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1. Simplitigs as an efficient and scalable representation of de Bruijn graphs

Author:
Břinda, Karel; Baym, Michael; Kucherov, Gregory
Source:
Genome biology 2021 v.22 no.1 pp. 96
ISSN:
1474-760X
Subject:
bioinformatics,   etc   ; algorithms; genome; memory;     Show all 4 Subjects
Abstract:
... de Bruijn graphs play an essential role in bioinformatics, yet they lack a universal scalable representation. Here, we introduce simplitigs as a compact, efficient, and scalable representation, and ProphAsm, a fast algorithm for their computation. For the example of assemblies of model organisms and two bacterial pan-genomes, we compare simplitigs to unitigs, the best existing representation, and ...
DOI:
10.1186/s13059-021-02297-z

2. Rice bioinformatics in the genomic era: Status and perspectives

Author:
Jia, Lei; Xie, Lingjuan; Lao, Sangting; Zhu, Qian-Hao; Fan, Longjiang
Source:
The crop journal 2021 v.9 no.3 pp. 609-621
ISSN:
2214-5141
Subject:
bioinformatics,   etc   ; genome; genomics; rice;     Show all 4 Subjects
Abstract:
... Rice is one of cereal crops and a model species for monocots. Since the release of the first draft rice genome sequences in 2002, considerable progress has been achieved in rice genomic researches, thanks to rapid development and efficient utilization of bioinformatics methods and tools. In this review, we summarize the progress of studies of rice genome sequencing and other omics and introduce th ...
DOI:
10.1016/j.cj.2021.03.003

3. The robustness of the chaos game representation to mutations and its application in free-alignment methods

Author:
Kania, Adrian; Sarapata, Krzysztof
Source:
Genomics 2021 v.113 no.3 pp. 1428-1437
ISSN:
0888-7543
Subject:
bioinformatics,   etc   ; genomics; phylogeny;     Show all 3 Subjects
Abstract:
... Numerical representation of biological sequences plays an important role in bioinformatics and has many practical applications. One of the most popular approaches is the chaos game representation. In this paper, the authors propose a novel look into chaos game construction - an analytical description of this procedure. This type enables to build more general number sequences using different weight ...
DOI:
10.1016/j.ygeno.2021.03.015

4. Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish

Author:
Mishra, Shital Kumar; Wang, Han
Source:
Biology 2021 v.10 no.5
ISSN:
2079-7737
Subject:
bioinformatics,   etc   ; Danio rerio; Internet;     Show all 3 Subjects
Abstract:
... Recent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next regulatory biology frontier. Thus, identification of coding lncRNAs from ever-increasing lncRNA databases would be a bioinformatic challenge. Here we employed the Coding Potential Alignment Tool ( ...
DOI:
10.3390/biology10050371

5. CircNFIX promotes progression of pituitary adenoma via CCNB1 by sponging miR-34a -5p

Author:
Cheng, Jianhua; Nie, Ding; Li, Bin; Gui, SongBai; Li, ChuZhong; Zhang, YaZhuo; Zhao, Peng
Source:
Molecular and cellular endocrinology 2021 v.525 pp. 111140
ISSN:
0303-7207
Subject:
bioinformatics,   etc   ; adenoma; endocrinology;     Show all 3 Subjects
Abstract:
... Previous studies have shown that CCNB1 affects the invasiveness of pituitary adenomas, and it is of great significance to find the upstream mechanism of regulating CCNB1.In this study, we explored a significantly overexpressed circRNA in invasive pituitary adenomas. Based on bioinformatics analysis and mechanism experiments, we determined that circNFIX (has-circ_0005660) affects cell invasion, mig ...
DOI:
10.1016/j.mce.2020.111140

6. Cancer Subtype Recognition Based on Laplacian Rank Constrained Multiview Clustering

Author:
Ge, Shuguang; Wang, Xuesong; Cheng, Yuhu; Liu, Jian
Source:
Genes 2021 v.12 no.4
ISSN:
2073-4425
Subject:
bioinformatics,   etc   ; algorithms; data collection;     Show all 3 Subjects
Abstract:
... Integrating multigenomic data to recognize cancer subtype is an important task in bioinformatics. In recent years, some multiview clustering algorithms have been proposed and applied to identify cancer subtype. However, these clustering algorithms ignore that each data contributes differently to the clustering results during the fusion process, and they require additional clustering steps to gener ...
DOI:
10.3390/genes12040526

7. Mathematical simulation of two-phase flow and slag entrainment during steel bloom continuous casting

Author:
Chen, Wei; Zhang, Lifeng; Wang, Yadong; Ji, Sha; Ren, Ying; Yang, Wen
Source:
Powder technology 2021 v.390 pp. 539-554
ISSN:
0032-5910
Subject:
bioinformatics,   etc   ; probability; slags; steel; technology;     Show all 5 Subjects
Abstract:
... A three-dimensional computational model, coupled with the Large Eddy Simulation (LES) model and Volume of Fluid (VOF) multiphase model, was established to investigate the two-phase flow and slag entrainment during steel bloom continuous casting. The influence of the in-mold electromagnetic stirring (M-EMS), casting speed, and submerged entry nozzle (SEN) immersion depth on the flow pattern and sla ...
DOI:
10.1016/j.powtec.2021.05.101

8. Detection of Highly Divergent Tandem Repeats in the Rice Genome

Author:
Korotkov, Eugene V.; Kamionskya, Anastasiya M.; Korotkova, Maria A.
Source:
Genes 2021 v.12 no.4
ISSN:
2073-4425
Subject:
bioinformatics,   etc   ; algorithms; nucleotides; rice; transposons;     Show all 5 Subjects
Abstract:
... Currently, there is a lack of bioinformatics approaches to identify highly divergent tandem repeats (TRs) in eukaryotic genomes. Here, we developed a new mathematical method to search for TRs, which uses a novel algorithm for constructing multiple alignments based on the generation of random position weight matrices (RPWMs), and applied it to detect TRs of 2 to 50 nucleotides long in the rice geno ...
DOI:
10.3390/genes12040473

9. A novel approach to teaching Hidden Markov Models to a diverse undergraduate population

Author:
Heller, Philip; Pogaru, Pratyusha
Source:
Heliyon 2021 v.7 no.3 pp. e06437
ISSN:
2405-8440
Subject:
bioinformatics,   etc   ; DNA; computer software; mathematics;     Show all 4 Subjects
Abstract:
... Hidden Markov Models (HMMs) are an essential tool for Bioinformatic analysis, with extensive success at finding patterns (e.g. CRISPR arrays or genes of interest) in DNA or protein sequences. HMMs are conceptually intricate, and the algorithms that make use of them are complicated. Thus they present a challenge to Bioinformatics instructors at the undergraduate level, particularly when the student ...
DOI:
10.1016/j.heliyon.2021.e06437

10. Early detection of cyanobacterial blooms and associated cyanotoxins using fast detection strategy

Author:
Teta, Roberta; Esposito, Germana; De Sterlich, Carlo; Lega, Massimiliano; Costantino, Valeria
Source:
Journal of visualized experiments 2021 no.168 pp. e61889
ISSN:
1940-087X
Subject:
bioinformatics,   etc   ; Bivalvia; cyanobacterial toxins; microscopy;     Show all 4 Subjects
Abstract:
... Fast detection of cyanobacteria and cyanotoxins is achieved using a Fast Detection Strategy (FDS). Only 24 h are needed to unravel the presence of cyanobacteria and related cyanotoxins in water samples and in an organic matrix, such as bivalve extracts. FDS combines remote/proximal sensing techniques with analytical/bioinformatics analyses. Sampling spots are chosen through multi-disciplinary, mul ...
DOI:
10.3791/61889

11. On the optimistic performance evaluation of newly introduced bioinformatic methods

Author:
Buchka, Stefan; Hapfelmeier, Alexander; Gardner, Paul P.; Wilson, Rory; Boulesteix, Anne-Laure
Source:
Genome biology 2021 v.22 no.1 pp. 152
ISSN:
1474-760X
Subject:
bioinformatics,   etc   ; data collection; epigenetics; genome; microarray technology;     Show all 5 Subjects
Abstract:
... Most research articles presenting new data analysis methods claim that “the new method performs better than existing methods,” but the veracity of such statements is questionable. Our manuscript discusses and illustrates consequences of the optimistic bias occurring during the evaluation of novel data analysis methods, that is, all biases resulting from, for example, selection of datasets or compe ...
DOI:
10.1186/s13059-021-02365-4

12. miRNAs through β-ARR2/p-ERK1/2 pathway regulate the VSMC proliferation and migration

Author:
Ghasempour, Ghasem; Mohammadi, Asghar; Zamani-Garmsiri, Fahimeh; Najafi, Mohammad
Source:
Life sciences 2021 v.279 pp. 119703
ISSN:
0024-3205
Subject:
bioinformatics,   etc   ; atherosclerosis; genes; microRNA; protein synthesis; therapeutics;     Show all 6 Subjects
Abstract:
... miRNAs are involved in plaque formation of atherosclerosis and vessel restenosis. In this study, we investigated the effects of miR-599, miR-204, and miR-181b on VSMC proliferation, and migration through TGFβ receptor 2 (TGFβR2), β-arrestin 2 (β-ARR2), SMAD2/p-SMAD2, and ERK1/2/p-ERK1/2.Genes and miRNAs were predicted by bioinformatics tools and were transfected by PEI-miRNAs (miR-599, miR-204, an ...
DOI:
10.1016/j.lfs.2021.119703

13. A broadly resolved molecular phylogeny of New Zealand cheilostome bryozoans as a framework for hypotheses of morphological evolution

Author:
Orr, R.J.S.; Di Martino, E.; Gordon, D.P.; Ramsfjell, M.H.; Mello, H.L.; Smith, A.M.; Liow, L.H.
Source:
Molecular phylogenetics and evolution 2021 v.161 pp. 107172
ISSN:
1055-7903
Subject:
bioinformatics,   etc   ; Bryozoa; fauna; mitochondria; phylogeny; New Zealand;     Show all 6 Subjects
Abstract:
... Larger molecular phylogenies based on ever more genes are becoming commonplace with the advent of cheaper and more streamlined sequencing and bioinformatics pipelines. However, many groups of inconspicuous but no less evolutionarily or ecologically important marine invertebrates are still neglected in the quest for understanding species- and higher-level phylogenetic relationships. Here, we allevi ...
DOI:
10.1016/j.ympev.2021.107172

14. MicroRNA-mRNA expression profiles and functional network after injection of botulinum toxin type A into submandibular glands

Author:
Mao, Qian-Ying; Xie, Shang; Wu, Li-Ling; Xiang, Ruo-Lan; Cai, Zhi-Gang
Source:
Toxicon 2021 v.199 pp. 31-40
ISSN:
0041-0101
Subject:
bioinformatics,   etc   ; botulinum toxin; microRNA; microarray technology; secretion;     Show all 5 Subjects
Abstract:
... Botulinum toxin type A (BTXA) is effective for the treatment of sialorrhea. MicroRNAs (miRNAs) have significant functions in salivary diseases, but the role of miRNAs during BTXA-inhibited salivary secretion is not yet clear. A total of 19 differentially expressed (DE) miRNAs and 1072 DE mRNAs were identified following BTXA injected into submandibular glands of rats (n = 4) through miRNA sequencin ...
DOI:
10.1016/j.toxicon.2021.05.011

15. A structure-based approach for the development of a bicyclic peptide acting as a miniaturized anti-CD55 antibody

Author:
Moreira, Miguel; Ruggiero, Alessia; Iaccarino, Emanuela; Barra, Giovanni; Sandomenico, Annamaria; Ruvo, Menotti; Berisio, Rita
Source:
International journal of biological macromolecules 2021 v.182 pp. 1455-1462
ISSN:
0141-8130
Subject:
bioinformatics,   etc   ; antibodies; blood; complement; immunotherapy; neoplasms; peptides;     Show all 7 Subjects
Abstract:
... CD55 is a major regulator of the complement system, a complex network of proteins that cooperate to clear tissue and blood pathogens from the organism. Indeed, overexpression of CD55 is associated with many diseases and is connected to the resistance mechanisms exhibited by several cancers towards immunotherapy approaches. High level of CD55 expression on tumour cells renders it a good target for ...
DOI:
10.1016/j.ijbiomac.2021.05.092

16. Addressing Research Bottlenecks to Crop Productivity

Author:
Reynolds, Matthew; Atkin, Owen K.; Bennett, Malcolm; Cooper, Mark; Dodd, Ian C.; Foulkes, M. John; Frohberg, Claus; Hammer, Graeme; Henderson, Ian R.; Huang, Bingru; Korzun, Viktor; McCouch, Susan R.; Messina, Carlos D.; Pogson, Barry J.; Slafer, Gustavo A.; Taylor, Nicolas L.; Wittich, Peter E.
Source:
Trends in plant science 2021 v.26 no.6 pp. 607-630
ISSN:
1360-1385
Subject:
bioinformatics,   etc   ; asymmetry; genetic improvement; genomics; phenomics; probability;     Show all 6 Subjects
Abstract:
... Asymmetry of investment in crop research leads to knowledge gaps and lost opportunities to accelerate genetic gain through identifying new sources and combinations of traits and alleles. On the basis of consultation with scientists from most major seed companies, we identified several research areas with three common features: (i) relatively underrepresented in the literature; (ii) high probabilit ...
DOI:
10.1016/j.tplants.2021.03.011

17. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis

Author:
Kim, Jihyeon; Na, Seong-In; Kim, Dongwook; Chun, Jongsik
Source:
The journal of microbiology 2021 v.59 no.6 pp. 609-615
ISSN:
1225-8873
Subject:
bioinformatics,   etc   ; genes; microbiology; nucleotide sequences; phylogeny;     Show all 5 Subjects
Abstract:
... Phylogenomic tree reconstruction has recently become a routine and critical task to elucidate the evolutionary relationships among bacterial species. The most widely used method utilizes the concatenated core genes, universally present in a single-copy throughout the bacterial domain. In our previous study, a bioinformatics pipeline termed Up-to-date Bacterial Core Genes (UBCG) was developed with ...
DOI:
10.1007/s12275-021-1231-4

18. RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive

Author:
Rose, Yana; Duarte, Jose M.; Lowe, Robert; Segura, Joan; Bi, Chunxiao; Bhikadiya, Charmi; Chen, Li; Rose, Alexander S.; Bittrich, Sebastian; Burley, Stephen K.; Westbrook, John D.
Source:
Journal of molecular biology 2021 v.433 no.11 pp. 166704
ISSN:
0022-2836
Subject:
bioinformatics,   etc   ; databases; molecular biology; nucleic acids;     Show all 4 Subjects
Abstract:
... The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves many millions of unique users worldwide by delivering experimentally-determined 3D structures of biomolecules integrated with >40 external data resources via RCSB.org, application programming interfaces (APIs), and FTP downloads. Herein, we present the architectural redesign of RCSB PDB data delivery se ...
DOI:
10.1016/j.jmb.2020.11.003

19. Network Protein Interaction in the Link between Stroke and Periodontitis Interplay: A Pilot Bioinformatic Analysis

Author:
Leira, Yago; Mascarenhas, Paulo; Blanco, Juan; Sobrino, Tomás; Mendes, José João; Machado, Vanessa; Botelho, João
Source:
Genes 2021 v.12 no.5
ISSN:
2073-4425
Subject:
bioinformatics,   etc   ; databases; inflammation; periodontitis; stroke; therapeutics;     Show all 6 Subjects
Abstract:
... The clinical interaction between stroke and periodontitis has been consistently studied and confirmed. Hence, exploring potentially new protein interactions in this association using bioinformatic strategies presents potential interest. In this exploratory study, we conducted a protein–protein network interaction (PPI) search with documented encoded proteins for both stroke and periodontitis. Gene ...
DOI:
10.3390/genes12050787

20. Bok binds to a largely disordered loop in the coupling domain of type 1 inositol 1,4,5-trisphosphate receptor

Author:
Szczesniak, Laura M.; Bonzerato, Caden G.; Schulman, Jacqualyn J.; Bah, Alaji; Wojcikiewicz, Richard J.H.
Source:
Biochemical and biophysical research communications 2021 v.553 pp. 180-186
ISSN:
0006-291X
Subject:
bioinformatics,   etc   ; amino acids; cytosol; inositols; peptides; research;     Show all 6 Subjects
Abstract:
... Bcl-2-related ovarian killer (Bok) binds tightly to inositol 1,4,5-trisphosphate receptors (IP₃Rs). To better understand this interaction, we sought to elucidate the Bok binding determinants in IP₃R1, focusing on the ∼75 amino acid loop (residues 1882–1957) between α helices 72 and 73. Bioinformatic analysis revealed that the majority of this loop is intrinsically disordered, with two flanking reg ...
DOI:
10.1016/j.bbrc.2021.03.047