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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. Correction to: Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

Author:
Olova, Nelly; Krueger, Felix; Andrews, Simon; Oxley, David; Berrens, Rebecca V.; Branco, Miguel R.; Reik, Wolf
Source:
Genome biology 2019 v.20 no.1 pp. 43
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; DNA libraries; DNA methylation; bisulfites;     Show all 4 Subjects
Abstract:
... Following publication of the original article [1], it was reported that the incorrect “Additional file 3” was published. The correct additional file is given below. ...
DOI:
10.1186/s13059-019-1656-9

3. A Diagnosis for All Rare Genetic Diseases: The Horizon and the Next Frontiers

Author:
Boycott, Kym M.; Hartley, Taila; Biesecker, Leslie G.; Gibbs, Richard A.; Innes, A. Micheil; Riess, Olaf; Belmont, John; Dunwoodie, Sally L.; Jojic, Nebojsa; Lassmann, Timo; Mackay, Deborah; Temple, I. Karen; Visel, Axel; Baynam, Gareth
Source:
Cell 2019 v.177 no.1 pp. 32-37
ISSN:
0092-8674
Subject:
sequence analysis,   etc   ; disease diagnosis; genetic disorders; patients;     Show all 4 Subjects
Abstract:
... The introduction of exome sequencing in the clinic has sparked tremendous optimism for the future of rare disease diagnosis, and there is exciting opportunity to further leverage these advances. To provide diagnostic clarity to all of these patients, however, there is a critical need for the field to develop and implement strategies to understand the mechanisms underlying all rare diseases and tra ...
DOI:
10.1016/j.cell.2019.02.040

4. Correction to: Optimised isolation method for RNA extraction suitable for RNA sequencing from feline teeth collected in a clinical setting and at post mortem

Author:
Lee, S.; Trivedi, U.; Johnson, C.; Farquharson, C.; Bergkvist, G. T.
Source:
Veterinary research communications 2019 v.43 no.1 pp. 29
ISSN:
0165-7380
Subject:
sequence analysis,   etc   ; RNA; cats; isolation techniques; teeth;     Show all 5 Subjects
Abstract:
... The authors regret that the original version of the above article contained errors in the Figs. 3, 4 and Tables 3 legends. The errors has been corrected. ...
DOI:
10.1007/s11259-018-9740-2

5. 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

6. A comparative evaluation of hybrid error correction methods for error-prone long reads

Author:
Fu, Shuhua; Wang, Anqi; Au, Kin Fai
Source:
Genome biology 2019 v.20 no.1 pp. 26
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; data quality; genomics; guidelines; haplotypes; nucleotide sequences;     Show all 6 Subjects
Abstract:
... BACKGROUND: Third-generation sequencing technologies have advanced the progress of the biological research by generating reads that are substantially longer than second-generation sequencing technologies. However, their notorious high error rate impedes straightforward data analysis and limits their application. A handful of error correction methods for these error-prone long reads have been devel ...
DOI:
10.1186/s13059-018-1605-z

7. CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing

Author:
Sato, Kenta; Tsuyuzaki, Koki; Shimizu, Kentaro; Nikaido, Itoshi
Source:
Genome biology 2019 v.20 no.1 pp. 31
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; computer software; data collection; genes; transcriptome;     Show all 5 Subjects
Abstract:
... Recent technical improvements in single-cell RNA sequencing (scRNA-seq) have enabled massively parallel profiling of transcriptomes, thereby promoting large-scale studies encompassing a wide range of cell types of multicellular organisms. With this background, we propose CellFishing.jl, a new method for searching atlas-scale datasets for similar cells and detecting noteworthy genes of query cells ...
DOI:
10.1186/s13059-019-1639-x

8. A comprehensive analysis of chimpanzee (Pan troglodytes)-specific LINE-1 retrotransposons

Author:
Lee, Sunyoung; Tang, Wanxiangfu; Liang, Ping; Han, Kyudong
Source:
Gene 2019 v.693 pp. 46-51
ISSN:
0378-1119
Subject:
sequence analysis,   etc   ; Pan troglodytes; evolution; genetic variation; genome; humans; retrotransposons;     Show all 7 Subjects
Abstract:
... Long interspersed element-1 (LINE-1 or L1) is one of the most abundant retrotransposons in the primate genomes and has contributed to their genome diversity and variations during the primate evolution. Among primate L1 subfamilies, L1Pt subfamilies include Pan troglodytes-specific L1s. L1Pt elements have been successfully expanded in the chimpanzee genome since the divergence of human and chimpanz ...
DOI:
10.1016/j.gene.2019.01.022

9. Sequence analysis of α-(1, 2)-fucosyltransferase gene in nine Chinese individuals with Para-Bombay phenotype

Author:
Lin, Jiajin; Chen, Rongcang; Zhu, Suiyong; Qiu, Xiaole; Huang, Ying; Wang, Xiudi
Source:
Gene 2019 v.685 pp. 21-23
ISSN:
0378-1119
Subject:
sequence analysis,   etc   ; genes; haplotypes; heterozygosity; hexosyltransferases; molecular cloning; mutation; phenotype;     Show all 8 Subjects
Abstract:
... To analyze the sequence of α-(1, 2)-fucosyltransferase gene (FUT1) in nine individuals with Para-Bombay phenotype.Para-Bombay phenotype was defined according to the serologic characteristics and ABO genotypes. The full coding region of FUT1 was amplified, genotype and haplotype were analyzed by direct and TOPO cloning sequencing which was used to discriminate heterozygous mutations of FUT1.These n ...
DOI:
10.1016/j.gene.2018.09.017

10. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

Author:
Schiebinger, Geoffrey; Shu, Jian; Tabaka, Marcin; Cleary, Brian; Subramanian, Vidya; Solomon, Aryeh; Gould, Joshua; Liu, Siyan; Lin, Stacie; Berube, Peter; Lee, Lia; Chen, Jenny; Brumbaugh, Justin; Rigollet, Philippe; Hochedlinger, Konrad; Jaenisch, Rudolf; Regev, Aviv; Lander, Eric S.
Source:
Cell 2019 v.176 no.4 pp. 928-943.e22
ISSN:
0092-8674
Subject:
sequence analysis,   etc   ; cytokines; gene expression; models; transcription factors;     Show all 5 Subjects
Abstract:
... Understanding the molecular programs that guide differentiation during development is a major challenge. Here, we introduce Waddington-OT, an approach for studying developmental time courses to infer ancestor-descendant fates and model the regulatory programs that underlie them. We apply the method to reconstruct the landscape of reprogramming from 315,000 single-cell RNA sequencing (scRNA-seq) pr ...
DOI:
10.1016/j.cell.2019.01.006

11. 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

12. 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

13. Nontuberculous mycobacteria: Insights on taxonomy and evolution

Author:
Turenne, Christine Y.
Source:
Infection, genetics, and evolution 2019
ISSN:
1567-1348
Subject:
sequence analysis,   etc   ; Mycobacterium; evolution; numerical taxonomy; phenotype; ribosomal RNA;     Show all 6 Subjects
Abstract:
... Seventy years have passed since Ernest H. Runyon presented a phenotypic classification approach for nontuberculous mycobacteria (NTM), primarily as a starting point in trying to understand their clinical relevance. From numerical taxonomy (biochemical testing) to 16S rRNA gene sequencing to whole genome sequencing (WGS), our understanding of NTM has also evolved. Novel species are described at a r ...
DOI:
10.1016/j.meegid.2019.01.017

14. Beyond bulk: a review of single cell transcriptomics methodologies and applications

Author:
Kulkarni, Ashwinikumar; Anderson, Ashley; Merullo, Devin; Konopka, Genevieve
Source:
Current opinion in biotechnology 2019
ISSN:
0958-1669
Subject:
sequence analysis,   etc   ; bioinformatics; brain; gene expression; neurophysiology; transcriptome; transcriptomics;     Show all 7 Subjects
Abstract:
... Single cell RNA sequencing (scRNA-seq) is a promising approach to study the transcriptomes of individual cells in the brain and the central nervous system (CNS). This technology acts as a bridge between neuroscience, computational biology, and systems biology, enabling an unbiased and novel understanding of the cellular composition of the brain and CNS. Gene expression at the single cell resolutio ...
DOI:
10.1016/j.copbio.2019.03.001

15. Correction to: Analysis of resistance genes of clinical Pannonibacter phragmitetus strain 31801 by complete genome sequencing

Author:
Ming, De-song; Chen, Qing-qing; Chen, Xiao-tin
Source:
Archives of microbiology 2018 v.200 no.10 pp. 1503
ISSN:
0302-8933
Subject:
sequence analysis,   etc   ; bacteria; resistance genes;     Show all 3 Subjects
Abstract:
... Subsequent to publication it has been noticed that the below listed text parts, figures and tables of the above paper were taken from paper ...
DOI:
10.1007/s00203-018-1579-y

16. 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

17. 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

18. 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

19. 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

20. 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