modEnrichr: a suite of gene set enrichment analysis tools for model organisms

MV Kuleshov, JEL Diaz, ZN Flamholz… - Nucleic acids …, 2019 - academic.oup.com
Z-score that is the deviation from expected rank as previously described (10), and (iv) a
combined score that is calculated by multiplying the Z-… 10 terms sorted by P-value, Z-score, or the …

Large language models improve annotation of prokaryotic viral proteins

ZN Flamholz, SJ Biller, L Kelly - Nature Microbiology, 2024 - nature.com
Viral genomes are poorly annotated in metagenomic samples, representing an obstacle to
understanding viral diversity and function. Current annotation approaches rely on alignment-…

H/ACA snRNP–dependent ribosome biogenesis regulates translation of polyglutamine proteins

SM Breznak, Y Peng, L Deng, NM Kotb, Z Flamholz… - Science …, 2023 - science.org
Stem cells in many systems, including Drosophila germline stem cells (GSCs), increase
ribosome biogenesis and translation during terminal differentiation. Here, we show that the H/…

[PDF][PDF] FAIRshake: toolkit to evaluate the FAIRness of research digital resources

…, KM Jagodnik, SL Jenkins, P McQuilton, Z Flamholz… - Cell systems, 2019 - cell.com
As more digital resources are produced by the research community, it is becoming
increasingly important to harmonize and organize them for synergistic utilization. The findable, …

[HTML][HTML] Large language models improve annotation of viral proteins

ZN Flamholz, SJ Biller, L Kelly - Research square, 2023 - ncbi.nlm.nih.gov
Viral sequences are poorly annotated in environmental samples, a major roadblock to
understanding how viruses influence microbial community structure. Current annotation …

[HTML][HTML] Word embeddings trained on published case reports are lightweight, effective for clinical tasks, and free of protected health information

ZN Flamholz, A Crane-Droesch, LH Ungar… - Journal of biomedical …, 2022 - Elsevier
Objective Quantify tradeoffs in performance, reproducibility, and resource demands across
several strategies for developing clinically relevant word embeddings. Materials and methods …

FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources

…, KM Jagodnik, SL Jenkins, P McQuilton, Z Flamholz… - BioRxiv, 2019 - biorxiv.org
As more datasets, tools, workflows, APIs, and other digital resources are produced by the
research community, it is becoming increasingly difficult to harmonize and organize these …

Pseudouridine-dependent ribosome biogenesis regulates translation of polyglutamine proteins during Drosophila oogenesis

S Breznak, Y Peng, L Deng, NM Kotb, Z Flamholz… - bioRxiv, 2022 - biorxiv.org
Stem cells in many systems, including Drosophila germline stem cells (GSCs), increase
ribosome biogenesis and translation during terminal differentiation. Here, we show that …

Glycolytic strategy as a tradeoff between energy yield and protein cost

A Flamholz, E Noor, A Bar-Even… - Proceedings of the …, 2013 - National Acad Sciences
… Tandem measurements of metabolic fluxes and protein levels in organisms like Pseudomonas
fluorescens and Z. mobilis—ED-using heterotrophs—would allow comparison of our …

Content Summaries of Best Papers for the Natural Lan-guage Processing Section of the 2022 IMIA Yearbook

ZN Flamholz, A Crane-Droesch, LH Ungar… - J Biomed …, 2022 - thieme-connect.com
The authors highlight two main points that may impact NLP research:(i) the importance of
clinical data to train NLP systems, although accessing those data may be complex out of …