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LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries

JOURNAL ARTICLE published 2023 in Computational and Structural Biotechnology Journal

Research funded by Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (180544)

Authors: David Patsch | Michael Eichenberger | Moritz Voss | Uwe T. Bornscheuer | Rebecca M. Buller

https://doi.org/10.1016/j.csbj.2023.09.013

A computational design approach for virtual screening of peptide interactions across K + channel families

JOURNAL ARTICLE published 2015 in Computational and Structural Biotechnology Journal

Authors: Craig A. Doupnik | Katherine C. Parra | Wayne C. Guida

https://doi.org/10.1016/j.csbj.2014.11.004

Finding new cancer epigenetic and genetic biomarkers from cell-free DNA by combining SALP-seq and machine learning

JOURNAL ARTICLE published 2020 in Computational and Structural Biotechnology Journal

Research funded by National Natural Science Foundation of China (61971122)

Authors: Shicai Liu | Jian Wu | Qiang Xia | Hongde Liu | Weiwei Li | Xinyi Xia | Jinke Wang

https://doi.org/10.1016/j.csbj.2020.06.042

Applying data mining techniques to medical time series: an empirical case study in electroencephalography and stabilometry

JOURNAL ARTICLE published 2016 in Computational and Structural Biotechnology Journal

Authors: A. Anguera | J.M. Barreiro | J.A. Lara | D. Lizcano

https://doi.org/10.1016/j.csbj.2016.05.002

A Structural Perspective on the Regulation of Human Single-Stranded DNA Binding Protein 1 (hSSB1, OBFC2B) Function in DNA Repair

JOURNAL ARTICLE published 2019 in Computational and Structural Biotechnology Journal

Authors: Teegan Lawson | Serene El-Kamand | Ruvini Kariawasam | Derek J. Richard | Liza Cubeddu | Roland Gamsjaeger

https://doi.org/10.1016/j.csbj.2019.03.014

Experimental and computational approaches to unravel microbial community assembly

JOURNAL ARTICLE published 2020 in Computational and Structural Biotechnology Journal

Authors: Daniel Aguirre de Cárcer

https://doi.org/10.1016/j.csbj.2020.11.031

Nextcast: A software suite to analyse and model toxicogenomics data

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Authors: Angela Serra | Laura Aliisa Saarimäki | Alisa Pavel | Giusy del Giudice | Michele Fratello | Luca Cattelani | Antonio Federico | Omar Laurino | Veer Singh Marwah | Vittorio Fortino | Giovanni Scala | Pia Anneli Sofia Kinaret | Dario Greco

https://doi.org/10.1016/j.csbj.2022.03.014

The synergistic interaction landscape of chromatin regulators reveals their epigenetic regulation mechanisms across five cancer cell lines

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Authors: Meng Cao | Liqiang Wang | Dahua Xu | Xiaoman Bi | Shengnan Guo | Zhizhou Xu | Liyang Chen | Dehua Zheng | Peihu Li | Jiankai Xu | Shaojiang Zheng | Hong Wang | Bo Wang | Jianping Lu | Kongning Li

https://doi.org/10.1016/j.csbj.2022.09.008

Multiple transcription auto regulatory loops can act as robust oscillators and decision-making motifs

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Research funded by Science and Engineering Research Board (CRG/2019/001208,MTR/2019/00002) | National Institutes of Health (R01EY026025)

Authors: Rajamanickam Murugan | Gabriel Kreiman

https://doi.org/10.1016/j.csbj.2022.08.065

First thermostable CLIP-tag by rational design applied to an archaeal O-alkyl-guanine-DNA-alkyl-transferase

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Authors: Rosa Merlo | Rosanna Mattossovich | Marianna Genta | Anna Valenti | Giovanni Di Mauro | Alberto Minassi | Riccardo Miggiano | Giuseppe Perugino

https://doi.org/10.1016/j.csbj.2022.09.015

Identification of new head and neck squamous cell carcinoma subtypes and development of a novel score system (PGSscore) based on variations in pathway activity between tumor and adjacent non-tumor samples

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Authors: Yufan Zhang | Ying Liu | Junfei Huang | Zhiqi Hu | Yong Miao

https://doi.org/10.1016/j.csbj.2022.08.057

Recognition of the ligand-induced spatiotemporal residue pair pattern of β2-adrenergic receptors using 3-D residual networks trained by the time series of protein distance maps

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Research funded by National Research Foundation of Korea (NRF- 2019M3E5D4065299)

Authors: Minwoo Han | Seungju Lee | Yuna Ha | Jee-Young Lee

https://doi.org/10.1016/j.csbj.2022.10.036

Electron density is not spherical: the many applications of the transferable aspherical atom model

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Authors: Marta Kulik | Paulina M. Dominiak

https://doi.org/10.1016/j.csbj.2022.10.018

MLSP: A bioinformatics tool for predicting molecular subtypes and prognosis in patients with breast cancer

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Research funded by National Natural Science Foundation of China (31671447,81903539)

Authors: Jie Zhu | Weikaixin Kong | Liting Huang | Shixin Wang | Suzhen Bi | Yin Wang | Peipei Shan | Sujie Zhu

https://doi.org/10.1016/j.csbj.2022.11.017

ProxyBind: A compendium of binding sites for proximity-induced pharmacology

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Authors: Evianne Rovers | Lihua Liu | Matthieu Schapira

https://doi.org/10.1016/j.csbj.2022.11.010

RNAME: A comprehensive database of RNA modification enzymes

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Research funded by National Natural Science Foundation of China (31771471) | Natural Science Foundation of Sichuan Province (2022NSFSC1770)

Authors: Fulei Nie | Qiang Tang | Ying Liu | Huaizhi Qin | Shilong Liu | Meng Wu | Pengmian Feng | Wei Chen

https://doi.org/10.1016/j.csbj.2022.11.022

The NPR/Hal family of protein kinases in yeasts: biological role, phylogeny and regulation under environmental challenges

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Research funded by Fundação para a Ciência e a Tecnologia (2022.01501,LA/P/0140/2020,PD/BD/142944/2018) | Institute for Bioengineering and Biosciences (UIDB/04565/2020,UIDP/04565/2020)

Authors: Miguel Antunes | Isabel Sá-Correia

https://doi.org/10.1016/j.csbj.2022.10.006

Mammalian RNA switches: Molecular rheostats in gene regulation, disease, and medicine

JOURNAL ARTICLE published 2019 in Computational and Structural Biotechnology Journal

Research funded by National Institutes of Health (R01 HL132899,R01HL147954) | American Heart Association (13SDG15970006)

Authors: Kadiam C. Venkata Subbaiah | Omar Hedaya | Jiangbin Wu | Feng Jiang | Peng Yao

https://doi.org/10.1016/j.csbj.2019.10.001

A conserved Neurite Outgrowth and Guidance motif with biomimetic potential in neuronal Cell Adhesion Molecules

JOURNAL ARTICLE published 2021 in Computational and Structural Biotechnology Journal

Research funded by Università degli Studi di Padova (PRAT2015 CPDA151948)

Authors: Giorgia Scapin | Matteo Gasparotto | Daniele Peterle | Simone Tescari | Elena Porcellato | Alberto Piovesan | Irene Righetto | Laura Acquasaliente | Vincenzo De Filippis | Francesco Filippini

https://doi.org/10.1016/j.csbj.2021.10.005

Mechanical and Systems Biology of Cancer

JOURNAL ARTICLE published 2018 in Computational and Structural Biotechnology Journal

Research funded by Stand Up to Cancer Campaign for Cancer Research UK (C37275/A20146)

Authors: Fabian Spill | Chris Bakal | Michael Mak

https://doi.org/10.1016/j.csbj.2018.07.002