The paper introduces SANDLE, a method for analyzing subcellular omics data that reduces false positives and analysis time while handling complex experimental designs.

bioRxiv · Jul 7, 2026 · PreprintBiochemistry

Operation of a TCA cycle subnetwork in the mammalian nucleus

Eleni Kafkia, Amparo Andrés‐Pons, Kerstin Ganter, Markus Seiler, Tom S. Smith, Anna Andrejeva, Paula Jouhten, Filipa M. Pereira, Catarina de Matos Ferraz Franco, Anna Kuroshchenkova, Sergio Leone, Ritwick Sawarkar, Rebecca H. Boston, James E. D. Thaventhiran, Judith B. Zaugg, , Kiran Raosaheb Patil

The paper shows that parts of the TCA cycle operate in the nucleus, challenging the canonical view of metabolic compartmentalization.

Science Advances · Aug 31, 2022Peer-reviewedSystems Biology

Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments

Tom S. Smith, Anna Andrejeva, Josie A. Christopher, Oliver M. Crook, Mohamed Elzek, Kathryn Susan Lilley

The paper evaluates the impact of prior Orbitrap software versions on low isobaric mass tag intensities and finds minimal detrimental effects on differential abundance experiments.

ACS Measurement Science Au · Mar 9, 2022Peer-reviewedBioinformatics