- Network Science – A.-L. Barabási (2016, Cambridge UP) – free online
- Pattern Recognition and Machine Learning – C. Bishop (2006, Springer)
- Hands-On Machine Learning with Scikit-Learn, Keras, and TensorFlow – A. Géron (2019, O’Reilly)
- Introduction to Bioinformatics – A. Lesk (2019, Oxford UP)
- Networks: An Introduction – M. Newman (2010, Oxford UP)
- Bayesian Data Analysis – Gelman et al. (2013, CRC Press)
- Data Analysis: A Bayesian Tutorial – Sivia & Skilling (2006, Oxford UP)
- Next-Generation DNA Sequencing Informatics – S. Brown (2015, Cold Spring Harbor Press)
- BLAST (Altschul et al., 1990) – sequence alignment
- Cluster analysis of genome-wide expression (Eisen et al., 1998)
- Lethality & centrality in protein networks (Jeong et al., 2001)
- WGCNA (Langfelder & Horvath, 2008)
- BWA short-read aligner (Li & Durbin, 2009)
- Normalization methods for arrays (Bolstad et al., 2003)
- Chemical-protein interaction networks (Cheng et al., 2012)
- EBI data growth & integration (Cook et al., 2016)
- ML in genomics (Libbrecht & Noble, 2015)
- Drug repurposing review (Pushpakom et al., 2019)
- Cancer genome landscapes (Vogelstein et al., 2013)
- Biopython Tutorial & Cookbook
- Bioconductor Project
- The Cancer Genome Atlas (TCGA)
- Genomic Data Commons API
- FastQC Documentation
- Cytoscape Tutorials
- NetworkX Documentation
- NCBI Education Resources
- FASTQ (Illumina)
- Biopython SeqIO
- Formatul SAM/VCF (htslib)
- SRA Run Selector — căutare și filtrare rulari SRA.
- Entrez Programming Utilities (E-utilities) — interfață pentru metadate și linkuri.
- NCBI Datasets API — API modern pentru secvențe și rulari.
- ENA Browser — interfață web pentru genomuri și rulari.
- ENA Portal API (filereport) — acces programatic la linkurile FASTQ.
- Biopython Entrez — pentru acces la NCBI