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- Author:
- Guterres, Alexandro; Gonçalves, Jonathan; de Lemos, Elba Regina Sampaio
- Source:
- Research in microbiology 2019 v.170 no.1 pp. 60-64
- ISSN:
- 0923-2508
- Subject:
- sequence analysis, etc ; Bartonella; genes; phylogeny; Show all 4 Subjects
- Abstract:
- ... Bartonellosis is an emerging serious diseases of zoonotic relevance caused by an expanding number of recently discovered species of Bartonella. Many studies use partial gltA gene sequencing as the method of choice for species attribution, and a plethora of studies have utilized only this gene to describe Bartonella diversity. We observe a lack of correspondence between the phylogenies constructed ...
- DOI:
- 10.1016/j.resmic.2018.08.007
-
https://dx.doi.org/10.1016/j.resmic.2018.08.007
- Author:
- Das, Subhram; Deb, Tamal; Dey, Nilanjan; Ashour, Amira S.; Bhattacharya, D.K.; Tibarewala, D.N.
- Source:
- Genomics 2018 v.110 no.5 pp. 263-273
- ISSN:
- 0888-7543
- Subject:
- sequence analysis, etc ; genes; proteins; Show all 3 Subjects
- Abstract:
- ... Several proteins and genes are members of families that share a public evolutionary. In order to outline the evolutionary relationships and to recognize conserved patterns, sequence comparison becomes an emerging process. The current work investigates critically the k-mer role in composition vector method for comparing genome sequences. Generally, composition vector methods using k-mer are applied ...
- DOI:
- 10.1016/j.ygeno.2017.11.003
-
https://dx.doi.org/10.1016/j.ygeno.2017.11.003
- Author:
- Hill, Joseph L; Hollender, Courtney A
- Source:
- Current opinion in plant biology 2019 v.47 pp. 73-80
- ISSN:
- 1369-5266
- Subject:
- sequence analysis, etc ; gene dosage; genes; gravitropism; models; perennials; trees; Show all 7 Subjects
- Abstract:
- ... Directional growth in all plants involves both phototropic and gravitropic responses. Accordingly, mechanisms controlling shoot architecture throughout the plant kingdom are likely similar. However, as forms vary between species due in part to gene copy number and functional divergence, some aspects of how plants predetermine and regulate architecture can differ. This is especially true when compa ...
- DOI:
- 10.1016/j.pbi.2018.09.010
-
http://dx.doi.org/10.1016/j.pbi.2018.09.010
- Author:
- Danda, Gopinath; Drndić, Marija
- Source:
- Current opinion in biotechnology 2019 v.55 pp. 124-133
- ISSN:
- 0958-1669
- Subject:
- sequence analysis, etc ; desalination; engineering; graphene; mechanical properties; nanopores; Show all 6 Subjects
- Abstract:
- ... Two-dimensional (2D) materials from graphene to metal dichalcogenides and beyond, have interesting electrical, optical and mechanical properties. Recent advances in their growth, transfer and device physics have led to the shrinking of 2D material-based devices to the atomic scale and expanding their functionality. Single or multiple nanometer-scale holes, as small as single-atom vacancies, can be ...
- DOI:
- 10.1016/j.copbio.2018.09.002
-
https://dx.doi.org/10.1016/j.copbio.2018.09.002
- Author:
- Gruber, Andreas J.; Schmidt, Ralf; Ghosh, Souvik; Martin, Georges; Gruber, Andreas R.; van Nimwegen, Erik; Zavolan, Mihaela
- Source:
- Genome biology 2018 v.19 no.1 pp. 44
- ISSN:
- 1474-760X
- Subject:
- sequence analysis, etc ; binding proteins; neoplasms; Show all 3 Subjects
- Abstract:
- ... 3′ Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on poly(A) site choice. Application of PAQR and KAPAC to RNA sequencing data f ...
- DOI:
- 10.1186/s13059-018-1415-3
-
https://dx.doi.org/10.1186/s13059-018-1415-3
- Author:
- Arzalluz-Luque, Ángeles; Conesa, Ana
- Source:
- Genome biology 2018 v.19 no.1 pp. 110
- ISSN:
- 1474-760X
- Subject:
- sequence analysis, etc ; RNA; alternative splicing; Show all 3 Subjects
- Abstract:
- ... Single-cell RNAseq and alternative splicing studies have recently become two of the most prominent applications of RNAseq. However, the combination of both is still challenging, and few research efforts have been dedicated to the intersection between them. Cell-level insight on isoform expression is required to fully understand the biology of alternative splicing, but it is still an open question ...
- DOI:
- 10.1186/s13059-018-1496-z
-
https://dx.doi.org/10.1186/s13059-018-1496-z
- Author:
- Trincado, Juan L.; Entizne, Juan C.; Hysenaj, Gerald; Singh, Babita; Skalic, Miha; Elliott, David J.; Eyras, Eduardo
- Source:
- Genome biology 2018 v.19 no.1 pp. 40
- ISSN:
- 1474-760X
- Subject:
- sequence analysis, etc ; exons; introns; neurons; Show all 4 Subjects
- Abstract:
- ... Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses these challenges, and enables streamlined analysis across multiple conditions taking into account biological variability. Using experimental and simulated data, we show that SUPP ...
- DOI:
- 10.1186/s13059-018-1417-1
-
https://dx.doi.org/10.1186/s13059-018-1417-1
- Author:
- Han, Xiaoping; Wang, Renying; Zhou, Yincong; Fei, Lijiang; Sun, Huiyu; Lai, Shujing; Saadatpour, Assieh; Zhou, Zimin; Chen, Haide; Ye, Fang; Huang, Daosheng; Xu, Yang; Huang, Wentao; Jiang, Mengmeng; Jiang, Xinyi; Mao, Jie; Chen, Yao; Lu, Chenyu; Xie, Jin; Fang, Qun; Wang, Yibin; Yue, Rui; Li, Tiefeng; Huang, He; Orkin, Stuart H.; Yuan, Guo-Cheng; Chen, Ming; Guo, Guoji
- Source:
- Cell 2018 v.172 pp. 1091-1107.e17
- ISSN:
- 0092-8674
- Subject:
- sequence analysis, etc ; Internet; mice; tissues; Show all 4 Subjects
- Abstract:
- ... Single-cell RNA sequencing (scRNA-seq) technologies are poised to reshape the current cell-type classification system. However, a transcriptome-based single-cell atlas has not been achieved for complex mammalian systems. Here, we developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices. Using Microwell-seq, we analyzed more than 400,000 single ce ...
- DOI:
- 10.1016/j.cell.2018.02.001
-
http://dx.doi.org/10.1016/j.cell.2018.02.001
- Author:
- Járvás, Gábor; Varga, Tamás; Szigeti, Márton; Hajba, László; Fürjes, Péter; Rajta, István; Guttman, András
- Source:
- Electrophoresis 2018 v.39 no.3 pp. 534-539
- ISSN:
- 0173-0835
- Subject:
- sequence analysis, etc ; electrophoresis; equipment; hydrodynamics; Show all 4 Subjects
- Abstract:
- ... As a continuation of our previously published work, this paper presents a detailed evaluation of a microfabricated cell capture device utilizing a doubly tilted micropillar array. The device was fabricated using a novel hybrid technology based on the combination of proton beam writing and conventional lithography techniques. Tilted pillars offer unique flow characteristics and support enhanced flu ...
- DOI:
- 10.1002/elps.201700268
-
http://dx.doi.org/10.1002/elps.201700268
- Author:
- Jia, Meng-Ru; Tang, Ni; Cao, Yue; Chen, Yanshan; Han, Yong-He; Ma, Lena Q.
- Source:
- Chemosphere 2019 v.218 pp. 1061-1070
- ISSN:
- 0045-6535
- Subject:
- sequence analysis, etc ; Bacillus (bacteria); Pteris vittata; arsenates; arsenic; arsenites; bacteria; bacterial biomass; operon; roots; toxicity; Show all 11 Subjects
- Abstract:
- ... Arsenate (AsV) reduction in bacteria is essential to alleviate their arsenic (As) toxicity. We isolated a Bacillus strain PVR-YHB1-1 from the roots of As-hyperaccumulator Pteris vittata. The strain was efficient in reducing AsV to arsenite (AsIII), but the associated mechanisms were unclear. Here, we investigated its As resistance and reduction behaviors and associated genes at genome level. Resul ...
- DOI:
- 10.1016/j.chemosphere.2018.11.145
-
https://dx.doi.org/10.1016/j.chemosphere.2018.11.145
- Author:
- Zou, Fenxiang; Ruan, Qingyu; Lin, Xiaoye; Zhang, Mingxia; Song, Yanling; Zhou, Leiji; Zhu, Zhi; Lin, Shuichao; Wang, Wei; Yang, Chaoyong James
- Source:
- Biosensors & bioelectronics 2019 v.126 pp. 551-557
- ISSN:
- 0956-5663
- Subject:
- sequence analysis, etc ; DNA; automation; bioluminescence; biosensors; genes; genetic testing; microfluidic technology; mutants; mutation; sex determination analysis; Show all 11 Subjects
- Abstract:
- ... To explore genome mutation meaningfully, it is in urgent need to develop an automated and inexpensive platform for DNA mutation analysis. Digital microfluidics is a powerful platform for a broad range of applications due to the advantages of high automatization and low reagent consumption. Pyrosequencing enables DNA sequencing based on non-electrophoresis bioluminescence, which is suitable for rap ...
- DOI:
- 10.1016/j.bios.2018.09.092
-
https://dx.doi.org/10.1016/j.bios.2018.09.092
- Author:
- Carrillo-Ávila, José Antonio; Bonilla-García, Laura; Navarro-Marí, José María; Gutiérrez-Fernández, José
- Source:
- Anaerobe 2019 v.55 pp. 93-95
- ISSN:
- 1075-9964
- Subject:
- sequence analysis, etc ; Actinobaculum; antibiotics; bacteria; desorption; diagnostic techniques; hospitals; mass spectrometry; pathogenesis; pathogens; ribosomal RNA; women; Show all 12 Subjects
- Abstract:
- ... We report the first case of pelvic inflammatory disease (PID) caused by Actinobaculum massiliense. A 53-year-old woman attended the emergency department with symptoms compatible with a PID episode, finally resolved by intramuscular antibiotic treatment. Actinobaculum sp. was isolated by culture, and A. massiliense was confirmed by matrix assisted laser desorption time-of-flight mass spectrometry a ...
- DOI:
- 10.1016/j.anaerobe.2018.11.006
-
http://dx.doi.org/10.1016/j.anaerobe.2018.11.006
- Author:
- Sriboonlert, Ajaraporn; Wonnapinij, Passorn
- Source:
- International journal of biological macromolecules 2019 v.121 pp. 671-676
- ISSN:
- 0141-8130
- Subject:
- sequence analysis, etc ; Lampyridae; genes; mitochondria; mitochondrial DNA; mitochondrial genome; mutation; phylogeny; ribosomal RNA; transfer RNA; Show all 10 Subjects
- Abstract:
- ... The first mitochondrial genome of the firefly genus Inflata Boontop, Inflata indica (Lampyridae, Luciolinae) is reported here. Thirteen protein coding genes, 22 tRNA, 2 rRNA genes and a 1570 bp non-coding region were annotated. The comparative analysis showed that the size, GC content, gene content and gene arrangement of this mitochondrial genome are similar to those of other Lampyridae. The mito ...
- DOI:
- 10.1016/j.ijbiomac.2018.10.124
-
https://dx.doi.org/10.1016/j.ijbiomac.2018.10.124
- Author:
- Wesolowska-Andersen, Agata; Everman, Jamie L.; Davidson, Rebecca; Rios, Cydney; Herrin, Rachelle; Eng, Celeste; Janssen, William J.; Liu, Andrew H.; Oh, Sam S.; Kumar, Rajesh; Fingerlin, Tasha E.; Rodriguez-Santana, Jose; Burchard, Esteban G.; Seibold, Max A.
- Source:
- Genome biology 2018 v.19 no.1 pp. 49
- ISSN:
- 1474-760X
- Subject:
- sequence analysis, etc ; children; respiratory tract diseases; transcriptome; Show all 4 Subjects
- Abstract:
- ... In our recent article [1], it has come to our attention that the sample labels are not consistent between Table 1, the data labels deposited in the Sequence Read Archive, and Additional file 1: Table S2. We are therefore providing an updated Additional file 1: Table S2 so identical samples now have the same label. ...
- DOI:
- 10.1186/s13059-018-1423-3
-
https://dx.doi.org/10.1186/s13059-018-1423-3
- Author:
- Barberán-Soler, Sergio; Vo, Jenny M.; Hogans, Ryan E.; Dallas, Anne; Johnston, Brian H.; Kazakov, Sergei A.
- Source:
- Genome biology 2018 v.19 no.1 pp. 105
- ISSN:
- 1474-760X
- Subject:
- sequence analysis, etc ; DNA libraries; biomarkers; microRNA; therapeutics; Show all 5 Subjects
- Abstract:
- ... The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter and circularizing the ligation products. When compared to other methods, RealSeq®-A ...
- DOI:
- 10.1186/s13059-018-1488-z
-
https://dx.doi.org/10.1186/s13059-018-1488-z
- Author:
- Petukhov, Viktor; Guo, Jimin; Baryawno, Ninib; Severe, Nicolas; Scadden, David T.; Samsonova, Maria G.; Kharchenko, Peter V.
- Source:
- Genome biology 2018 v.19 no.1 pp. 78
- ISSN:
- 1474-760X
- Subject:
- sequence analysis, etc ; barcoding; computer software; droplets; transcriptome; Show all 5 Subjects
- Abstract:
- ... Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data creates challenges for subsequent computational processing and troubleshooting of these experiments, with few software options currently available. Here, we describe a ...
- DOI:
- 10.1186/s13059-018-1449-6
-
https://dx.doi.org/10.1186/s13059-018-1449-6
- Author:
- Lee, Heewook; Kingsford, Carl
- Source:
- Genome biology 2018 v.19 no.1 pp. 16
- ISSN:
- 1474-760X
- Subject:
- sequence analysis, etc ; HLA antigens; alleles; immune response; Show all 4 Subjects
- Abstract:
- ... Accurate typing of human leukocyte antigen (HLA) is important because HLA genes play important roles in immune responses and disease genesis. Previously available computational methods are database-matching approaches and their outputs are inherently limited by the completeness of already known types, making them unsuitable for discovery of novel alleles. We have developed a graph-guided assembly ...
- DOI:
- 10.1186/s13059-018-1388-2
-
https://dx.doi.org/10.1186/s13059-018-1388-2
- Author:
- Van den Berge, Koen; Perraudeau, Fanny; Soneson, Charlotte; Love, Michael I.; Risso, Davide; Vert, Jean-Philippe; Robinson, Mark D.; Dudoit, Sandrine; Clement, Lieven
- Source:
- Genome biology 2018 v.19 no.1 pp. 24
- ISSN:
- 1474-760X
- Subject:
- sequence analysis, etc ; gene expression regulation; models; Show all 3 Subjects
- Abstract:
- ... Dropout events in single-cell RNA sequencing (scRNA-seq) cause many transcripts to go undetected and induce an excess of zero read counts, leading to power issues in differential expression (DE) analysis. This has triggered the development of bespoke scRNA-seq DE methods to cope with zero inflation. Recent evaluations, however, have shown that dedicated scRNA-seq tools provide no advantage compare ...
- DOI:
- 10.1186/s13059-018-1406-4
-
https://dx.doi.org/10.1186/s13059-018-1406-4
- Author:
- Ma, Cong; Shao, Mingfu; Kingsford, Carl
- Source:
- Genome biology 2018 v.19 no.1 pp. 52
- ISSN:
- 1474-760X
- Subject:
- sequence analysis, etc ; algorithms; genes; models; neoplasms; transcriptomics; Show all 6 Subjects
- Abstract:
- ... Transcripts are frequently modified by structural variations, which lead to fused transcripts of either multiple genes, known as a fusion gene, or a gene and a previously non-transcribed sequence. Detecting these modifications, called transcriptomic structural variations (TSVs), especially in cancer tumor sequencing, is an important and challenging computational problem. We introduce SQUID, a nove ...
- DOI:
- 10.1186/s13059-018-1421-5
-
https://dx.doi.org/10.1186/s13059-018-1421-5
- Author:
- Ospina‐Sarria, Jhon Jairo; Cabra‐García, Jimmy
- Source:
- Cladistics 2018 v.34 no.5 pp. 574-577
- ISSN:
- 0748-3007
- Subject:
- sequence analysis, etc ; data analysis; nucleotide sequences; phylogeny; Show all 4 Subjects
- Abstract:
- ... De Laet (2015) claimed that minimization of ad hoc hypotheses of homoplasy does not lead to a preference for trivial optimizations when analysing unaligned sequence data, as claimed by Wheeler (2012; see also Kluge and Grant, 2006). In addition, De Laet asserted that Kluge and Grant's (2006) parsimony rationale is internally inconsistent in terms of Baker's (2003) theoretical framework. We argue t ...
- DOI:
- 10.1111/cla.12229
-
http://dx.doi.org/10.1111/cla.12229