Evidence map›Paper›PMID 41347229›Full record

ArticleNAR genomics and bioinformatics2025

Uncovering position-specific patterns in codon and codon-pair usage in candidate genes associated with blood coagulation diseases.

Nathan J Clement, Nobuko Hamasaki-Katagiri, Brian Lin, Anton A Komar, Michael DiCuccio, Haim Bar, Chava Kimchi-Sarfaty

Abstract read
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In one paragraph

Article in NAR genomics and bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Nathan J ClementHemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, United States.
Nobuko Hamasaki-KatagiriHemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, United States.
Brian LinHemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, United States.
Anton A KomarCenter for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, United States.
Michael DiCuccioRockville, MD 20853, United States.
Haim BarDepartment of Statistics, University of Connecticut, Storrs, CT 06269, United States.
Chava Kimchi-SarfatyHemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, United States.ORCID https://orcid.org/0000-0002-9355-8585

Funding

Safer and more effective FIX therapeutics: impact of codon optimizationR01HL151392 · NHLBI · CLEVELAND STATE UNIVERSITY · PI KOMAR, ANTON A. · 2020 to 2023
$1.5M
NHLBI NIH HHS R01 HL151392
6 · The paper itself

Abstract

Current strategies for optimizing gene therapeutics and recombinant protein production typically rely on universal host codon usage indices. However, there is a growing shift toward incorporating gene-specific traits to enhance therapeutic characteristics. In this study, we investigate position-specific variations in codon and adjacent codon-pair usage biases (CPUBs), offering potential for more tailored gene engineering approaches. We focus our analysis on the coding sequences of four coagulation factors: ADAMTS13, von Willebrand factor, factor VIII, and factor IX, which have been used in therapeutic applications. By aligning transcript homologs with human sequences for each gene using Discontiguous Megablast and MACSE, we assess "sequence-position-specific" codon and CPUBs; 157 homologous sequences for

Indexed as

Blood Coagulation DisordersCodonCodon UsageADAMTS13 ProteinAnimalsFactor IXFactor VIIIHumansvon Willebrand FactorADAMTS13 ProteinADAMTS13 protein, humanCodonFactor IXFactor VIIIvon Willebrand Factor

Identifiers

PMID41347229
PMCPMC12673856

What Socratic holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.