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 …
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
Viral genomes are poorly annotated in metagenomic samples, representing an obstacle to
understanding viral diversity and function. Current annotation approaches rely on alignment-…
understanding viral diversity and function. Current annotation approaches rely on alignment-…
H/ACA snRNP–dependent ribosome biogenesis regulates translation of polyglutamine proteins
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/…
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
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, …
increasingly important to harmonize and organize them for synergistic utilization. The findable, …
[HTML][HTML] Large language models improve annotation of viral proteins
Viral sequences are poorly annotated in environmental samples, a major roadblock to
understanding how viruses influence microbial community structure. Current annotation …
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 …
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
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 …
research community, it is becoming increasingly difficult to harmonize and organize these …
Pseudouridine-dependent ribosome biogenesis regulates translation of polyglutamine proteins during Drosophila oogenesis
Stem cells in many systems, including Drosophila germline stem cells (GSCs), increase
ribosome biogenesis and translation during terminal differentiation. Here, we show that …
ribosome biogenesis and translation during terminal differentiation. Here, we show that …
Glycolytic strategy as a tradeoff between energy yield and protein cost
… Tandem measurements of metabolic fluxes and protein levels in organisms like Pseudomonas
fluorescens and Z. mobilis—ED-using heterotrophs—would allow comparison of our …
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 …
clinical data to train NLP systems, although accessing those data may be complex out of …