HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http:// htsstation.epfl.ch

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.Peer Reviewe

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

A multitude of factors contribute to complex diseases and can be measured with ‘omics’ methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the Virtual Metabolic Human (VMH, www.vmh.life) database encapsulating current knowledge of human metabolism within five interlinked resources ‘Human metabolism’, ‘Gut microbiome’, ‘Disease’, ‘Nutrition’, and ‘ReconMaps’. The VMH captures 5180 unique metabolites, 17 730 unique reactions, 3695 human genes, 255 Mendelian diseases, 818 microbes, 632 685 microbial genes and 8790 food items. The VMH’s unique features are (i) the hosting of the metabolic reconstructions of human and gut microbes amenable for metabolic modeling; (ii) seven human metabolic maps for data visualization; (iii) a nutrition designer; (iv) a user-friendly webpage and application-programming interface to access its content; (v) user feedback option for community engagement and (vi) the connection of its entities to 57 other web resources. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community

Quantifying ChIP-seq data:A spiking method providing an internal reference for sample-to-sample normalization

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments are widely used to determine, within entire genomes, the occupancy sites of any protein of interest, including, for example, transcription factors, RNA polymerases, or histones with or without various modifications. In addition to allowing the determination of occupancy sites within one cell type and under one condition, this method allows, in principle, the establishment and comparison of occupancy maps in various cell types, tissues, and conditions. Such comparisons require, however, that samples be normalized. Widely used normalization methods that include a quantile normalization step perform well when factor occupancy varies at a subset of sites, but may miss uniform genome-wide increases or decreases in site occupancy. We describe a spike adjustment procedure (SAP) that, unlike commonly used normalization methods intervening at the analysis stage, entails an experimental step prior to immunoprecipitation. A constant, low amount from a single batch of chromatin of a foreign genome is added to the experimental chromatin. This "spike" chromatin then serves as an internal control to which the experimental signals can be adjusted. We show that the method improves similarity between replicates and reveals biological differences including global and largely uniform changes

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

© 2024 Niarakis, Ostaszewski, Mazein, Kuperstein, Kutmon, Gillespie, Funahashi, Acencio, Hemedan, Aichem, Klein, Czauderna, Burtscher, Yamada, Hiki, Hiroi, Hu, Pham, Ehrhart, Willighagen, Valdeolivas, Dugourd, Messina, Esteban-Medina, Peña-Chilet, Rian, Soliman, Aghamiri, Puniya, Naldi, Helikar, Singh, Fernández, Bermudez, Tsirvouli, Montagud, Noël, Ponce-de-Leon, Maier, Bauch, Gyori, Bachman, Luna, Piñero, Furlong, Balaur, Rougny, Jarosz, Overall, Phair, Perfetto, Matthews, Rex, Orlic-Milacic, Gomez, De Meulder, Ravel, Jassal, Satagopam, Wu, Golebiewski, Gawron, Calzone, Beckmann, Evelo, D’Eustachio, Schreiber, Saez-Rodriguez, Dopazo, Kuiper, Valencia, Wolkenhauer, Kitano, Barillot, Auffray, Balling, Schneider and the COVID-19 Disease Map Community. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing.Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors.Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19.Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.The author(s) declare financial support was received for the research, authorship, and/or publication of this article. AN acknowledges support from SANOFI-AVENTIS R&D via the CIFRE contract, n° 2020/0766. MK, FH, NP, FE, and CE acknowledge the support of the ZonMw COVID-19 programme (Grant No. 10430012010015). JD Spanish Ministry of Science and Innovation (Grant no. PID2020-117979RB-I00) and Instituto de Salud Carlos III (Grant no. IMP/00019). MAi, KK, FS: Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 251654672 - TRR 161 and under Germany’s Excellence Strategy - EXC 2117 - 422037984. FM: “5 per 1000–2021” grant of the Italian Ministry of Health (Grant No. 5M-2021-23683787) and European Commission with HORIZON programme, BY-COVID project (Grant No. 101046203—BY-COVID). National Institute for Infectious Diseases Lazzaro Spallanzani–IRCCS received financial support from the Italian Ministry of Health grant “Ricerca Corrente”. JP, LF: IMI2-JU grants, resources which are composed of financial contributions from the European Union’s Horizon 2020 Research and Innovation Programme and EFPIA [GA: 777365 eTRANSAFE], and the EU H2020 Programme [GA:964537 RISKHUNT3R]; Project 001-P-001647—Valorisation of EGA for Industry and Society funded by the European Regional Development Fund (ERDF) and Generalitat de Catalunya; Institute of Health Carlos III (project IMPaCT-Data, exp. IMP/00019), co-funded by the European Union, European Regional Development Fund (ERDF, “A way to make Europe”). AMo, MP and AV acknowledge the support of the European Commission under the INFORE project (H2020-ICT-825070) and the PerMedCoE (H2020-ICT-951773). Contributions by TH and BLP were supported by NIH grant #R35GM119770 to TH. MaGo acknowledges funding from Deutsche Forschungsgemeinschaft (DFG) through grants no. 442326535 (NFDI4Health) and 451265285 (NFDI4Health Task Force COVID-19), from the European Commission through the Horizon 2020 framework program under grant no. 825843 (EU-STANDS4PM) and through the Digital Europe program under grant no. 101083771 (EDITH), as well as from the Klaus Tschira Foundation. AL acknowledges support from the Intramural Research Program of the National Library of Medicine (NLM), National Institutes of Health (NIH).Peer reviewe

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

IntroductionThe COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. MethodsExtensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors.ResultsResults revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. DiscussionThe key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies

IMP ver. 1.4 docker image

<p>This upload contains the the IMP docker image ver. 1.4</p> <p>For more information visit the IMP website: http://r3lab.uni.lu/web/imp/</p> <p>Documentation available at: http://r3lab.uni.lu/web/imp/</p

IMP HTML reports

This file contains all the HTML reports generated by IMP for the analysis of datasets reported in the article

IMP small scale test dataset

<p>This file contains the test data set used within the article:</p> <p><strong>IMP: a reproducible pipeline for reference-independent integrated metagenomic and metatranscriptomic analyses</strong></p> <p>Shaman Narayanasamy^†, Yohan Jarosz^†, Emilie E.L. Muller, Cédric C. Laczny, Malte Herold, Anne Kaysen, Anna Heintz-Buschart, Nicolás Pinel, Patrick May, and Paul Wilmes^*</p> <p>Preprint: http://biorxiv.org/content/early/2016/02/10/039263</p> <p> </p> <p>This test data set was used for benchmarking the run times of IMP. They are derived by selecting the first 5% of reads from a wastewater sludge microbial community dataset (see manuscript and original publication of data: 10.1038/ncomms6603). Also included are the respective preprocessed FASTQ files such that IMP can be tested without running the preprocessing step. A README file inside the folder briefly describes the different FASTQ files contained in the folder.</p

IMP test data set

<p>This file contains the test data set used within the article:</p> <p><strong>IMP: a reproducible pipeline for reference-independent integrated metagenomic and metatranscriptomic analyses</strong></p> <p>Shaman Narayanasamy^†, Yohan Jarosz^†, Emilie E.L. Muller, Cédric C. Laczny, Malte Herold, Anne Kaysen, Anna Heintz-Buschart, Nicolás Pinel, Patrick May, and Paul Wilmes^*</p> <p>Preprint: http://biorxiv.org/content/early/2016/02/10/039263</p> <p>This test data set was used for benchmarking the run times of IMP. They are derived by selecting the first 5% of reads from a wastewater sludge microbial community dataset (see manuscript). Also included are the respective preprocessed FASTQ files such that IMP can be tested without running the preprocessing step. A README file inside the folder briefly describes the different FASTQ files contained in the folder.</p