AUDACITY: a comprehensive approach for the detection and classification of Runs of Homozygosity in medical and population genomics
Publication date: Available online 14 July 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Alberto Magi, Tania Giangregorio, Roberto Semeraro, Giulia Carangelo, Flavia Palombo, Giovanni Romeo, Marco Seri, Tommaso Pippucci (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 15, 2020 Category: Biotechnology Source Type: research

Genome-wide Circadian Regulation: a Unique System for Computational Biology
Publication date: Available online 10 July 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Lingying Sun, Junjie Ma, Christoph W Turck, Pin Xu, Guang-Zhong Wang (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 12, 2020 Category: Biotechnology Source Type: research

A convenient protein library for spectroscopic calibrations
Publication date: Available online 10 July 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Joëlle De Meutter, Erik Goormaghtigh (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 10, 2020 Category: Biotechnology Source Type: research

Exploring Protein Phosphorylation by Combining Computational Approaches and Biochemical Methods
Publication date: Available online 7 July 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Gonzalo Pérez-Mejías, Alejandro Velázquez-Cruz, Alejandra Guerra-Castellano, Blanca Baños-Jaime, Antonio Díaz-Quintana, Katiuska González-Arzola, Miguel Ángel De la Rosa, Irene Díaz-Moreno (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 8, 2020 Category: Biotechnology Source Type: research

Finding new cancer epigenetic and genetic biomarkers from cell-free DNA by combining SALP-seq and machine learning
Publication date: Available online 7 July 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Shicai Liu, Jian Wu, Qiang Xia, Hongde Liu, Weiwei Li, Xinyi Xia, Jinke Wang (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 8, 2020 Category: Biotechnology Source Type: research

Pot1-tpp1 telomere length regulation and disease
Publication date: Available online 3 July 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Tomas Aramburu, Sarah Plucinsky Emmanuel Skordalakes (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 5, 2020 Category: Biotechnology Source Type: research

Integration of Single-Cell Multi-Omics for Gene Regulatory Network Inference
Publication date: Available online 29 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Xinlin Hu, Yaohua Hu, Fanjie Wu, Ricky Wai Tak Leung, Jing Qin (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 30, 2020 Category: Biotechnology Source Type: research

Directed evolution of the aryl-alcohol oxidase: beyond the lab bench
Publication date: Available online 29 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Javier Viña-Gonzalez, Miguel Alcalde (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 30, 2020 Category: Biotechnology Source Type: research

ProtExA: A Tool for Post-Processing Proteomics Data Providing Differential Expression Metrics, Co-Expression Networks and Functional Analytics
Publication date: Available online 29 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): George Minadakis, Kleitos Sokratous, George M. Spyrou (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 30, 2020 Category: Biotechnology Source Type: research

Rich-Club in the Brain’s Macrostructure: Insights from Graph Theoretical Analysis
Publication date: Available online 29 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Dae-Jin Kim, Byoung-Kyong Min (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 30, 2020 Category: Biotechnology Source Type: research

Protein Electrostatics: from Computational and Structural Analysis to Discovery of Functional Fingerprints and Biotechnological Design
Publication date: Available online 30 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Filippo Vascon, Matteo Gasparotto, Marta Giacomello, Laura Cendron, Elisabetta Bergantino, Francesco Filippini, Irene Righetto (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 30, 2020 Category: Biotechnology Source Type: research

COSMO: A dynamic programming algorithm for multicriteria codon optimization
Publication date: Available online 30 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Akito Taneda, Kiyoshi Asai (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 30, 2020 Category: Biotechnology Source Type: research

Advances of super-resolution fluorescence polarization microscopy and its applications in life sciences
Publication date: Available online 26 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Long Chen, Xingye Chen, Xusan Yang, Chao He, Miaoyan Wang, Michael Zhang, Peng Xi, Juntao Gao (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 27, 2020 Category: Biotechnology Source Type: research

Assessment of vector-host-pathogen relationships using data mining and machine learning
Publication date: Available online 25 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Diing D.M. Agany, Jose E. Pietri, Etienne Z. Gnimpieba (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 27, 2020 Category: Biotechnology Source Type: research

Genome mining strategies for ribosomally synthesised and post-translationally modified peptides
Publication date: Available online 25 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Alicia H. Russell, Andrew W. Truman (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 27, 2020 Category: Biotechnology Source Type: research

Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: molecular dynamics and ab initio molecular orbital simulations
Publication date: Available online 25 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Shusuke Suzuki, Toshiya Nakamura, Ryosuke Saito, Yuta Terauchi, Kentaro Kawai, Midori Takimoto-Kamimura, Noriyuki Kurita (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 27, 2020 Category: Biotechnology Source Type: research

From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes
Publication date: Available online 25 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Clémence Frioux, Dipali Singh, Tamas Korcsmaros, Falk Hildebrand (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 27, 2020 Category: Biotechnology Source Type: research

CRISPR-Sub: analysis of DNA substitution mutations caused by CRISPR-Cas9 in human cells
Publication date: Available online 25 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Gue-Ho Hwang, Jihyeon Yu, Soyeon Yang, Woo Jae Son, Kayeong Lim, Heon Seok Kim, Jin-Soo Kim, Sangsu Bae (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 27, 2020 Category: Biotechnology Source Type: research

Exploring the catalytic cascade of cembranoid biosynthesis by combination of genetic engineering and molecular simulations
Publication date: Available online 25 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Patrick Schrepfer, Ilke Ugur, Sven Klumpe, Bernhard Loll, Ville R.I. Kaila, Thomas Brück (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 27, 2020 Category: Biotechnology Source Type: research

Statistical methods for the estimation of contagion effects in human disease and health networks
Publication date: Available online 25 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Ran Xu (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 27, 2020 Category: Biotechnology Source Type: research

Energy flow and intersubunit signalling in gsam: a non-equilibrium molecular dynamics study
Publication date: Available online 25 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): C. Harder-Viddal, R.M. Roshko, J. Stetefeld (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 25, 2020 Category: Biotechnology Source Type: research

Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces
Publication date: Available online 21 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Namil Lee, Soonkyu Hwang, Jihun Kim, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 22, 2020 Category: Biotechnology Source Type: research

Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities
Publication date: Available online 21 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Susan Idicula-Thomas, Ulka Gawde, Sameeksha Bhaye, Khushal Pokar, Gary D. Bader (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 22, 2020 Category: Biotechnology Source Type: research

Modeling and analysis of site-specific mutations in cancer identifies known plus putative novel hotspots and bias due to contextual sequences
Publication date: Available online 20 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Victor Trevino (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 21, 2020 Category: Biotechnology Source Type: research

Computational approaches in viral ecology
Publication date: Available online 19 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Varada Khot, Marc Strous, Alyse K. Hawley (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 19, 2020 Category: Biotechnology Source Type: research

Structures of Hyperstable Ancestral Haloalkane Dehalogenases Show Restricted Conformational Dynamics
Publication date: Available online 19 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Petra Babkova, Zuzana Dunajova, Radka Chaloupkova, Jiri Damborsky, David Bednar, Martin Marek (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 19, 2020 Category: Biotechnology Source Type: research

The search of sequence variants using a constrained protein evolution simulation approach
Publication date: Available online 17 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Pierre Tuffery, Sjoerd de Vries (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 18, 2020 Category: Biotechnology Source Type: research

Essential Site Scanning Analysis: a new approach for detecting sites that modulate the dispersion of protein global motions
Publication date: Available online 18 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Burak T. Kaynak, Ivet Bahar, Pemra Doruker (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 18, 2020 Category: Biotechnology Source Type: research

Statistical methods for SNP heritability estimation and partition: A review
Publication date: Available online 18 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Huanhuan Zhu, Xiang Zhou (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 18, 2020 Category: Biotechnology Source Type: research

Rapid preliminary purity evaluation of tumor biopsies using deep learning approach
Publication date: Available online 16 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Fei Fan, Dan Chen, Yu Zhao, Huating Wang, Hao Sun, Kun Sun (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 18, 2020 Category: Biotechnology Source Type: research

Deep learning models in genomics; are we there yet?
Publication date: Available online 17 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Lefteris Koumakis (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 18, 2020 Category: Biotechnology Source Type: research

Exploring the structural basis of conformational heterogeneity and autoinhibition of human cGMP-specific Protein Kinase Iα through computational modelling and molecular dynamics simulations
Publication date: Available online 12 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Arooma Maryam, Rana Rehan Khalid, Sundeep Chaitanya Vedithi, Abdulilah Ece, Suleyman Selim Çınaroğlu, Abdul Rauf Siddiqi, Tom L. Blundell (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 13, 2020 Category: Biotechnology Source Type: research

Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation
Publication date: Available online 12 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Seungbyn Baek, Insuk Lee (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 13, 2020 Category: Biotechnology Source Type: research

Turning genome-wide association study findings into opportunities for drug repositioning
Publication date: Available online 12 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Alexandria Li-Ching Lau, Hon-Cheong So (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 13, 2020 Category: Biotechnology Source Type: research

C-Jun N-terminal kinase inhibitors: structural insight into kinase-inhibitor complexes
Publication date: Available online 12 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Men Thi Hoai Duong, Joon-Hwa Lee, Hee-Chul Ahn (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 13, 2020 Category: Biotechnology Source Type: research

Handling multi-mapped reads in RNA-seq
Publication date: Available online 12 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Gabrielle Deschamps-Francoeur, Joël Simoneau, Michelle S Scott (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 13, 2020 Category: Biotechnology Source Type: research

Machine learning approach to predict medication overuse in migraine patients
Publication date: Available online 12 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Patrizia Ferroni, Fabio M. Zanzotto, Noemi Scarpato, Antonella Spila, Luisa Fofi, Gabriella Egeo, Alessandro Rullo, Raffaele Palmirotta, Piero Barbanti, Fiorella Guadagni (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 13, 2020 Category: Biotechnology Source Type: research

Bioinformatics approaches for deciphering the epitranscriptome: recent progress and emerging topics
Publication date: Available online 13 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Lian Liu, Bowen Song, Jiani Ma, Yi Song, Song-Yao Zhang, Yujiao Tang, Xiangyu Wu, Zhen Wei, Kunqi Chen, Jionglong Su, Rong Rong, Zhiliang Lu, João Pedro de Magalhães, Daniel J. Rigden, Lin Zhang, Shao-Wu Zhang, Yufei Huang, Xiujuan Lei, Hui Liu, Jia Meng (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 13, 2020 Category: Biotechnology Source Type: research

Electron Microscopy-based semi-automated characterization of aggregation in monoclonal antibody products
Publication date: Available online 11 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Mohit Kumar, Apoorv Pant, Rohit Bansal, Ashutosh Pandey, James Gomes, Kedar Khare, Anurag Singh Rathore, Manidipa Banerjee (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 12, 2020 Category: Biotechnology Source Type: research

A systematic strategy for the investigation of vaccines and drugs targeting bacteria
Publication date: Available online 12 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Fangfang Yan, Feng Gao (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 12, 2020 Category: Biotechnology Source Type: research

Glycosyltransferase GT1 Family: phylogenetic distribution, substrates coverage, and representative structural features
Publication date: Available online 10 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Peng Zhang, Zheng Zhang, Lijuan Zhang, Jingjing Wang, Changsheng Wu (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 11, 2020 Category: Biotechnology Source Type: research

Structural modeling, mutation analysis, and in vitro expression of usherin, a major protein in inherited retinal degeneration and hearing loss
Publication date: Available online 10 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Dongmei Yu, Junhuang Zou, Qian Chen, Tian Zhu, Ruifang Sui, Jun Yang (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 11, 2020 Category: Biotechnology Source Type: research

Computational prediction of protein aggregation: advances in proteomics, conformation-specific algorithms and biotechnological applications
Publication date: Available online 10 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Jaime Santos, Jordi Pujols, Irantzu Pallarès, Valentín Iglesias, Salvador Ventura (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 10, 2020 Category: Biotechnology Source Type: research

Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions
Publication date: Available online 10 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Seungjin Na, Eunok Paek (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 10, 2020 Category: Biotechnology Source Type: research

IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity
Publication date: Available online 2 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Alireza Sahaf Naeini, Amna Farooq, Magnar Bjørås, Junbai Wang (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 9, 2020 Category: Biotechnology Source Type: research

HiPR: High-throughput Probabilistic RNA structure inference
Publication date: Available online 8 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Pavel P. Kuksa, Fan Li, Sampath Kannan, Brian D. Gregory, Yuk Yee Leung, Li-San Wang (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 9, 2020 Category: Biotechnology Source Type: research

Plasma lipidomic biomarker analysis reveals distinct lipid changes in vascular dementia
Publication date: Available online 9 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Yue Liu, Daniel KY Chan, Anbupalam Thalamuthu, Wei Wen, Jiyang Jiang, Matthew Paradise, Teresa Lee, John Crawford, Matthew Wai Kin Wong, Ying Hua Xu, Anne Poljak, Russell Pickford, Perminder S Sachdev, Nady Braidy (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 9, 2020 Category: Biotechnology Source Type: research

Single-molecule optical microscopy of protein dynamics and computational analysis of images to determine cell structure development in differentiating Bacillus subtilis
Publication date: Available online 9 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Adam J.M. Wollman, Katarína Muchová, Zuzana Chromiková, Anthony J. Wilkinson, Imrich Barák, Mark C. Leake (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 9, 2020 Category: Biotechnology Source Type: research

Software tools for 3D nuclei segmentation and quantitative analysis in multicellular aggregates
Publication date: Available online 3 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Filippo Piccinini, Tamas Balassa, Antonella Carbonaro, Akos Diosdi, Timea Toth, Nikita Moshkov, Ervin A. Tasnadi, Peter Horvath (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 4, 2020 Category: Biotechnology Source Type: research

Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family
Publication date: Available online 3 June 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Martin Marek, Radka Chaloupkova, Tatyana Prudnikova, Yukari Sato, Pavlina Rezacova, Yuji Nagata, Ivana Kuta Smatanova, Jiri Damborsky (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 4, 2020 Category: Biotechnology Source Type: research