David A Knowles
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Explore the profile of David A Knowles including associated specialties, affiliations and a list of published articles.
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43
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Recent Articles
1.
OConnell S, Brown B, Cannon D, Broin P, Knowles D, Parker N, et al.
medRxiv
. 2024 Dec;
PMID: 39711695
Neuroanatomical variation in individuals with bipolar disorder (BD) has been previously described in observational studies. However, the causal dynamics of these relationships remain unexplored. We performed Mendelian Randomization of 297...
2.
Das A, Lakhani C, Terwagne C, Lin J, Naito T, Raj T, et al.
medRxiv
. 2024 Dec;
PMID: 39677477
The increasing availability of whole-genome sequencing (WGS) has begun to elucidate the contribution of rare variants (RVs), both coding and non-coding, to complex disease. Multiple RV association tests are available...
3.
Um D, Knowles D, Kaiser G
Comput Biol Chem
. 2024 Nov;
114:108251.
PMID: 39602973
This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ). By assigning a unique vector embedding to each short sequence,...
4.
Su J, Knowles D, Rabadan R
ArXiv
. 2024 Nov;
PMID: 39575118
The success of machine learning models relies heavily on effectively representing high-dimensional data. However, ensuring data representations capture human-understandable concepts remains difficult, often requiring the incorporation of prior knowledge and...
5.
Park C, Mani S, Beltran-Velez N, Maurer K, Huang T, Li S, et al.
Genome Res
. 2024 Sep;
34(9):1384-1396.
PMID: 39237300
Characterizing cell-cell communication and tracking its variability over time are crucial for understanding the coordination of biological processes mediating normal development, disease progression, and responses to perturbations such as therapies....
6.
Su J, Reynier J, Fu X, Zhong G, Jiang J, Escalante R, et al.
Genome Biol
. 2023 Dec;
24(1):291.
PMID: 38110959
Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a unified framework that integrates...
7.
Park C, Mani S, Beltran-Velez N, Maurer K, Gohil S, Li S, et al.
bioRxiv
. 2023 Nov;
PMID: 38014338
Characterizing cell-cell communication and tracking its variability over time is essential for understanding the coordination of biological processes mediating normal development, progression of disease, or responses to perturbations such as...
8.
Fernando M, Fan Y, Zhang Y, Tokolyi A, Murphy A, Kammourh S, et al.
bioRxiv
. 2023 Nov;
PMID: 37961635
Given the large number of genes significantly associated with risk for neuropsychiatric disorders, a critical unanswered question is the extent to which diverse mutations --sometimes impacting the same gene-- will...
9.
Brown B, Morris J, Lappalainen T, Knowles D
bioRxiv
. 2023 Oct;
PMID: 37905013
Inference of directed biological networks is an important but notoriously challenging problem. We introduce , an approach to learning causal networks that leverages large-scale intervention-response data. Applied to 788 genes...
10.
Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox
Schertzer M, Stirn A, Isaev K, Pereira L, Das A, Harbison C, et al.
bioRxiv
. 2023 Sep;
PMID: 37745416
Alternative splicing is an essential mechanism for diversifying proteins, in which mature RNA isoforms produce proteins with potentially distinct functions. Two major challenges in characterizing the cellular function of isoforms...