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1. SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data

Author:
Peng, Tao; Zhu, Qin; Yin, Penghang; Tan, Kai
Source:
Genome biology 2019 v.20 no.1 pp. 88
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; algorithms; genes;     Show all 3 Subjects
Abstract:
... Single-cell RNA-seq data contain a large proportion of zeros for expressed genes. Such dropout events present a fundamental challenge for various types of data analyses. Here, we describe the SCRABBLE algorithm to address this problem. SCRABBLE leverages bulk data as a constraint and reduces unwanted bias towards expressed genes during imputation. Using both simulation and several types of experim ...
DOI:
10.1186/s13059-019-1681-8

2. TransLiG: a de novo transcriptome assembler that uses line graph iteration

Author:
Liu, Juntao; Yu, Ting; Mu, Zengchao; Li, Guojun
Source:
Genome biology 2019 v.20 no.1 pp. 81
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; graphs; transcriptome;     Show all 3 Subjects
Abstract:
... We present TransLiG, a new de novo transcriptome assembler, which is able to integrate the sequence depth and pair-end information into the assembling procedure by phasing paths and iteratively constructing line graphs starting from splicing graphs. TransLiG is shown to be significantly superior to all the salient de novo assemblers in both accuracy and computing resources when tested on artificia ...
DOI:
10.1186/s13059-019-1690-7

3. DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis

Author:
Xiong, Bin; Yang, Yiben; Fineis, Frank R.; Wang, Ji-Ping
Source:
Genome biology 2019 v.20 no.1 pp. 75
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; RNA; transcription (genetics);     Show all 3 Subjects
Abstract:
... RNA degradation affects RNA-seq quality when profiling transcriptional activities in cells. Here, we show that transcript degradation is both gene- and sample-specific and is a common and significant factor that may bias the results in RNA-seq analysis. Most existing global normalization approaches are ineffective to correct for degradation bias. We propose a novel pipeline named DegNorm to adjust ...
DOI:
10.1186/s13059-019-1682-7

4. 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

5. 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

6. EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

Author:
Lun, Aaron T. L.; Riesenfeld, Samantha; Andrews, Tallulah; Dao, The Phuong; Gomes, Tomas; Marioni, John C.
Source:
Genome biology 2019 v.20 no.1 pp. 63
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; RNA; data collection; droplets; transcriptomics;     Show all 5 Subjects
Abstract:
... Droplet-based single-cell RNA sequencing protocols have dramatically increased the throughput of single-cell transcriptomics studies. A key computational challenge when processing these data is to distinguish libraries for real cells from empty droplets. Here, we describe a new statistical method for calling cells from droplet-based data, based on detecting significant deviations from the expressi ...
DOI:
10.1186/s13059-019-1662-y

7. 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

8. 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

9. 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

10. 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

11. 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

12. Comparative analysis of sequencing technologies for single-cell transcriptomics

Author:
Natarajan, Kedar Nath; Miao, Zhichao; Jiang, Miaomiao; Huang, Xiaoyun; Zhou, Hongpo; Xie, Jiarui; Wang, Chunqing; Qin, Shishang; Zhao, Zhikun; Wu, Liang; Yang, Naibo; Li, Bo; Hou, Yong; Liu, Shiping; Teichmann, Sarah A.
Source:
Genome biology 2019 v.20 no.1 pp. 70
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; RNA; cell lines; complementary DNA; transcriptomics;     Show all 5 Subjects
Abstract:
... Single-cell RNA-seq technologies require library preparation prior to sequencing. Here, we present the first report to compare the cheaper BGISEQ-500 platform to the Illumina HiSeq platform for scRNA-seq. We generate a resource of 468 single cells and 1297 matched single cDNA samples, performing SMARTer and Smart-seq2 protocols on two cell lines with RNA spike-ins. We sequence these libraries on b ...
DOI:
10.1186/s13059-019-1676-5

13. Neoascochyta species cause leaf scorch on wheat in Australia

Author:
Golzar, H.; Thomas, G.; Jayasena, K. W.; Wright, D.; Wang, C.; Kehoe, M.
Source:
Australasian plant disease notes 2019 v.14 no.1 pp. 1
ISSN:
1833-928X
Subject:
sequence analysis,   etc   ; Didymellaceae; fungi; leaves; pathogenicity; scorch; wheat; Western Australia;     Show all 8 Subjects
Abstract:
... A conspicuous leaf scorch of wheat associated with Didymellaceae family was observed on commercial wheat varieties in Western Australia during recent years. Two fungal species isolated from leaf lesions were identified based on morphological characteristics and DNA sequencing. Neoascochyta europaea was isolated from symptomatic leaf lesions on the wheat varieties Trojan and Wyalkatchem also Neoasc ...
DOI:
10.1007/s13314-018-0332-3

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

Author:
Kulkarni, Ashwinikumar; Anderson, Ashley G.; Merullo, Devin P.; Konopka, Genevieve
Source:
Current opinion in biotechnology 2019 v.58 pp. 129-136
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. Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated?

Author:
Ittisoponpisan, Sirawit; Islam, Suhail A.; Khanna, Tarun; Alhuzimi, Eman; David, Alessia; Sternberg, Michael J.E.
Source:
Journal of molecular biology 2019 v.431 no.11 pp. 2197-2212
ISSN:
0022-2836
Subject:
sequence analysis,   etc   ; algorithms; humans; models; mutants; phenotype; protein structure; proteome;     Show all 8 Subjects
Abstract:
... Knowledge of protein structure can be used to predict the phenotypic consequence of a missense variant. Since structural coverage of the human proteome can be roughly tripled to over 50% of the residues if homology-predicted structures are included in addition to experimentally determined coordinates, it is important to assess the reliability of using predicted models when analyzing missense varia ...
DOI:
10.1016/j.jmb.2019.04.009

16. Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines

Author:
Jacobson, Elsie C.; Grand, Ralph S.; Perry, Jo K.; Vickers, Mark H.; Olins, Ada L.; Olins, Donald E.; O'Sullivan, Justin M.
Source:
Genomics 2019
ISSN:
0888-7543
Subject:
sequence analysis,   etc   ; cell lines; karyotyping; loci; myeloid leukemia; neoplasm cells;     Show all 6 Subjects
Abstract:
... Cancer cell lines often have large structural variants (SVs) that evolve over time. There are many reported differences in large scale SVs between HL-60 and HL-60/S4, two cell lines derived from the same acute myeloid leukemia sample. However, the stability and variability of inter- and intra-chromosomal structural variants between different sources of the same cell line is unknown. Here, we used ...
DOI:
10.1016/j.ygeno.2019.05.009

17. Prp8 in a Reduced Spliceosome Lacks a Conserved Toggle that Correlates with Splicing Complexity across Diverse Taxa

Author:
Garside, E.L.; Whelan, T.A.; Stark, M.R.; Rader, S.D.; Fast, N.M.; MacMillan, A.M.
Source:
Journal of molecular biology 2019
ISSN:
0022-2836
Subject:
sequence analysis,   etc   ; Rhodophyta; X-radiation; catalytic activity; introns; spliceosomes;     Show all 6 Subjects
Abstract:
... Conformational rearrangements are critical to regulating the assembly and activity of the spliceosome. The spliceosomal protein Prp8 undergoes multiple conformational changes during the course of spliceosome assembly, activation, and catalytic activity. Most of these rearrangements of Prp8 involve the disposition of the C-terminal Jab-MPN and RH domains with respect to the core of Prp8. Here we us ...
DOI:
10.1016/j.jmb.2019.04.047

18. 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

19. A computational system for identifying operons based on RNA-seq data

Author:
Tjaden, Brian
Source:
Methods 2019
ISSN:
1046-2023
Subject:
sequence analysis,   etc   ; biochemical pathways; databases; operon; probabilistic models; transcription (genetics);     Show all 6 Subjects
Abstract:
... An operon is a set of neighboring genes in a genome that is transcribed as a single polycistronic message. Genes that are part of the same operon often have related functional roles or participate in the same metabolic pathways. The majority of all bacterial genes are co-transcribed with one or more other genes as part of a multi-gene operon. Thus, accurate identification of operons is important i ...
DOI:
10.1016/j.ymeth.2019.03.026

20. Efficient transposition of Tn4556 by alterations in inverted repeats using a delivery vector carrying a counter-selectable marker for Streptomyces

Author:
Sota, Masahiro; Sakoda, Akiko; Ikeda, Haruo
Source:
Journal of industrial microbiology & biotechnology 2019 v.46 no.3-4 pp. 477-482
ISSN:
1367-5435
Subject:
sequence analysis,   etc   ; Streptomyces; methyltransferases; open reading frames; transposons;     Show all 5 Subjects
Abstract:
... A 6625-base pair transposon, Tn4556, was initially isolated from a Streptomyces strain and a sequence analysis was performed; however, its annotation data remain incomplete. At least three positions were identified as frameshift and base-exchange errors by resequencing. The revised sequence revealed that Tn4556 contains four open reading frames that encode transposase, methyltransferase, isoprenyl ...
DOI:
10.1007/s10295-018-2101-x