PeerJ Editor, Author & Reviewer

3,790 Points

Contributions by role

Contributions by subject area

Ugo Bastolla

PeerJ Editor, Author & Reviewer

Summary

I got my PhD in Physics at Rome University, working with Luca Peliti and Giorgio Parisi on biologically inspired problems: evolutionary models and Boolean networks. Since then, I have always been interested in computational biology: Protein folding, Stability and population biology constraints in protein evolution, Conformation changes in proteins, Structural evolution of proteins, Theoretical ecology, Ecological interactions among microorganisms.

Bioinformatics Computational Biology Ecology Evolutionary Studies

Editorial Board Member

PeerJ - the Journal of Life & Environmental Sciences

Past or current institution affiliations

Universidad Autónoma de Madrid

Work details

Researcher

Center for Molecular Biology Severo Ochoa, Madrid

Bioinformatics Unit

Researcher

Consejo Superior de Investigaciones Científicas (CSIC)

Bioinformatics Unit

Websites

PeerJ Contributions

October 5, 2018

Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution

María José Jiménez-Santos, Miguel Arenas, Ugo Bastolla

https://doi.org/10.7717/peerj.5549 PubMed 30310736

December 5, 2016

Learning structural bioinformatics and evolution with a snake puzzle

Gonzalo S. Nido, Ludovica Bachschmid-Romano, Ugo Bastolla, Alberto Pascual-García

https://doi.org/10.7717/peerj-cs.100

April 18, 2018 - Version: 1

Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution

María José Jiménez-Santos, Miguel Arenas, Ugo Bastolla

https://doi.org/10.7287/peerj.preprints.26868v1

July 1, 2016 - Version: 1

Learning protein folding and evolution with a snake puzzle

Gonzalo S Nido, Ludovica Bachschmid-Romano, Ugo Bastolla, Alberto Pascual-García

https://doi.org/10.7287/peerj.preprints.2201v1

Academic Editor on

April 28, 2025

Robust phylogenetic profile clustering for Saccharomyces cerevisiae proteins

Paul M. Harrison

https://doi.org/10.7717/peerj.19370 PubMed 40313378

April 22, 2024

Kernel density estimation of allele frequency including undetected alleles

Satoshi Aoki, Keita Fukasawa

https://doi.org/10.7717/peerj.17248 PubMed 38666077

August 18, 2022

Incorporating nonlinearity with generalized functional responses to simulate multiple predator effects

Michael W. McCoy, Elizabeth Hamman, Molly Albecker, Jeremy Wojdak, James R. Vonesh, Benjamin M. Bolker

https://doi.org/10.7717/peerj.13920 PubMed 35999847

November 2, 2021

Senescence as a trade-off between successful land colonisation and longevity: critical review and analysis of a hypothesis

Tomasz Bilinski, Aneta Bylak, Krzysztof Kukuła, Renata Zadrag-Tecza

https://doi.org/10.7717/peerj.12286 PubMed 34760360

August 20, 2021

Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer’s disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study

Kelly Cardona, Javier Medina, Mary Orrego-Cardozo, Francia Restrepo de Mejía, Xabier Elcoroaristizabal, Carlos Andrés Naranjo Galvis

https://doi.org/10.7717/peerj.12016 PubMed 34484988

May 12, 2021

Differentially expressed genes, lncRNAs, and competing endogenous RNAs in Kawasaki disease

Changsheng Guo, Yuanqing Hua, Zuanhao Qian

https://doi.org/10.7717/peerj.11169 PubMed 34026343

February 24, 2021

Low compositions of human toll-like receptor 7/8-stimulating RNA motifs in the MERS-CoV, SARS-CoV and SARS-CoV-2 genomes imply a substantial ability to evade human innate immunity

Chu-Wen Yang, Mei-Fang Chen

https://doi.org/10.7717/peerj.11008 PubMed 33665043

May 11, 2020

The spindle assembly checkpoint and speciation

Robert C. Jackson, Hitesh B. Mistry

https://doi.org/10.7717/peerj.9073 PubMed 32435535

March 20, 2020

Identification of key gene modules and hub genes of human mantle cell lymphoma by coexpression network analysis

Dongmei Guo, Hongchun Wang, Li Sun, Shuang Liu, Shujing Du, Wenjing Qiao, Weiyan Wang, Gang Hou, Kaigang Zhang, Chunpu Li, Qingliang Teng

https://doi.org/10.7717/peerj.8843 PubMed 32219041

January 6, 2020

Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species

Zhanjun Wang, Beibei Xu, Bao Li, Qingqing Zhou, Guiyi Wang, Xingzhou Jiang, Chenchen Wang, Zhongdong Xu

https://doi.org/10.7717/peerj.8251 PubMed 31934501

May 28, 2019

Identify CRNDE and LINC00152 as the key lncRNAs in age-related degeneration of articular cartilage through comprehensive and integrative analysis

Pengfei Hu, Fangfang Sun, Jisheng Ran, Lidong Wu

https://doi.org/10.7717/peerj.7024 PubMed 31179196

September 17, 2018

Zooming into plant-flower visitor networks: an individual trait-based approach

Beatriz Rumeu, Danny J. Sheath, Joseph E. Hawes, Thomas C. Ings

https://doi.org/10.7717/peerj.5618 PubMed 30245938

July 24, 2018

Imputing missing distances in molecular phylogenetics

Xuhua Xia

https://doi.org/10.7717/peerj.5321 PubMed 30065887

June 12, 2018

A relationship between species richness and evenness that depends on specific relative abundance distribution

Qiang Su

https://doi.org/10.7717/peerj.4951 PubMed 29910980

March 8, 2017

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

Elaina D. Graham, John F. Heidelberg, Benjamin J. Tully

https://doi.org/10.7717/peerj.3035 PubMed 28289564

February 9, 2017

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

Alex D. Washburne, Justin D. Silverman, Jonathan W. Leff, Dominic J. Bennett, John L. Darcy, Sayan Mukherjee, Noah Fierer, Lawrence A. David

https://doi.org/10.7717/peerj.2969 PubMed 28289558

December 6, 2016

Aging and cardiovascular complexity: effect of the length of RR tachograms

Karthi Balasubramanian, Nithin Nagaraj

https://doi.org/10.7717/peerj.2755 PubMed 27957395

September 21, 2016

Chromosomal rearrangements and protein globularity changes in Mycobacterium tuberculosis isolates from cerebrospinal fluid

Seow Hoon Saw, Joon Liang Tan, Xin Yue Chan, Kok Gan Chan, Yun Fong Ngeow

https://doi.org/10.7717/peerj.2484 PubMed 27688977

September 20, 2016

Are sites with multiple single nucleotide variants in cancer genomes a consequence of drivers, hypermutable sites or sequencing errors?

Thomas C.A. Smith, Antony M. Carr, Adam C. Eyre-Walker

https://doi.org/10.7717/peerj.2391 PubMed 27688957

July 19, 2016

Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures

Kok-Gan Chan, Kumutha Priya, Chien-Yi Chang, Ahmad Yamin Abdul Rahman, Kok Keng Tee, Wai-Fong Yin

https://doi.org/10.7717/peerj.2223 PubMed 27547539

June 29, 2016

Emergent properties of a computational model of tumour growth

Pan Pantziarka

https://doi.org/10.7717/peerj.2176 PubMed 27413638

January 14, 2016

Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus

Felipe Coutinho, Diogo Antonio Tschoeke, Fabiano Thompson, Cristiane Thompson

https://doi.org/10.7717/peerj.1522 PubMed 26839740

March 24, 2015

Bayesian inference of protein structure from chemical shift data

Lars A. Bratholm, Anders S. Christensen, Thomas Hamelryck, Jan H. Jensen

https://doi.org/10.7717/peerj.861 PubMed 25825683

October 3, 2013

iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins

Yan Xu, Xiao-Jian Shao, Ling-Yun Wu, Nai-Yang Deng, Kuo-Chen Chou

https://doi.org/10.7717/peerj.171 PubMed 24109555