 11/28/2022]
8
Schiml VC, Delogu F, Kumar P, Kunath B, Batut B, Mehta S, Johnson JE, Grüning B, Pope PB, Jagtap PD, Griffin TJ, Arntzen MØ. Integrative meta-omics in Galaxy and beyond. ENVIRONMENTAL MICROBIOME 2023;18:56. [PMID: 37420292 PMCID: PMC10329324 DOI: 10.1186/s40793-023-00514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/05/2023] [Indexed: 07/09/2023]
9
Hadar N, Narkis G, Amar S, Varnavsky M, Palti GC, Safran A, Birk OS. STRavinsky STR database and PGTailor PGT tool demonstrate superiority of CHM13-T2T over hg38 and hg19 for STR-based applications. Eur J Hum Genet 2023;31:738-743. [PMID: 37055538 PMCID: PMC10325972 DOI: 10.1038/s41431-023-01352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 04/15/2023]  Open
10
Camilli A. De Novo Genome Sequencing, Annotation, and Taxonomy of Unknown Bacteria. Cold Spring Harb Protoc 2023;2023:1-3. [PMID: 36283838 PMCID: PMC10586727 DOI: 10.1101/pdb.top107847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
11
Church DM. A next-generation human genome sequence. Science 2022;376:34-35. [PMID: 35357937 DOI: 10.1126/science.abo5367] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
12
The Vista of Application of Specific Anaphylaxis Accurate Diagnosis Based on DNA Single-Nucleotide Methylation Sites. CONTRAST MEDIA & MOLECULAR IMAGING 2021;2021:8202068. [PMID: 34908915 PMCID: PMC8635942 DOI: 10.1155/2021/8202068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/21/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
13
Rahman A, Pachter L. SWALO: scaffolding with assembly likelihood optimization. Nucleic Acids Res 2021;49:e117. [PMID: 34417615 PMCID: PMC8599790 DOI: 10.1093/nar/gkab717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/16/2021] [Accepted: 08/16/2021] [Indexed: 01/01/2023]  Open
14
Berger B, Waterman MS, Yu YW. Levenshtein Distance, Sequence Comparison and Biological Database Search. IEEE TRANSACTIONS ON INFORMATION THEORY 2021;67:3287-3294. [PMID: 34257466 PMCID: PMC8274556 DOI: 10.1109/tit.2020.2996543] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
15
Gómez-Muñoz C, García-Ortega LF, Montalvo-Arredondo J, Pérez-Ortega E, Damas-Buenrostro LC, Riego-Ruiz L. Long insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast. G3-GENES GENOMES GENETICS 2021;11:6188626. [PMID: 33768233 PMCID: PMC8495930 DOI: 10.1093/g3journal/jkab088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/12/2021] [Indexed: 11/18/2022]
16
Biological computation and computational biology: survey, challenges, and discussion. Artif Intell Rev 2021. [DOI: 10.1007/s10462-020-09951-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
17
Nakabayashi R, Morishita S. HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C. Bioinformatics 2020;36:3966-3974. [PMID: 32369554 PMCID: PMC7672694 DOI: 10.1093/bioinformatics/btaa288] [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: 11/09/2019] [Revised: 03/09/2020] [Accepted: 04/27/2020] [Indexed: 01/18/2023]  Open
18
Hao M, Qiao H, Gao Y, Wang Z, Qiao X, Chen X, Qi H. A mixed culture of bacterial cells enables an economic DNA storage on a large scale. Commun Biol 2020;3:416. [PMID: 32737399 PMCID: PMC7395121 DOI: 10.1038/s42003-020-01141-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/02/2020] [Indexed: 11/25/2022]  Open
19
Giani AM, Gallo GR, Gianfranceschi L, Formenti G. Long walk to genomics: History and current approaches to genome sequencing and assembly. Comput Struct Biotechnol J 2019;18:9-19. [PMID: 31890139 PMCID: PMC6926122 DOI: 10.1016/j.csbj.2019.11.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/03/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022]  Open
20
Andonov R, Djidjev H, François S, Lavenier D. Complete assembly of circular and chloroplast genomes based on global optimization. J Bioinform Comput Biol 2019;17:1950014. [PMID: 31288643 DOI: 10.1142/s0219720019500148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
21
Characterization and evolutionary dynamics of complex regions in eukaryotic genomes. SCIENCE CHINA-LIFE SCIENCES 2019;62:467-488. [PMID: 30810961 DOI: 10.1007/s11427-018-9458-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/05/2018] [Indexed: 01/07/2023]
22
Li W, Freudenberg J, Freudenberg J. Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome. Gene 2019;691:141-152. [PMID: 30630097 DOI: 10.1016/j.gene.2018.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/14/2018] [Indexed: 10/27/2022]
23
Maxson Jones K, Ankeny RA, Cook-Deegan R. The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project. JOURNAL OF THE HISTORY OF BIOLOGY 2018;51:693-805. [PMID: 30390178 PMCID: PMC7307446 DOI: 10.1007/s10739-018-9538-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
24
Harrison OB, Schoen C, Retchless AC, Wang X, Jolley KA, Bray JE, Maiden MCJ. Neisseria genomics: current status and future perspectives. Pathog Dis 2018;75:3861976. [PMID: 28591853 PMCID: PMC5827584 DOI: 10.1093/femspd/ftx060] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/05/2017] [Indexed: 12/17/2022]  Open
25
Silva PJ, Schaibley VM, Ramos KS. Academic medical centers as innovation ecosystems to address population -omics challenges in precision medicine. J Transl Med 2018;16:28. [PMID: 29448963 PMCID: PMC5815198 DOI: 10.1186/s12967-018-1401-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/05/2018] [Indexed: 01/08/2023]  Open
26
Markowetz F. All biology is computational biology. PLoS Biol 2017;15:e2002050. [PMID: 28278152 PMCID: PMC5344307 DOI: 10.1371/journal.pbio.2002050] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
27
Huang J, Zhang C, Zhao X, Fei Z, Wan K, Zhang Z, Pang X, Yin X, Bai Y, Sun X, Gao L, Li R, Zhang J, Li X. The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit Trees. PLoS Genet 2016;12:e1006433. [PMID: 28005948 PMCID: PMC5179053 DOI: 10.1371/journal.pgen.1006433] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/20/2016] [Indexed: 12/26/2022]  Open
28
Carvalho AB, Dupim EG, Goldstein G. Improved assembly of noisy long reads by k-mer validation. Genome Res 2016;26:1710-1720. [PMID: 27831497 PMCID: PMC5131822 DOI: 10.1101/gr.209247.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 09/29/2016] [Indexed: 11/24/2022]
29
Making sense of genomes of parasitic worms: Tackling bioinformatic challenges. Biotechnol Adv 2016;34:663-686. [DOI: 10.1016/j.biotechadv.2016.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/25/2016] [Accepted: 03/01/2016] [Indexed: 01/25/2023]
30
Beier S, Himmelbach A, Schmutzer T, Felder M, Taudien S, Mayer KFX, Platzer M, Stein N, Scholz U, Mascher M. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes. PLANT BIOTECHNOLOGY JOURNAL 2016;14:1511-22. [PMID: 26801048 PMCID: PMC5066668 DOI: 10.1111/pbi.12511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 05/02/2023]
31
Bermudez-Santana CI. APLICACIONES DE LA BIOINFORMÁTICA EN LA MEDICINA: EL GENOMA HUMANO. ¿CÓMO PODEMOS VER TANTO DETALLE? ACTA BIOLÓGICA COLOMBIANA 2016. [DOI: 10.15446/abc.v21n1supl.51233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
32
Chaisson MJP, Wilson RK, Eichler EE. Genetic variation and the de novo assembly of human genomes. Nat Rev Genet 2015;16:627-40. [PMID: 26442640 DOI: 10.1038/nrg3933] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
33
Fierst JL. Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools. Front Genet 2015;6:220. [PMID: 26150829 PMCID: PMC4473057 DOI: 10.3389/fgene.2015.00220] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/08/2015] [Indexed: 01/05/2023]  Open
34
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 2015;33:623-30. [DOI: 10.1038/nbt.3238] [Citation(s) in RCA: 687] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 04/08/2015] [Indexed: 02/07/2023]
35
Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol 2015. [PMID: 25637298 DOI: 10.1186/s13059‐015‐0582‐8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
36
Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol 2015;16:26. [PMID: 25637298 PMCID: PMC4373400 DOI: 10.1186/s13059-015-0582-8] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/06/2015] [Indexed: 11/10/2022]  Open
37
Wang FQ, Zhong J, Zhao Y, Xiao J, Liu J, Dai M, Zheng G, Zhang L, Yu J, Wu J, Duan B. Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum. BMC Genomics 2014;15 Suppl 1:S11. [PMID: 24564352 PMCID: PMC4046689 DOI: 10.1186/1471-2164-15-s1-s11] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]  Open
38
Simpson JT. Exploring genome characteristics and sequence quality without a reference. ACTA ACUST UNITED AC 2014;30:1228-35. [PMID: 24443382 PMCID: PMC3998141 DOI: 10.1093/bioinformatics/btu023] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
39
Li W, Freudenberg J, Miramontes P. Diminishing return for increased Mappability with longer sequencing reads: implications of the k-mer distributions in the human genome. BMC Bioinformatics 2014;15:2. [PMID: 24386976 PMCID: PMC3927684 DOI: 10.1186/1471-2105-15-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 12/17/2013] [Indexed: 11/10/2022]  Open
40
Patel LR, Nykter M, Chen K, Zhang W. Cancer genome sequencing: understanding malignancy as a disease of the genome, its conformation, and its evolution. Cancer Lett 2013;340:152-60. [PMID: 23111104 PMCID: PMC3632661 DOI: 10.1016/j.canlet.2012.10.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 10/15/2012] [Accepted: 10/19/2012] [Indexed: 12/11/2022]
41
Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M. De novo likelihood-based measures for comparing genome assemblies. BMC Res Notes 2013;6:334. [PMID: 23965294 PMCID: PMC3765854 DOI: 10.1186/1756-0500-6-334] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/13/2013] [Indexed: 12/12/2022]  Open
42
A novel approach to estimating heterozygosity from low-coverage genome sequence. Genetics 2013;195:553-61. [PMID: 23934885 DOI: 10.1534/genetics.113.154500] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
43
BIOCOMPUTATION: Some history and prospects. Biosystems 2013;112:196-203. [DOI: 10.1016/j.biosystems.2012.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/10/2012] [Accepted: 12/13/2012] [Indexed: 11/24/2022]
44
Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Bhat PR, Wu Y, Ciardo G, Alsaihati B, Ma Y, Wanamaker S, Resnik J, Bozdag S, Luo MC, Close TJ. Combinatorial pooling enables selective sequencing of the barley gene space. PLoS Comput Biol 2013;9:e1003010. [PMID: 23592960 PMCID: PMC3617026 DOI: 10.1371/journal.pcbi.1003010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/05/2013] [Indexed: 11/23/2022]  Open
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Forde BM, O'Toole PW. Next-generation sequencing technologies and their impact on microbial genomics. Brief Funct Genomics 2013;12:440-53. [PMID: 23314033 DOI: 10.1093/bfgp/els062] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
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Wit P, Pespeni MH, Ladner JT, Barshis DJ, Seneca F, Jaris H, Therkildsen NO, Morikawa M, Palumbi SR. The simple fool's guide to population genomics via RNA ‐Seq: an introduction to high‐throughput sequencing data analysis. Mol Ecol Resour 2012;12:1058-67. [DOI: 10.1111/1755-0998.12003] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 07/16/2012] [Accepted: 07/27/2012] [Indexed: 11/30/2022]
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Fouhy F, Ross RP, Fitzgerald GF, Stanton C, Cotter PD. Composition of the early intestinal microbiota: knowledge, knowledge gaps and the use of high-throughput sequencing to address these gaps. Gut Microbes 2012;3:203-20. [PMID: 22572829 PMCID: PMC3427213 DOI: 10.4161/gmic.20169] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
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Medvedev P, Pham S, Chaisson M, Tesler G, Pevzner P. Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. J Comput Biol 2011;18:1625-34. [PMID: 21999285 DOI: 10.1089/cmb.2011.0151] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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Kim Y, Jo AR, Jang DH, Cho YJ, Chun J, Min BM, Choi Y. Toll-like receptor 9 mediates oral bacteria-induced IL-8 expression in gingival epithelial cells. Immunol Cell Biol 2011;90:655-63. [PMID: 21968713 DOI: 10.1038/icb.2011.85] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Jackson SA, Iwata A, Lee SH, Schmutz J, Shoemaker R. Sequencing crop genomes: approaches and applications. THE NEW PHYTOLOGIST 2011;191:915-925. [PMID: 21707621 DOI: 10.1111/j.1469-8137.2011.03804.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
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