Visualization of omics data for systems biology

N Gehlenborg, SI O'donoghue, NS Baliga… - Nature …, 2010 - nature.com
High-throughput studies of biological systems are rapidly accumulating a wealth of'omics'-
scale data. Visualization is a key aspect of both the analysis and understanding of these …

Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool

I Letunic, P Bork - Nucleic acids research, 2024 - academic.oup.com
Abstract The Interactive Tree Of Life (https://itol. embl. de) is an online tool for the
management, display, annotation and manipulation of phylogenetic and other trees. It is …

Visualization of biomedical data

SI O'Donoghue, BF Baldi, SJ Clark… - Annual Review of …, 2018 - annualreviews.org
The rapid increase in volume and complexity of biomedical data requires changes in
research, communication, and clinical practices. This includes learning how to effectively …

ggmsa: A visual exploration tool for multiple sequence alignment and associated data

L Zhou, T Feng, S Xu, F Gao, TT Lam… - Briefings in …, 2022 - academic.oup.com
The identification of the conserved and variable regions in the multiple sequence alignment
(MSA) is critical to accelerating the process of understanding the function of genes. MSA …

Continuous distributed representation of biological sequences for deep proteomics and genomics

E Asgari, MRK Mofrad - PloS one, 2015 - journals.plos.org
We introduce a new representation and feature extraction method for biological sequences.
Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors …

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

I Letunic, P Bork - Nucleic acids research, 2016 - academic.oup.com
Abstract Interactive Tree Of Life (http://itol. embl. de) is a web-based tool for the display,
manipulation and annotation of phylogenetic trees. It is freely available and open to …

Visual comparison for information visualization

M Gleicher, D Albers, R Walker, I Jusufi… - Information …, 2011 - journals.sagepub.com
Data analysis often involves the comparison of complex objects. With the ever increasing
amounts and complexity of data, the demand for systems to help with these comparisons is …

The ocean sampling day consortium

A Kopf, M Bicak, R Kottmann, J Schnetzer, I Kostadinov… - Gigascience, 2015 - Springer
Abstract Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial
Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine …

Visualization of macromolecular structures

SI O'donoghue, DS Goodsell, AS Frangakis… - Nature …, 2010 - nature.com
Structural biology is rapidly accumulating a wealth of detailed information about protein
function, binding sites, RNA, large assemblies and molecular motions. These data are …

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

GA Pavlopoulos, D Malliarakis, N Papanikolaou… - …, 2015 - academic.oup.com
Abstract “Α picture is worth a thousand words.” This widely used adage sums up in a few
words the notion that a successful visual representation of a concept should enable easy …