Publicaciones Year 2019
  • Heirendt, Laurent; Arreckx, Sylvain; Pfau, Thomas; Mendoza, Sebastian N.; Richelle, Anne; Heinken, Almut; Haraldsdottir, Hulda S.; Wachowiak, Jacek; Keating, Sarah M.; Vlasov, Vanja; Magnusdottir, Stefania; Ng, Chiam Yu; Preciat, German; Zagare, Alise; Chan, Siu H. J.; Aurich, Maike K.; Clancy, Catherine M.; Modamio, Jennifer; Sauls, John T.; Noronha, Alberto; Bordbar, Aarash; Cousins, Benjamin; El Assal, Diana C.; Valcarcel, Luis V.; Apaolaza, Inigo; Ghaderi, Susan; Ahookhosh, Masoud; Ben Guebila, Marouen; Kostromins, Andrejs; Sompairac, Nicolas; Le, Hoai M.; Ma, Ding; Sun, Yuekai; Wang, Lin; Yurkovich, James T.; Oliveira, Miguel A. P.; Vuong, Phan T.; El Assal, Lemmer P.; Kuperstein, Inna; Zinovyev, Andrei; Hinton, H. Scott; Bryant, William A.; Aragon Artacho, Francisco J.; Planes, Francisco J.; Stalidzans, Egils; Maass, Alejandro; Vempala, Santosh; Hucka, Michael; Saunders, Michael A.; Maranas, Costas D.; Lewis, Nathan E.; Sauter, Thomas; Palsson, Bernhard O.; Thiele, Ines; Fleming, Ronan M. T. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. NATURE PROTOCOLS

  • Apaolaza, Inigo; Valcarcel, Luis Vitores; Planes, Francisco J. gMCS: fast computation of genetic minimal cut sets in large networks. BIOINFORMATICS

  • Carazo, Fernando; Campuzano, Lucia; Cendoya, Xabier; Planes, Francisco J.; Rubio, Angel. TranscriptAchilles: a genome-wide platform to predict isoform biomarkers of gene essentiality in cancer. GIGASCIENCE

  • Carazo, Fernando; Gimeno, Marian; Ferrer-Bonsoms, Juan A.; Rubio, Angel. Integration of CLIP experiments of RNA-binding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic data. BMC GENOMICS

  • Fuertes, Alvaro; Perez-Burillo, Sergio; Apaolaza, Inigo; Valles, Yvonne; Pilar Francino, M.; Angel Rufian-Henares, Jose; Planes, Francisco J. Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth. FRONTIERS IN MICROBIOLOGY

  • Carazo, Fernando; Romero, Juan P.; Rubio, Angel. Upstream analysis of alternative splicing: a review of computational approaches to predict context-dependent splicing factors. BRIEFINGS IN BIOINFORMATICS

  • Valcarcel, Luis V.; Torrano, Veronica; Tobalina, Luis; Carracedo, Arkaitz; Planes, Francisco J. rMTA: robust metabolic transformation analysis. BIOINFORMATICS

  • Chandak, Shubham; Tatwawadi, Kedar; Ochoa, Idoia; Hernaez, Mikel; Weissman, Tsachy. SPRING: a next-generation compressor for FASTQ data. BIOINFORMATICS

  • Yang, Ruochen; Chen, Xi; Ochoa, Idoia. MassComp, a lossless compressor for mass spectrometry data. BMC BIOINFORMATICS

  • Hernaez, Mikel; Pavlichin, Dmitri; Weissman, Tsachy; Ochoa, Idoia. Genomic Data Compression. ANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE, VOL 2, 2019

  • Fischer-Hwang, Irena; Ochoa, Idoia; Weissman, Tsachy; Hernaez, Mikel. Denoising of Aligned Genomic Data. SCIENTIFIC REPORTS

  • Zhang, Chuanyi; Ochoa, Idoia. VEF: a Variant Filtering tool based on Ensemble methods. BIOINFORMATICS

  • Voges, Jan; Paridaens, Tom; Müntefering, Fabian;  Mainzer, Liudmila S.; Bliss, Brian;  Yang, Mingyu; Ochoa, Idoia; Fostier, Jan;  Ostermann,Jörn; Hernaez , Mikel. GABAC: an arithmetic coding solution for genomic data. BIOINFORMATICS

Publicaciones Year 2018

  • Cortazar, Ana R.; Torrano, Veronica; Martin-Martin, Natalia; Caro-Maldonado, Alfredo; Camacho, Laura; Hermanova, Ivana; Guruceaga, Elizabeth; Lorenzo-Martin, Luis F.; Caloto, Ruben; Gomis, Roger R.; Apaolaza, Inigo; Quesada, Victor; Trka, Jan; Gomez-Munoz, Antonio; Vincent, Silvestre; Bustelo, Xose R.; Planes, Francisco J.; Aransay, Ana M.; Carracedo, Arkaitz. CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets. CANCER RESEARCH

  • Apaolaza, Inigo; San Jose-Eneriz, Edurne; Agirre, Xabier; Prosper, Felipe; Planes, Francisco J. COBRA methods and metabolic drug targets in cáncer. MOLECULAR & CELLULAR ONCOLOGY

  • Romero, J.P., Ortiz-Estévez, M., Muniategui, A., Carrancio, S., De Miguel, F.J., Carazo, F., Montuenga, L.M., Loos, R., Pío, R., Trotter, M.W.B., Rubio, A. Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm. BMC GENOMICS

  • Tubía, I., Carazo, F., Apezteguía, A., Pérez-Lorenzo, E., Paredes, J., Arana, S. Analysis of temperature and pH shifts on the impedance characteristic using interdigitated microelectrode based sensors for industrial applications. SENSORS AND ACTUATORS A-PHYSICAL

  • Aldave, G., Gonzalez-Huarriz, M., Rubio, A., Romero, J.P., Ravi, D., Miñana, B., Cuadrado-Tejedor, M., García-Osta, A., Verhaak, R., Xipell, E., Martinez-Vélez, N., De La Rocha, A.A., Puigdelloses, M., García-Moure, M., Marigil, M., Pérez-Larraya, J.G., Marín-Bejar, O., Huarte, M., Carro, M.S., Ferrarese, R., Belda-Iniesta, C., Ayuso, A., Prat-Acín, R. The aberrant splicing of BAF45d links splicing regulation and transcription in glioblastoma. NEURO-ONCOLOGY

  • Roguski, Lukasz; Ochoa, Idoia; Hernaez, Mikel; Deorowicz, Sebastian. FaStore: a space-saving solution for raw sequencing data. BIOINFORMATICS

  • Peng, Jianhao; Milenkovic, Olgica; Ochoa, Idoia. METHCOMP: a special purpose compression platform for DNA methylation data    . BIOINFORMATICS

Publicaciones Year 2017

  • Pey, Jon; San Jose-Eneriz, Edurne; Carmen Ochoa, Maria; Apaolaza, Inigo; de Atauri, Pedro; Rubio, Angel; Cendoya, Xabier; Miranda, Estibaliz; Garate, Leire; Cascante, Marta; Carracedo, Arkaitz; Agirre, Xabier; Prosper, Felipe; Planes, Francisco J. In-silico gene essentiality analysis of polyamine biosynthesis reveals APRT as a potential target in cancer. SCIENTIFIC REPORTS

  • Apaolaza, Inigo; San Jose-Eneriz, Edurne; Tobalina, Luis; Miranda, Estibaliz; Garate, Leire; Agirre, Xabier; Prosper, Felipe; Planes, Francisco J. An in-silico approach to predict and exploit synthetic lethality in cancer metabolism . NATURE COMMUNICATIONS

  • Garcia, I., Aldaregia, J., Vicentic, J.M., Aldaz, P., Moreno-Cugnon, L., Torres-Bayona, S., Carrasco-Garcia, E., Garros-Regulez, L., Egaña, L., Rubio, A., Pollard, S., Stevanovic, M., Sampron, N., Matheu, A. Oncogenic activity of SOX1 in glioblastoma. SCIENTIFIC REPORTS

  • Ochoa, Idoia; Hernaez, Mikel; Goldfeder, Rachel; Weissman, Tsachy; Ashley, Euan. Effect of lossy compression of quality scores on variant calling. BRIEFINGS IN BIOINFORMATICS

Publicaciones Year 2016

  • Tobalina, Luis; Pey, Jon; Planes, Francisco J. Direct calculation of minimal cut sets involving a specific reaction knock-out. BIOINFORMATICS

  • Tobalina, Luis; Pey, Jon; Rezola, Alberto; Planes, Francisco J. Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context-Specific Network Reconstruction Method. PLOS ONE

  • Romero, J.P., Muniategui, A., De Miguel, F.J., Aramburu, A., Montuenga, L., Pio, R., Rubio, A. EventPointer: an effective identification of alternative splicing events using junction arrays. BMC GENOMICS

  • de Miguel, F.J. ,Pajares, M.J. , Martínez-Terroba, E. ,  Ajona, D. , Morales, X. , Sharma, R.D. ,  Pardo, F.J. , Rouzaut, A. , Rubio, A. , Montuenga, L.M. , Pio, R. A large-scale analysis of alternative splicing reveals a key role of QKI in lung cancer. MOLECULAR ONCOLOGY

  • Tatwawadi, Kedar; Hernaez, Mikel; Ochoa, Idoia; Weissman, Tsachy. GTRAC: fast retrieval from compressed collections of genomic variants. BIOINFORMATICS

Publicaciones Year 2015

  • Rezola, Alberto; Pey, Jon; Tobalina, Luis; Rubio, Angel; Beasley, John E.; Planes, Francisco J. Advances in network-based metabolic pathway analysis and gene expression data integration. BRIEFINGS IN BIOINFORMATICS

  • Tobalina, Luis; Bargiela, Rafael; Pey, Jon; Herbst, Florian-Alexander; Lores, Ivan; Rojo, David; Barbas, Coral; Pelaez, Ana I.; Sanchez, Jesus; von Bergen, Martin; Seifert, Jana; Ferrer, Manuel; Planes, Francisco J. Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data. BIOINFORMATICS

  • Pey, Jon; Villar, Juan A.; Tobalina, Luis; Rezola, Alberto; Manuel Garcia, Jose; Beasley, John E.; Planes, Francisco J. TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm. BIOINFORMATICS

  • Rubio Díaz-Cordovés, Ángel; Del Villar, Fernando. Code profiling in R: a review of existing methods and an Introduction to package GUIProfiler. THE R JOURNAL

  • Malysa, Greg; Hernaez, Mikel; Ochoa, Idoia; Rao, Milind; Ganesan, Karthik; Weissman, Tsachy. QVZ: lossy compression of quality values. BIOINFORMATICS

  • Ochoa, Idoia; Hernaez, Mikel; Weissman, Tsachy. iDoComp: a compression scheme for assembled genomes. BIOINFORMATICS

Publicaciones Year 2014

  • Pey, Jon; Planes, Francisco J. Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks. BIOINFORMATICS

  • Pey, Jon; Planes, Francisco J.; Beasley, John E. Refining carbon flux paths using atomic trace data. BIOINFORMATICS

  • Rezola, Alberto; Pey, Jon; Rubio, Angel; Planes, Francisco J. In-Silico Prediction of Key Metabolic Differences between Two Non-Small Cell Lung Cancer Subtypes. PLOS ONE

  • Idoate, M. A.; Gonzalez-Huarriz, M.; Aldave, G.; Echeveste, J.; Tejada, S.; Pastor, F.; Rubio, A.; Aramburu, A.; Xipell, E.; Alonso, A. Aberrant Alternative Splicing of DPF2 (BAF45D) in the Maintenance of an Undifferentiated Cellular State in Glioblastoma. MODERN PATHOLOGY

  • Manolakos, Alexandros; Ochoa, Idoia; Venkat, Kartik; Goldsmith, Andrea J.; Gevaert, Olivier. CaMoDi: a new method for cancer module discovery. BMC GENOMICS

  • Ochoa, Idoia; Hernaez, Mikel; Weissman, Tsachy. Aligned genomic data compression via improved modeling. JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY