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1. What is the minimum length of gltA gene required for phylogenetic analyzes in Bartonella?

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

2. Optimal choice of k-mer in composition vector method for genome sequence comparison

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

3. Branching out: new insights into the genetic regulation of shoot architecture in trees

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

4. Two-dimensional nanopores and nanoporous membranes for ion and molecule transport

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

5. Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC

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

6. Single-cell RNAseq for the study of isoforms—how is that possible?

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

7. SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

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

8. Mapping the Mouse Cell Atlas by Microwell-Seq

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

9. Tilted pillar array fabrication by the combination of proton beam writing and soft lithography for microfluidic cell capture Part 2: Image sequence analysis based evaluation and biological application

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

10. Efficient arsenate reduction by As-resistant bacterium Bacillus sp. strain PVR-YHB1-1: Characterization and genome analysis

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

11. Rapid, real-time chemiluminescent detection of DNA mutation based on digital microfluidics and pyrosequencing

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

12. The first reported case of pelvic inflammatory disease caused by Actinobaculum massiliense

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

13. Comparative mitochondrial genome analysis of the firefly, Inflata indica (Coleoptera: Lampyridae) and the first evidence of heteroplasmy in fireflies

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

14. Correction to: Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome

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

15. Decreasing miRNA sequencing bias using a single adapter and circularization approach

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

16. dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments

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

17. Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery

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

18. Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications

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

19. SQUID: transcriptomic structural variation detection from RNA-seq

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

20. Parsimony analysis of unaligned sequence data: some clarifications

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