ParkDB: a Parkinson's disease gene expression database. - Cristian Taccioli; Vincenza Maselli; Jesper Tegnér; David Gomez-Cabrero; Gioia Altobelli; Warren Emmett; Francesco Lescai; Stefano Gustincich; Elia Stupka (Database J. Biol. Databases Curation, 2011)

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. - Andrew E. Teschendorff; Francesco Marabita; Matthias Lechner; Thomas E. Bartlett; Jesper Tegnér; David Gomez-Cabrero; Stephan Beck 002 (Bioinform., 2013)

Data integration in the era of omics: current and future challenges. - David Gomez-Cabrero; Imad Abugessaisa; Dieter Maier; Andrew E. Teschendorff; Matthias Merkenschlager; Andreas Gisel; Esteban Ballestar; Erik Bongcam-Rudloff; Ana Conesa; Jesper Tegnér (BMC Syst. Biol., 2014)

STATegra EMS: an Experiment Management System for complex next-generation omics experiments. - Rafael Hernández-de-Diego; Noemi Boix-Chova; David Gomez-Cabrero; Jesper Tegnér; Imad Abugessaisa; Ana Conesa (BMC Syst. Biol., 2014)

Assessing the consistency of public human tissue RNA-seq data sets. - Frida Danielsson; Tojo James; David Gomez-Cabrero; Mikael Huss (Briefings Bioinform., 2015)

Public data and open source tools for multi-assay genomic investigation of disease. - Lavanya Kannan; Marcel Ramos; Angela Re; Nehme Hachem; Zhaleh Safikhani; Deena M. A. Gendoo; Sean Davis 001; David Gomez-Cabrero; Robert Castelo; Kasper D. Hansen; Vincent J. Carey; Martin Morgan; et al. (Briefings Bioinform., 2016)

From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration. - David Gomez-Cabrero; Jörg Menche; Claudia Vargas; Isaac Cano; Dieter Maier; Albert-László Barabási; Jesper Tegnér; Josep Roca (BMC Bioinform., 2016)

Erratum to: A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions. - Vincenzo Lagani; Argyro D. Karozou; David Gomez-Cabrero; Gilad Silberberg; Ioannis Tsamardinos (BMC Bioinform., 2016)

A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions. - Vincenzo Lagani; Argyro D. Karozou; David Gomez-Cabrero; Gilad Silberberg; Ioannis Tsamardinos (BMC Bioinform., 2016)

ChainRank, a chain prioritisation method for contextualisation of biological networks. - Ákos Tényi; Pedro de Atauri; David Gomez-Cabrero; Isaac Cano; Kim Clarke; Francesco Falciani; Marta Cascante; Josep Roca; Dieter Maier (BMC Bioinform., 2016)

Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies. - Maria Needhamsen; Ewoud Ewing; Harald Lund; David Gomez-Cabrero; Robert Adam Harris; Lara Kular; Maja Jagodic (BMC Bioinform., 2017)

Controllability, Multiplexing, and Transfer Learning in Networks using Evolutionary Learning. - Rise Ooi; Chao-Han Huck Yang; Pin-Yu Chen; Víctor M. Eguíluz; Narsis Aftab Kiani; Hector Zenil; David Gomez-Cabrero; Jesper Tegnér (CoRR, 2018)

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps. - Camden Jansen; Ricardo N. Ramirez; Nicole C. El-Ali; David Gomez-Cabrero; Jesper Tegnér; Matthias Merkenschlager; Ana Conesa; Ali Mortazavi (PLoS Comput. Biol., 2019)

GeneSetCluster: a tool for summarizing and integrating gene-set analysis results. - Ewoud Ewing; Nuria Planell-Picola; Maja Jagodic; David Gomez-Cabrero (BMC Bioinform., 2020)

Whispering LLaMA: A Cross-Modal Generative Error Correction Framework for Speech Recognition. - Srijith Radhakrishnan; Chao-Han Huck Yang; Sumeer Ahmad Khan; Rohit Kumar; Narsis A. Kiani; David Gomez-Cabrero; Jesper Tegnér (EMNLP, 2023)

A Parameter-Efficient Learning Approach to Arabic Dialect Identification with Pre-Trained General-Purpose Speech Model. - Srijith Radhakrishnan; Chao-Han Huck Yang; Sumeer Ahmad Khan; Narsis A. Kiani; David Gomez-Cabrero; Jesper N. Tegnér (INTERSPEECH, 2023)

LIBRA: an adaptative integrative tool for paired single-cell multi-omics data. - Xabier Martinez de Morentin; Sumeer Ahmad Khan; Robert Lehmann 002; Sally Sisi Qu; Alberto Maillo; Narsis A. Kiani; Felipe Prósper; Jesper Tegnér; David Gomez-Cabrero (Quant. Biol., 2023)

Reusability report: Learning the transcriptional grammar in single-cell RNA-sequencing data using transformers. - Sumeer Ahmad Khan; Alberto Maillo; Vincenzo Lagani; Robert Lehmann 002; Narsis A. Kiani; David Gomez-Cabrero; Jesper Tegnér (Nat. Mac. Intell., 2023)

ClustAll: An R package for patient stratification in complex diseases. - Asier Ortega-Legarreta; Sara Palomino-Echeverria; Estefania Huergo; Vincenzo Lagani; Narsis A. Kiani; Pierre-Emmanuel Rautou; Nuria Planell-Picola; Jesper Tegnér; David Gomez-Cabrero (PLoS Comput. Biol., 2024)

Interpretable Causal Representation Learning for Biological Data in the Pathway Space. - Jesus de la Fuente Cedeño; Robert Lehmann 002; Carlos Ruiz-Arenas; Jan Voges; Irene Marín-Goñi; Xabier Martinez de Morentin; David Gomez-Cabrero; Idoia Ochoa; Jesper Tegnér; Vincenzo Lagani; Mikel Hernaez (ICLR, 2025)

GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis. - Asier Ortega-Legarreta; Alberto Maillo; Daniel Mouzo; Ana Rosa López-Pérez; Lara Kular; Majid Pahlevan Kakhki; Maja Jagodic; Jesper Tegnér; Vincenzo Lagani; Ewoud Ewing; David Gomez-Cabrero (BMC Bioinform., 2025)