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1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. Go with the flow or solitary confinement: a look inside the single-cell toolbox for isolation of rare and uncultured microbes

Author:
Huys, Geert RB; Raes, Jeroen
Source:
Current opinion in microbiology 2018 v.44 pp. 1-8
ISSN:
1369-5274
Subject:
sequence analysis,   etc   ; metagenomics; microbial growth; microorganisms;     Show all 4 Subjects
Abstract:
... With the vast majority of the microbial world still considered unculturable or undiscovered, microbiologists not only require more fundamental insights concerning microbial growth requirements but also need to implement miniaturized, versatile and high-throughput technologies to upscale current microbial isolation strategies. In this respect, single-cell-based approaches are increasingly finding t ...
DOI:
10.1016/j.mib.2018.05.002

16. Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

Author:
van Dijk, David; Sharma, Roshan; Nainys, Juozas; Yim, Kristina; Kathail, Pooja; Carr, Ambrose J.; Burdziak, Cassandra; Moon, Kevin R.; Chaffer, Christine L.; Pattabiraman, Diwakar; Bierie, Brian; Mazutis, Linas; Wolf, Guy; Krishnaswamy, Smita; Pe’er, Dana
Source:
Cell 2018 v.174 no.3 pp. 716-729.e27
ISSN:
0092-8674
Subject:
sequence analysis,   etc   ; gene interaction; messenger RNA; phenotype;     Show all 4 Subjects
Abstract:
... Single-cell RNA sequencing technologies suffer from many sources of technical noise, including under-sampling of mRNA molecules, often termed “dropout,” which can severely obscure important gene-gene relationships. To address this, we developed MAGIC (Markov affinity-based graph imputation of cells), a method that shares information across similar cells, via data diffusion, to denoise the cell cou ...
DOI:
10.1016/j.cell.2018.05.061

17. Primer Reporte de Tineola bisselliella Hummel1 Causando Daños en una Colección Biológica en México

Author:
May-Vega, W. Patricio; Espinosa-Carrillo, L. Othón; Domínguez-Monge, Santiago; Campos-Figueroa, Manuel
Source:
TheSouthwestern entomologist 2018 v.43 no.2 pp. 551-553
ISSN:
0147-1724
Subject:
sequence analysis,   etc   ; Tineola bisselliella; insects; pests; Mexico;     Show all 5 Subjects
Abstract:
... During April and May 2016 damage on preserved insect specimens was observed in a biological collection in Mexico. Based on morphological characteristics and mDNA-COII and CytB sequence analysis, the pest was Tineola bisselliella Hummel. This is the first report of T. bisselliella causing damage in a biological collection in Mexico. ...
DOI:
10.3958/059.043.0230

18. Bacteria That Make a Meal of Sulfonamide Antibiotics: Blind Spots and Emerging Opportunities

Author:
Deng, Yu; Li, Bing; Zhang, Tong
Source:
Environmental science & technology 2018 v.52 no.7 pp. 3854-3868
ISSN:
1520-5851
Subject:
sequence analysis,   etc   ; antibiotics; bacteria; biodegradation; bioremediation; metagenomics;     Show all 6 Subjects
Abstract:
... The release of sulfonamide antibiotics into the environment is alarming because the existence of these antibiotics in the environment may promote resistance in clinically relevant microorganisms, which is a potential threat to the effectiveness of antibiotic therapies. Controllable biodegradation processes are of particular significance for the inexpensive yet effective restoration of sulfonamide- ...
DOI:
10.1021/acs.est.7b06026

19. Responsible RAD: Striving for best practices in population genomic studies of adaptation

Author:
Lowry, David B.; Hoban, Sean; Kelley, Joanna L.; Lotterhos, Katie E.; Reed, Laura K.; Antolin, Michael F.; Storfer, Andrew
Source:
Molecular ecology resources 2017 v.17 no.3 pp. 366-369
ISSN:
1755-098X
Subject:
sequence analysis,   etc   ; genomics; loci;     Show all 3 Subjects
Abstract:
... Two recent articles were written in response to our paper “Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing scans of adaptation.” While we agree with some of the comments made by the authors of these two response papers, we still believe caution should be employed in RADseq studies that aim to detect loci that contribute to adaptation. In this rebuttal, we e ...
DOI:
10.1111/1755-0998.12677

20. Functional Enhancer Screening in Single Cells

Author:
van Arensbergen, Joris; van Steensel, Bas
Source:
Molecular cell 2017 v.66 no.2 pp. 167-168
ISSN:
1097-2765
Subject:
sequence analysis,   etc   ; genes; screening;     Show all 3 Subjects
Abstract:
... In this issue of Molecular Cell, Xie et al. (2017) introduce Mosaic-seq, a powerful technology that combines CRISPRi and single-cell RNA-seq. This method enables the high-throughput assessment of contributions of enhancers to gene regulation. ...
DOI:
10.1016/j.molcel.2017.03.018