Scientific articles

  1. De Panis, D; J Padró; P Furió-Tarí; S Tarazona; IM Soto; P Milla Carmona; H Dopazo; A Conesa; E Hasson. Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila. Molecular Ecology 25: 4534-4550. DOI: 10.1111/mec.13785
  2. Santpere G, Lopez-Valenzuela M, Petit-Marty N, Navarro A, Espinosa-Parrilla Y (2016). Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes. BMC Genomics. 17:528
  3. Moreyra, N; J. Mensch; JP hurtado and E Hasson. Differential expression analysis of cold tolerance adaptation by RNAseq de novo approach. 15th European Conference on Computational Biology. The Hague, Holland.
  4. Gallego A, Melé M, Balcells I, García-Ramallo E, Torruella-Loran I, Hernández-Bellon H, Abelló T, Kondova I, Bontrop R, Hvilsom C, Navarro A, Marquès-Bonet T, Espinosa-Parrilla Y (2016). Functional Implications of Human-Specific Changes in Great Ape microRNAs. PLoS One. 11(4):e0154194.
  5. Rougon-Cardoso, A., Flores-Ponce, M., Ramos-Aboites, H.E., Martínez-Guerrero, C.E., Hao, Y-J., Cunha, L., Rodríguez-Martinez J. A., Ovando-Vázquez, C., Bermúdez-Barrientos, J.R., Abreu-Goodger, C., Chavarria-Hernández, N., Simões, N., Montiel, R. 2016. The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle. Scientific Reports. 6: 37536.
  6. Sandes, Edans Flavius De Oliveira, Azzedine Boukerche, and Alba Cristina Magalhaes Alves De Melo. “Parallel Optimal Pairwise Biological Sequence Comparison: Algorithms, Platforms, and Classification.” ACM Computing Surveys (CSUR) 48, no. 4 (2016): 63. DOI:10.1145/2893488
  7. Sandes, Edans Flavius O., Guillermo Miranda, Xavier Martorell, Eduard Ayguade, George Teodoro, and Alba Cristina Magalhaes A. Melo. “CUDAlign 4.0: Incremental Speculative Traceback for Exact Chromosome-Wide Alignment in GPU Clusters.” IEEE Transactions on Parallel and Distributed Systems 27, no. 10, (2016): 2838. DOI:10.1109/TPDS.2016.2515597
  8. Sandes, De O., F. Edans, Guillermo Miranda, Xavier Martorell, Eduard Ayguade, George Teodoro, and Alba CMA De Melo. “MASA: A Multiplatform Architecture for Sequence Aligners with Block Pruning.” ACM Transactions on Parallel Computing 2, no. 4 (2016): 28. DOI:10.1145/2858656
  9. Louyakis, A. S., Gourlé, H., Casaburi, G., Bonjawo, R. M. E., Duscher, A. A. and Foster, J. S. (2018), A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles. Environ Microbiol, 20: 842–861. doi:10.1111/1462-2920.14029
  10. Tardaguila M, de la Fuente L, Marti C, Pereira C, del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V and Conesa A. SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Research, 2018. February 9, 2018 doi:10.1101/gr.222976.117.
  11. León-Novelo L, Gerken AR, Graze RM, McIntyre LM, Marroni F. Direct Testing for Allele-Specific Expression Differences Between Conditions. G3 (Bethesda). 2018 Feb 2;8(2):447-460. doi: 10.1534/g3.117.300139
  12. Sergio Gonzalez, Bernardo Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo, and Norma Paniego. “ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data”. BMC Bioinformatics. 2017; 18: 121. doi: 1186/s12859-017-1494-2
  13. Moschen, Di Rienzo JA, Higgins J, Tohge T, Watanabe M, González S, Rivarola M, García-García F, Dopazo J, Hopp HE, Hoefgen R, Fernie AR, Paniego N, Fernández P, Heinz RA. “Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.).” Plant Mol Biol. 2017 Jul;94(4-5):549-564. doi: 10.1007/s11103-017-0625-5.
  14. Flores-Ponce, M, Vallebueno-Estrada, M., González-Orozco, E. Ramos-Aboites, H.E., García-Chávez, J.N., Simões, N., Montiel, R. Signatures of co-evolutionary host-pathogen interactions in the genome of the entomopathogenic nematode Steinernema carpocapsae. BMC Evol Biol. 2017 Apr 26;17(1):108. doi: 10.1186/s12862-017-0935-x.
  15. Defelipe LA, Do Porto DF, Pereira Ramos PI, Nicolás MF, Sosa E, Radusky L, Lanzarotti E, Turjanski AG, Marti MA A whole genome bioinformatic approach to determine potential latent phase specific targets in Mycobacterium tuberculosis.. Tuberculosis (Edinb) 1472-9792. 10.1016/j.tube.2015.11.009
  16. Rochi L, Diéguez MJ, Burguener G, Darino MA, Pergolesi M, Ingala LR, Cuyeu AR, Turjanski A, Kreff ED, Sacco F. Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust. Fungal Genet Biol 1087-1845. 10.1016/j.fgb.2016.10.001.
  17. Chaves A, Eberle SE, Defelipe L, Pepe C, Milanesio B, Aguirre F, Fernandez D, Turjanski A, Feliú-Torres A. Two novel DNA variants associated with glucose-6-phosphate dehydrogenase deficiency found in Argentine pediatric patients. Clinical Biochemistry. 0009-912010.1016/j.clinbiochem.2016.01.018
  18. Arcon JP, Defelipe L, Modenutti CP, López ED, Alvarez-Garcia D, Barril X, Turjanski AG, Martí MA. Molecular Dynamics in Mixed Solvents Reveals Protein–Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions. J Chem Inf Model. 1549-959610.1021/acs.jcim.6b00678-0935-x.
  19. A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies. Merino GA, Conesa A, Fernández EA. Brief Bioinform. 2017 Oct 13. doi: 10.1093/bib/bbx122