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Multidisciplinary Sciences
Sumera Zaib, Fatima Akram, Syed Talha Liaqat, Muhammad Zain Altaf, Imtiaz Khan, Ayed A. Dera, Jalal Uddin, Ajmal Khan, Ahmed Al-Harrasi
Summary: The aim of this study is to develop a specific vaccine using bioinformatics approaches to target SARS-CoV-2 infections. By predicting and selecting new epitopes, a vaccine subunit with immunogenic properties was constructed, and a good immune response was observed. The study identified this multi-epitope vaccine as a significant candidate for combating SARS-CoV-2 infections on a global scale.
SCIENTIFIC REPORTS
(2022)
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Biochemical Research Methods
Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali
Summary: This article introduces an application called MALVIRUS, which assists users in efficiently analyzing viral populations, particularly SARS-CoV-2 strain samples. The application has demonstrated higher efficiency and accuracy compared to other tools.
BMC BIOINFORMATICS
(2022)
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Biochemical Research Methods
Chayan Kumar Saha, Rodrigo Sanches Pires, Harald Brolin, Maxence Delannoy, Gemma Catherine Atkinson
Summary: FlaGs is a tool for analyzing the conservation of gene neighborhoods, showing utility in molecular evolutionary analysis with its ability to uncover new systems and predict functional associations.
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Microbiology
Orawee Kaewprasert, Sissades Tongsima, Rick Twee-Hee Ong, Kiatichai Faksri
Summary: This study demonstrates the importance of optimizing parameters and using high-quality variants in whole-genome sequence analysis for accurate bacterial phylogeny reconstruction.
ARCHIVES OF MICROBIOLOGY
(2022)
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Chemistry, Analytical
Antonios Prapas, Konstantinos F. Kantelis, Petros Nicopolitidis, Georgios I. Papadimitriou
Summary: This paper presents a novel Medium Access Control protocol utilizing long-range technology, which improves performance in Low Power Wide Area Network applications through better network awareness and dynamic time slot rescheduling.
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Biotechnology & Applied Microbiology
Eleonora Pedrazzoli, Andrea Bianchi, Alessandro Umbach, Simone Amistadi, Megane Brusson, Giacomo Frati, Matteo Ciciani, Kalina Aleksandra Badowska, Daniele Arosio, Annarita Miccio, Anna Cereseto, Antonio Casini
Summary: In this study, a high-fidelity SpCas9 variant suitable for RNP delivery, rCas9HF, was developed and compared with the only available high-fidelity Cas9 variant, HiFi Cas9. The comparative analysis showed different targeting capabilities of the two variants throughout the genome. The development of rCas9HF increases the genome editing solutions for the highest precision and efficient applications.
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Biochemical Research Methods
Melanie Kirsche, Gautam Prabhu, Rachel Sherman, Bohan Ni, Alexis Battle, Sergey Aganezov, Michael C. C. Schatz
Summary: Jasmine and Iris, as fast and accurate tools, provide solutions for the comparison and analysis of structural variants (SVs) in a population. Jasmine outperforms six widely used comparison methods and identifies a set of high-confidence de novo SVs. Additionally, a unified callset of SVs and indels is provided for genotyping and assessing their impact on gene expression.
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Chemistry, Organic
Daniel Polyak, Isaac J. Krauss
Summary: An efficient multigram synthesis method for alkynyl amino acid Fmoc-L-homopropargylglycine-OH is described. The optimized Boc protection and Seyferth-Gilbert homologation resulted in high material throughput and avoidance of racemization, respectively. The enantiopure (>98% ee) noncanonical amino acid can be readily generated for solid phase synthesis of functionalized peptides.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Biochemical Research Methods
Jeffrey N. Dudley, Celine S. Hong, Marwan A. Hawari, Jasmine Shwetar, Julie C. Sapp, Justin Lack, Henoke Shiferaw, Jennifer J. Johnston, Leslie G. Biesecker
Summary: PBVI is a method for Position-Based Variant Identification that improves the detection of low-level mosaic variants by using empirically-derived distributions of alternate nucleotides from a control dataset. Modeled on 11 segmental overgrowth genes, this method shows superior detection of single nucleotide mosaic variants of 0.01-0.05 variant allele fraction. Sensitivity of over 85% and 95% was observed at depths of 600 x and 1200 x, respectively, demonstrating its utility in identifying pathogenic variants in individuals with somatic overgrowth disorders.
BMC BIOINFORMATICS
(2021)
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Biochemical Research Methods
Shatha Alosaimi, Noelle van Biljon, Denis Awany, Prisca K. Thami, Joel Defo, Jacquiline W. Mugo, Christian D. Bope, Gaston K. Mazandu, Nicola J. Mulder, Emile R. Chimusa
Summary: The study found that current variant calling tools produce high false positive and false negative rates when analyzing African data, emphasizing the need for the development of high sensitivity and precision variant calling approaches tailored for populations with high genetic variations and low linkage disequilibrium. VarDict and BCFtools performed the best when using African population data, showing potential for improved accuracy in variant calling in diverse populations.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Cleber A. Trujillo, Edward S. Rice, Nathan K. Schaefer, Isaac A. Chaim, Emily C. Wheeler, Assael A. Madrigal, Justin Buchanan, Sebastian Preissl, Allen Wang, Priscilla D. Negraes, Ryan A. Szeto, Roberto H. Herai, Alik Huseynov, Mariana S. A. Ferraz, Fernando S. Borges, Alexandre H. Kihara, Ashley Byrne, Maximillian Marin, Christopher Vollmers, Angela N. Brooks, Jonathan D. Lautz, Katerina Semendeferi, Beth Shapiro, Gene W. Yeo, Stephen E. P. Smith, Richard E. Green, Alysson R. Muotri
Summary: The evolutionarily conserved splicing regulator NOVA1 plays a crucial role in neural development and function, with a protein-coding difference between modern humans and Neanderthals. Reintroducing the archaic allele of NOVA1 into human induced pluripotent cells resulted in slower neural development and increased surface complexity, reflecting potential functional consequences for human evolution.
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Multidisciplinary Sciences
Alexander S. Leonard, Danang Crysnanto, Zih-Hua Fang, Michael P. Heaton, Brian L. Vander Ley, Carolina Herrera, Heinrich Bollwein, Derek M. Bickhart, Kristen L. Kuhn, Timothy P. L. Smith, Benjamin D. Rosen, Hubert Pausch
Summary: This study demonstrates the consistency of structural variant-based pangenomes regardless of sequence platform, assembler, or coverage using bovine haplotype-resolved assemblies. The study also reveals numerous structural variants overlapping with coding sequences that have the potential to affect phenotype.
NATURE COMMUNICATIONS
(2022)
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Infectious Diseases
Zongyi Bo, Yurun Miao, Rui Xi, Xiaoyu Gao, Denian Miao, Huan Chen, Yong-Sam Jung, Yingjuan Qian, Jianjun Dai
Summary: Two PRV variants, named JSY7 and JSY13 strains, were isolated from a Bartha-K61-vaccinated swine farm. These variants showed different cytopathic effects and plaque sizes, but had the same Aspartate insertions in the gE protein. Genomic analysis clustered JSY7 and JSY13 strains in the same clade with other PRV isolates in China. The study also revealed evidence of genomic recombination between the JSY13 strain and the Bartha and JSY7 strains, highlighting the importance of this process in PRV evolution and virulence.
TRANSBOUNDARY AND EMERGING DISEASES
(2021)
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Engineering, Electrical & Electronic
Zachary D. Drummond, Kevin E. Claytor, David R. Allee, David M. Hull
Summary: This study introduces two improvements to the subspace-based PMU algorithms based on ESPRIT frequency estimation, including a dynamic real-time thresholding method and reducing the computational burden of ESPRIT. The proposed algorithm shows near flat estimation error over changes in nominal system frequency, harmonic distortion, and out-of-band interference, while also running in real time on resource-constrained platforms.
IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT
(2021)
Article
Mathematics
Giuseppe Alessio D'Inverno, Sara Brunetti, Maria Lucia Sampoli, Dafin Fior Muresanu, Alessandra Rufa, Monica Bianchini
Summary: This study presents an algorithmic approach to analyze the Visual Sequential Search Test (VSST) using the episode matching method, showing different behaviors among patients with different pathologies under specific tasks.
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Chemistry, Analytical
C. Gassner, F. Lipsmeier, P. Metzger, H. Beck, A. Schnueriger, J. T. Regula, J. Moelleken
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2015)
Review
Chemistry, Medicinal
Alexander Jarasch, Hans Koll, Joerg T. Regula, Martin Bader, Apollon Papadimitriou, Hubert Kettenberger
JOURNAL OF PHARMACEUTICAL SCIENCES
(2015)
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Medicine, Research & Experimental
Wolfgang Schaefer, Hans R. Voelger, Stefan Lorenz, Sabine Imhof-Jung, Joerg T. Regula, Christian Klein, Michael Molhoj
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Medicine, Research & Experimental
Joerg T. Regula, Peter Lundh von Leithner, Richard Foxton, Veluchamy A. Barathi, Chui Ming Gemmy Cheung, Sai Bo Bo Tun, Yeo Sia Wey, Daiju Iwata, Miroslav Dostalek, Joerg Moelleken, Kay G. Stubenrauch, Everson Nogoceke, Gabriella Widmer, Pamela Strassburger, Michael J. Koss, Christian Klein, David T. Shima, Guido Hartmann
EMBO MOLECULAR MEDICINE
(2016)
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Medicine, Research & Experimental
Werner Scheuer, Markus Thomas, Petra Hanke, Johannes Sam, Franz Osl, Diana Weininger, Monika Baehner, Stefan Seeber, Hubert Kettenberger, Juergen Schanzer, Ulrich Brinkmann, K. Michael Weidner, Joerg Regula, Christian Klein
Review
Medicine, Research & Experimental
Christian Klein, Wolfgang Schaefer, Joerg T. Regula
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Chemistry, Analytical
W. Meschendoerfer, C. Gassner, F. Lipsmeier, J. T. Regula, J. Moelleken
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2017)
Review
Medicine, Research & Experimental
Christian Klein, Claudio Sustmann, Markus Thomas, Kay Stubenrauch, Rebecca Croasdale, Juergen Schanzer, Ulrich Brinkmann, Hubert Kettenberger, Joerg T. Regula, Wolfgang Schaefer
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Multidisciplinary Sciences
Markus Thomas, Yvonne Kienast, Werner Scheuer, Monika Baehner, Klaus Kaluza, Christian Gassner, Frank Herting, Ulrich Brinkmann, Stefan Seeber, Anita Kavlie, Martin Welschof, Stefan Ries, K. Michael Weidner, Joerg T. Regula, Christian Klein
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Multidisciplinary Sciences
Sebastian Fenn, Christian B. Schiller, Julia J. Griese, Harald Duerr, Sabine Imhof-Jung, Christian Gassner, Joerg Moelleken, Joerg Thomas Regula, Wolfgang Schaefer, Markus Thomas, Christian Klein, Karl-Peter Hopfner, Hubert Kettenberger
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Multidisciplinary Sciences
Jasmin F. Sydow, Florian Lipsmeier, Vincent Larraillet, Maximiliane Hilger, Bjoern Mautz, Michael Molhoj, Jan Kuentzer, Stefan Klostermann, Juergen Schoch, Hans R. Voelger, Joerg T. Regula, Patrick Cramer, Apollon Papadimitriou, Hubert Kettenberger
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Biochemistry & Molecular Biology
Joerg Thomas Regula, Sabine Imhof-Jung, Michael Molhoj, Joerg Benz, Andreas Ehler, Alexander Bujotzek, Wolfgang Schaefer, Christian Klein
PROTEIN ENGINEERING DESIGN & SELECTION
(2018)
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Biochemical Research Methods
Christian Klein, Wolfgang Schaefer, Joerg T. Regula, Charles Dumontet, Ulrich Brinkmann, Marina Bacac, Pablo Umana
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Medicine, Research & Experimental
Claudio Sustmann, Steffen Dickopf, Joerg T. Regula, Hubert Kettenberger, Michael Molhoj, Christian Gassner, Diana Weininger, Sebastian Fenn, Tobias Manigold, Lothar Kling, Klaus-Peter Kuenkele, Manfred Schwaiger, Birgit Bossenmaier, Julia J. Griese, Karl-Peter Hopfner, Alexandra Graff-Meyer, Henning Stahlberg, Philippe Ringler, Matthias E. Lauer, Ulrich Brinkmann, Wolfgang Schaefer, Christian Klein
Correction
Medicine, Research & Experimental
Jorg T. Regula, Peter Lundh von Leithner, Richard Foxton, Veluchamy A. Barathi, Chui Ming Gemmy Cheung, Sai Bo Bo Tun, Yeo Sia Wey, Daiju Iwata, Miroslav Dostalek, Jorg Moelleken, Kay G. Stubenrauch, Everson Nogoceke, Gabriella Widmer, Pamela Strassburger, Michael J. Koss, Christian Klein, David T. Shima, Guido Hartmann
EMBO MOLECULAR MEDICINE
(2017)