For a full list of publications, please visit my google scholar profile.
List of selected publications:
- SE Johnstone*, A Reyes*, …, MJ Aryee+ and BE Bernstein+. Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell, 2020. doi: 10.1016/j.cell.2020.07.030.
- J Chavez*, C Barberena-Jonas*, JE Sotelo-Fonseca*, …, L Collado-Torres+ and A Reyes+. Programmatic access to bacterial regulatory networks with regutools. Bioinformatics, 2020. doi: 10.1093/bioinformatics/btaa575.
- P Kimes+ and A Reyes+. Reproducible and replicable comparisons using SummarizedBenchmark. Bioinformatics, 2018. doi: 10.1093/bioinformatics/bty627.
- A Reyes+ and W Huber+. Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues. Nucleic Acids Research, 2017. doi: 10.1093/nar/gkx1165.
- P Brennecke*, A Reyes*, S Pinto*, K Rattay*, …, and LM Steinmetz. Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells. Nature Immunology, 2015. doi: 10.1038/ni.3246.
- D Klimmeck*, N Cabezas-Wallscheid*, A Reyes*, …, and A Trumpp. Transcriptome-wide profiling and posttranscrip- tional analysis of hematopoietic stem/progenitor cell differentiation toward myeloid commitment. Stem Cell Reports, 2014. doi: 10.1016/j.stemcr.2014.08.012.
- N Cabezas-Wallscheid*, D Klimmeck*, J Hansson*, DB Lipka*, A Reyes*, …, and A Trumpp. Identification of regulatory networks in HSCs and their immediate progeny via integrated proteome, transcriptome, and DNA methylome analysis. Cell Stem Cell, 2014. doi: 10.1016/j.stem.2014.07.005.
- A Reyes*, S Anders*, …, and W Huber. Drift and conservation of differential exon usage across tissues in primate species. PNAS, 2013. doi: 10.1073/pnas.1307202110.
- S Anders*, A Reyes* and W Huber. Detecting differential usage of exons from RNA-seq data. Genome Research, 2012. doi: 10.1101/gr.133744.111.
* Denotes co-first authors
+ Denotes co-corresponding authors