The paper performs spatial transcriptomics on the human prefrontal cortex across the lifespan to identify aging-related changes in different cortical layers.

bioRxiv · Jan 12, 2026 · PreprintNeuroscience

Conserved and Divergent Modulation of Calcification in Atherosclerosis and Aortic Valve Disease by Tissue Extracellular Vesicles

Mark C. Blaser, Fabrizio Buffolo, Arda Halu, Mandy E. Turner, Florian Schlotter, Hideyuki Higashi, Lorena Pantano, Cassandra L. Clift, Louis Saddic, Samantha K. Atkins, Maximillian A. Rogers, Tan Pham, Amélie Vromman, Eugenia Shvartz, Galina K. Sukhova, , Elena Rabkin Aikawa

The paper isolates and analyzes extracellular vesicles from atherosclerotic plaques and aortic valves, identifying shared and distinct molecular pathways involved in calcification.

Circulation · Jul 10, 2023Peer-reviewedSystems Biology

Probing the functions of microglial cyclin-dependent kinase 5 under physiological and pathological conditions

Zhuyu Peng, Wen‐Chin Huang, Maggie Chen, Jay Penney, Hugh P. Cam, Fatema Abdurrob, Leyla Anne Akay, Xiao Chen, William T. Ralvenius, Lorena Pantano, Li‐Huei Tsai

This study investigates the role of Cdk5 in microglia under physiological and pathological conditions, finding transcriptional changes but minimal effects on morphology and behavior.

bioRxiv · May 12, 2020 · PreprintNeuroscience

COMPASS: a COMprehensive Platform for smAll RNA-Seq data analySis

Jiang Li, Alvin T. Kho, Robert Chase, Lorena Pantano, Leanna Farnam, Sami Samir Amr, Kelan G. Tantisira

COMPASS identifies and quantifies small RNAs from sequencing data, showing greater diversity and abundance compared to existing tools in a human serum dataset.

Scientific Reports · Mar 12, 2020Peer-reviewedBioinformatics

Functional and evolutionary impact of polymorphic inversions in the human genome

Carla Giner-Delgado, Sergi Villatoro, Jon Lerga-Jaso, Magdalena Gayà‐Vidal, Meritxell Oliva, David Castellano, Lorena Pantano, Bárbara Domingues Bitarello, David Izquierdo, Isaac Noguera, Íñigo Olalde, Alejandra Delprat, Antoine Blancher, Carles Lalueza‐Fox, Tõnu Esko, , Mario Cáceres

The paper studies 45 common human polymorphic inversions, showing their functional and evolutionary impact, including gene disruption and association with phenotypic traits.

Nature Communications · Sep 17, 2019Peer-reviewedGenomics

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API

Thomas Desvignes, Phillipe Loher, Karen L Eilbeck, Jeffery Ma, Gianvito Urgese, Bastian Fromm, Jason Sydes, Ernesto Aparicio‐Puerta, Víctor Barrera, Roderic Espín, Florian Thibord, Xavier Bofill‐De Ros, Eric R. Londin, Aristeidis G. Telonis, Elisa Ficarra, , Lorena Pantano

The paper introduces mirGFF3, a standardized format for miRNA/isomiR analysis, and mirtop, a tool to convert outputs into this format, enabling data sharing and comparative analysis.

Bioinformatics · Aug 28, 2019Peer-reviewedBioinformatics

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Björn Grüning, Ryan Dale, Andreas Sjödin, Brad Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S. Pedersen, Youri Hoogstrate, Anthony Bretaudeau, , Matthew L. Workentine

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

Nature Methods · Jun 25, 2018Peer-reviewedBioinformatics