Donna K. Slonim
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View article: Improved gene regulatory network inference from single cell data with dropout augmentation
Improved gene regulatory network inference from single cell data with dropout augmentation Open
A major challenge in working with single-cell RNA sequencing data is the prevalence of “dropout,” when some transcripts’ expression values are erroneously not captured. Addressing this issue, which produces zero-inflated count data, is cru…
View article: From Noise to Knowledge: Diffusion Probabilistic Model-Based Neural Inference of Gene Regulatory Networks
From Noise to Knowledge: Diffusion Probabilistic Model-Based Neural Inference of Gene Regulatory Networks Open
Understanding gene regulatory networks (GRNs) is crucial for elucidating cellular mechanisms and advancing therapeutic interventions. Original methods for GRN inference from bulk expression data often struggled with the high dimensionality…
View article: The splicing factor <scp>hnRNPL</scp> demonstrates conserved myocardial regulation across species and is altered in heart failure
The splicing factor <span>hnRNPL</span> demonstrates conserved myocardial regulation across species and is altered in heart failure Open
Heart failure (HF) is highly prevalent. Mechanisms underlying HF remain incompletely understood. Splicing factors (SF), which control pre‐mRNA alternative splicing, regulate cardiac structure and function. This study investigated regulatio…
View article: Maternal SARS-CoV-2 impacts fetal placental macrophage programs and placenta-derived microglial models of neurodevelopment
Maternal SARS-CoV-2 impacts fetal placental macrophage programs and placenta-derived microglial models of neurodevelopment Open
Background The SARS-CoV-2 virus activates maternal and placental immune responses. Such activation in the setting of other infections during pregnancy is known to impact fetal brain development. The effects of maternal immune activation on…
View article: Current and future directions in network biology
Current and future directions in network biology Open
Summary Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although t…
View article: Hofbauer cells and fetal brain microglia share transcriptional profiles and responses to maternal diet-induced obesity
Hofbauer cells and fetal brain microglia share transcriptional profiles and responses to maternal diet-induced obesity Open
Summary Maternal immune activation is associated with adverse offspring neurodevelopmental outcomes, many mediated by in utero microglial programming. As microglia remain inaccessible throughout development, identification of noninvasive b…
View article: From Noise to Knowledge: Diffusion Probabilistic Model-Based Neural Inference of Gene Regulatory Networks
From Noise to Knowledge: Diffusion Probabilistic Model-Based Neural Inference of Gene Regulatory Networks Open
A bstract Understanding gene regulatory networks (GRNs) is crucial for elucidating cellular mechanisms and advancing therapeutic interventions. Original methods for GRN inference from bulk expression data often struggled with the high dime…
View article: Current and future directions in network biology
Current and future directions in network biology Open
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field…
View article: MELISSA: Semi-Supervised Embedding for Protein Function Prediction Across Multiple Networks
MELISSA: Semi-Supervised Embedding for Protein Function Prediction Across Multiple Networks Open
Motivation Several popular methods exist to predict function from multiple protein-protein association networks. For example, both the Mashup algorithm, introduced by Cho, Peng and Berger, and deepNF, introduced by Gligorijević, Barotand, …
View article: Leukemia data by T.R. Golub et al.
Leukemia data by T.R. Golub et al. Open
This is the processed data, the original data is from exprSets for golub leukemia data. Used in the paper "Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring" by T.R. Golub et al.; this i…
View article: Leukemia data by T.R. Golub et al.
Leukemia data by T.R. Golub et al. Open
This is the processed data, the original data is from exprSets for golub leukemia data. Used in the paper "Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring" by T.R. Golub et al.; this i…
View article: Cell-specific imputation of drug connectivity mapping with incomplete data
Cell-specific imputation of drug connectivity mapping with incomplete data Open
Drug repositioning allows expedited discovery of new applications for existing compounds, but re-screening vast compound libraries is often prohibitively expensive. “Connectivity mapping” is a process that links drugs to diseases by identi…
View article: Improving Gene Regulatory Network Inference using Dropout Augmentation
Improving Gene Regulatory Network Inference using Dropout Augmentation Open
Motivation Many methods have been proposed to infer gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data. One major challenge when working with single-cell data is the prevalence of dropout events, when some exp…
View article: <scp>hnRNP L</scp> is essential for myogenic differentiation and modulates myotonic dystrophy pathologies
<span>hnRNP L</span> is essential for myogenic differentiation and modulates myotonic dystrophy pathologies Open
Introduction RNA‐binding proteins (RBPs) play an important role in skeletal muscle development and disease by regulating RNA splicing. In myotonic dystrophy type 1 (DM1), the RBP MBNL1 (muscleblind‐like) is sequestered by toxic CUG repeats…
View article: Cell-specific imputation of drug connectivity mapping with incomplete data
Cell-specific imputation of drug connectivity mapping with incomplete data Open
Motivation Drug repositioning allows expedited discovery of new applications for existing compounds, but re-screening vast compound libraries is often prohibitively expensive. “Connectivity mapping” is a process that links drugs to disease…
View article: A history of opioid exposure in females increases the risk of metabolic disorders in their future male offspring
A history of opioid exposure in females increases the risk of metabolic disorders in their future male offspring Open
Worldwide consumption of opioids remains at historic levels. Preclinical studies report intergenerational effects on the endogenous opioid system of future progeny following preconception morphine exposure. Given the role of endogenous opi…
View article: aTEMPO: Pathway-Specific Temporal Anomalies for Precision Therapeutics
aTEMPO: Pathway-Specific Temporal Anomalies for Precision Therapeutics Open
Dynamic processes are inherently important in disease, and identifying disease-related disruptions of normal dynamic processes can provide information about individual patients. We have previously characterized individuals' disease states …
View article: Assessment of network module identification across complex diseases
Assessment of network module identification across complex diseases Open
Many bioinformatics methods have been proposed for reducing the complexity of large gene or protein networks into relevant subnetworks or modules. Yet, how such methods compare to each other in terms of their ability to identify disease-re…
View article: Assessment of network module identification across complex diseases
Assessment of network module identification across complex diseases Open
Many bioinformatics methods have been proposed for reducing the complexity of large gene or protein networks into relevant subnetworks or modules. Yet, how such methods compare to each other in terms of their ability to identify disease-re…
View article: TEMPO: Detecting Pathway-Specific Temporal Dysregulation of Gene Expression in Disease
TEMPO: Detecting Pathway-Specific Temporal Dysregulation of Gene Expression in Disease Open
While many transcriptional profiling experiments measure dynamic processes that change over time, few include enough time points to adequately capture temporal changes in expression. This is especially true for data from human subjects, fo…
View article: Pathway centrality in protein interaction networks identifies putative functional mediating pathways in pulmonary disease
Pathway centrality in protein interaction networks identifies putative functional mediating pathways in pulmonary disease Open
Identification of functional pathways mediating molecular responses may lead to better understanding of disease processes and suggest new therapeutic approaches. We introduce a method to detect such mediating functions using topological pr…
View article: Putting benchmarks in their rightful place: The heart of computational biology
Putting benchmarks in their rightful place: The heart of computational biology Open
Research in computational biology has given rise to a vast number of methods developed to solve scientific problems. For areas in which many approaches exist, researchers have a hard time deciding which tool to select to address a scientif…
View article: Faculty Opinions recommendation of Analysis of shared heritability in common disorders of the brain.
Faculty Opinions recommendation of Analysis of shared heritability in common disorders of the brain. Open
Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association stud…