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Elena Papaleo
Bronze Contributor
5,955 Points

Contributions by role

Author 270
Editor 5,685

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Biochemistry
Computational Biology
Bioinformatics
Genomics
Evolutionary Studies
Genetics
Molecular Biology
Zoology
Dermatology
Oncology
Orthopedics
Rheumatology
Gastroenterology and Hepatology
Hematology
Cell Biology
Agricultural Science
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Biogeography
Ecology
Mathematical Biology
Paleontology
Urology
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Medical Genetics
Nephrology
Respiratory Medicine
Computational Science
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Otorhinolaryngology
Data Mining and Machine Learning
Biotechnology
Surgery and Surgical Specialties
Biophysics
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Bronze Contributor

Elena Papaleo

PeerJ Author

Summary

Elena Papaleo completed her PhD in 2006 and Post-doctoral from 2007-2009 at the Department of Biotechnology and Bioscience at the University of Milano-Bicocca (Italy) in the group of Prof. Luca De Gioia and Prof. Piercarlo Fantucci. She was then appointed as Adjunct Professor in Computational Biology at the University of Milano-Bicocca from 2010-2012. Afterwards, she was Senior Post-Doctoral Researcher in the group of Prof. Lindorff-Larsen at the Department of Biology of the University of Copenhagen (Denmark) from 2011-2015. She has been Visiting Researcher at many international institutes including the group of Prof. Salvador Ventura at the Institute of Biotechnology and Biomedicine (IBB, Barcelona, Spain) and the group of Prof. Francesco Luigi Gervasio at the Spanish National Cancer Research Center (CNIO, Madrid, Spain). In August 2015, she joined as Group Leader of the Computational Biology (CBL) Laboratory at the Danish Cancer Society Research Center (Copenhagen, Denmark). In 2018, she also become Associate Professor at the University of Copenhagen (Center for Protein Research). She has authored more than 90 publications, of which 50 scientific papers as main or senior author and she is Academic Editor of PLOS One, Frontiers in Molecular Biosciences, PeerJ, and Journal of Molecular Graphics and Modelling.

Adaptive & Self-Organizing Systems Algorithms & Analysis of Algorithms Biochemistry Bioinformatics Biomolecules Biophysical Chemistry Biophysics Biotechnology Computational Biology Computer Aided Design Data Mining & Machine Learning Data Science Databases Genomics Mathematical Biology Molecular Biology Optimization Theory & Computation Physical Chemistry (other) Programming Languages Scientific Computing & Simulation Theoretical & Computational Chemistry

Past or current institution affiliations

University of Copenhagen

Work details

Head of the Computational Biology Laboratory

Danish Cancer Society Research Center, Copenhagen, Denmark
Computational Biology Laboratory
The main research of CBL focuses on molecular modelling and simulations integrated with experimental data and network theory to the study structure-function relationship in key cancer proteins as well as on the analyses of high-throughput sequencing and omics data from profiling of cancer patients.

Associate Professor

University of Copenhagen
Center For Protein Research

Websites

  • Google Scholar
  • ResearchGate
  • LinkedIn
  • Academia.edu
  • PubMed Search

PeerJ Contributions

  • Articles 2
  • Edited 27
July 4, 2018
Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs
Elena Papaleo, Carlo Camilloni, Kaare Teilum, Michele Vendruscolo, Kresten Lindorff-Larsen
https://doi.org/10.7717/peerj.5125 PubMed 30013831
June 11, 2018
How well do force fields capture the strength of salt bridges in proteins?
Mustapha Carab Ahmed, Elena Papaleo, Kresten Lindorff-Larsen
https://doi.org/10.7717/peerj.4967 PubMed 29910983

Academic Editor on

July 8, 2020
pulseTD: RNA life cycle dynamics analysis based on pulse model of 4sU-seq time course sequencing data
Xin Wang, Siyu He, Jian Li, Jun Wang, Chengyi Wang, Mingwei Wang, Danni He, Xingfeng Lv, Qiuyan Zhong, Hongjiu Wang, Zhenzhen Wang
https://doi.org/10.7717/peerj.9371 PubMed 32714656
March 17, 2020
Biochemical and biophysical characterisation of immunoglobulin free light chains derived from an initially unbiased population of patients with light chain disease
Rebecca Sternke-Hoffmann, Amelie Boquoi, David Lopez Y. Niedenhoff, Florian Platten, Roland Fenk, Rainer Haas, Alexander K. Buell
https://doi.org/10.7717/peerj.8771 PubMed 32211238
February 19, 2020
SCelVis: exploratory single cell data analysis on the desktop and in the cloud
Benedikt Obermayer, Manuel Holtgrewe, Mikko Nieminen, Clemens Messerschmidt, Dieter Beule
https://doi.org/10.7717/peerj.8607 PubMed 32117635
December 5, 2019
TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
Gökhan Karakülah, Nazmiye Arslan, Cihangir Yandım, Aslı Suner
https://doi.org/10.7717/peerj.8192 PubMed 31824778
September 9, 2019
Characterization of ceRNA network to reveal potential prognostic biomarkers in triple-negative breast cancer
Xiang Song, Chao Zhang, Zhaoyun Liu, Qi Liu, Kewen He, Zhiyong Yu
https://doi.org/10.7717/peerj.7522 PubMed 31565554
May 27, 2019
Detection of condition-specific marker genes from RNA-seq data with MGFR
Khadija El Amrani, Gregorio Alanis-Lobato, Nancy Mah, Andreas Kurtz, Miguel A. Andrade-Navarro
https://doi.org/10.7717/peerj.6970 PubMed 31179178
January 24, 2019
Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma
Jie Chen, Chaofeng Xing, Li Yan, Yabing Wang, Haosen Wang, Zongmeng Zhang, Daolun Yu, Jie Li, Honglin Li, Jun Li, Yafei Cai
https://doi.org/10.7717/peerj.6352 PubMed 30697495
January 11, 2019
Non-H3 CDR template selection in antibody modeling through machine learning
Xiyao Long, Jeliazko R. Jeliazkov, Jeffrey J. Gray
https://doi.org/10.7717/peerj.6179 PubMed 30648015
November 12, 2018
CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks
Ruijiang Li, Hebing Chen, Shuai Jiang, Wanying Li, Hao Li, Zhuo Zhang, Hao Hong, Xin Huang, Chenghui Zhao, Yiming Lu, Xiaochen Bo
https://doi.org/10.7717/peerj.5951 PubMed 30473937
July 31, 2018
Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data
Alexandre Coudray, Anna M. Battenhouse, Philipp Bucher, Vishwanath R. Iyer
https://doi.org/10.7717/peerj.5362 PubMed 30083469
June 7, 2018
Metal-binding polymorphism in late embryogenesis abundant protein AtLEA4-5, an intrinsically disordered protein
Leidys French-Pacheco, Cesar L. Cuevas-Velazquez, Lina Rivillas-Acevedo, Alejandra A. Covarrubias, Carlos Amero
https://doi.org/10.7717/peerj.4930 PubMed 29892507
August 30, 2017
Atropos: specific, sensitive, and speedy trimming of sequencing reads
John P. Didion, Marcel Martin, Francis S. Collins
https://doi.org/10.7717/peerj.3720 PubMed 28875074
August 21, 2017
RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers
Van L.T. Hoang, Lisa N. Tom, Xiu-Cheng Quek, Jean-Marie Tan, Elizabeth J. Payne, Lynlee L. Lin, Sudipta Sinnya, Anthony P. Raphael, Duncan Lambie, Ian H. Frazer, Marcel E. Dinger, H. Peter Soyer, Tarl W. Prow
https://doi.org/10.7717/peerj.3631 PubMed 28852586
August 14, 2017
MicroRNAs tend to synergistically control expression of genes encoding extensively-expressed proteins in humans
Xue Chen, Wei Zhao, Ye Yuan, Yan Bai, Yong Sun, Wenliang Zhu, Zhimin Du
https://doi.org/10.7717/peerj.3682 PubMed 28828274
June 27, 2017
Differential gene expression analysis by RNA-seq reveals the importance of actin cytoskeletal proteins in erythroleukemia cells
Vanessa Fernández-Calleja, Pablo Hernández, Jorge B. Schvartzman, Mario García de Lacoba, Dora B. Krimer
https://doi.org/10.7717/peerj.3432 PubMed 28663935
June 22, 2017
Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments
Won Cheol Yim, John C. Cushman
https://doi.org/10.7717/peerj.3486 PubMed 28652936
May 18, 2017
Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents
Jonathan Maiangwa, Mohd Shukuri Mohamad Ali, Abu Bakar Salleh, Raja Noor Zaliha Raja Abd Rahman, Yahaya M. Normi, Fairolniza Mohd Shariff, Thean Chor Leow
https://doi.org/10.7717/peerj.3341 PubMed 28533982
March 15, 2017
Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis
Ruihu Hao, Haiwei Du, Lin Guo, Fengde Tian, Ning An, Tiejun Yang, Changcheng Wang, Bo Wang, Zihao Zhou
https://doi.org/10.7717/peerj.3078 PubMed 28316886
February 28, 2017
LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks
Alberto J. Martin, Sebastián Contreras-Riquelme, Calixto Dominguez, Tomas Perez-Acle
https://doi.org/10.7717/peerj.3052 PubMed 28265516
January 31, 2017
Identification of four potential predicting miRNA biomarkers for multiple myeloma from published datasets
Tian Xiang, Ai-Xin Hu, Peng Sun, Gao Liu, Gang Liu, Yan Xiao
https://doi.org/10.7717/peerj.2831 PubMed 28168095
October 27, 2016
The PARA-suite: PAR-CLIP specific sequence read simulation and processing
Andreas Kloetgen, Arndt Borkhardt, Jessica I. Hoell, Alice C. McHardy
https://doi.org/10.7717/peerj.2619 PubMed 27812418
October 20, 2016
Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer
Samra Khalid, Rumeza Hanif, Samar H.K. Tareen, Amnah Siddiqa, Zurah Bibi, Jamil Ahmad
https://doi.org/10.7717/peerj.2542 PubMed 27781158
June 28, 2016
Design and validation of a next generation sequencing assay for hereditary BRCA1 and BRCA2 mutation testing
Hyunseok P. Kang, Jared R. Maguire, Clement S. Chu, Imran S. Haque, Henry Lai, Rebecca Mar-Heyming, Kaylene Ready, Valentina S. Vysotskaia, Eric A. Evans
https://doi.org/10.7717/peerj.2162 PubMed 27375968
June 16, 2016
Utilizing mutual information for detecting rare and common variants associated with a categorical trait
Leiming Sun, Chan Wang, Yue-Qing Hu
https://doi.org/10.7717/peerj.2139 PubMed 27350900
May 24, 2016
DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations
T. Daniel Andrews, Yogesh Jeelall, Dipti Talaulikar, Christopher C. Goodnow, Matthew A. Field
https://doi.org/10.7717/peerj.2074 PubMed 27257550
February 25, 2016
A comparison of clustering methods for biogeography with fossil datasets
Matthew J. Vavrek
https://doi.org/10.7717/peerj.1720 PubMed 26966658
October 20, 2015
miRMOD: a tool for identification and analysis of 5′ and 3′ miRNA modifications in Next Generation Sequencing small RNA data
Abhinav Kaushik, Shradha Saraf, Sunil K. Mukherjee, Dinesh Gupta
https://doi.org/10.7717/peerj.1332 PubMed 26623179