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View article: Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD): the interplay of gut microbiome, insulin resistance, and diabetes
Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD): the interplay of gut microbiome, insulin resistance, and diabetes Open
The global prevalence of Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) has reached alarming levels, affecting nearly one-third of the world's population. This review analyzes current evidence on the intricate relationshi…
View article: Locality-aware pooling enhances protein language model performance across varied applications
Locality-aware pooling enhances protein language model performance across varied applications Open
Motivation Protein language models (PLMs) are amongst the most exciting recent advances for characterizing protein sequences, and have enabled a diverse set of applications, including structure determination, functional property prediction…
View article: KINAID: an orthology-based kinase-substrate prediction and analysis tool for phosphoproteomics
KINAID: an orthology-based kinase-substrate prediction and analysis tool for phosphoproteomics Open
Summary Proteome-wide datasets of phosphorylated peptides, either measured in a condition of interest or in response to perturbations, are increasingly becoming available for model organisms across the evolutionary spectrum. We introduce K…
View article: Toward equitable major histocompatibility complex binding predictions
Toward equitable major histocompatibility complex binding predictions Open
Deep learning tools that predict peptide binding by major histocompatibility complex (MHC) proteins play an essential role in developing personalized cancer immunotherapies and vaccines. In order to ensure equitable health outcomes from th…
View article: Integrative Computational Framework,<i>Dyscovr</i>, Links Mutated Driver Genes to Expression Dysregulation Across 19 Cancer Types
Integrative Computational Framework,<i>Dyscovr</i>, Links Mutated Driver Genes to Expression Dysregulation Across 19 Cancer Types Open
SUMMARY Though somatic mutations play a critical role in driving cancer initiation and progression, the systems-level functional impacts of these mutations—particularly, how they alter expression across the genome and give rise to cancer h…
View article: A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening
A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening Open
Prime editing installs precise edits into the genome with minimal unwanted byproducts, but low and variable editing efficiencies have complicated application of the approach to high-throughput functional genomics. Here we assembled a prime…
View article: The Mechanism and Inflammatory Markers Involved in the Potential Use of N-acetylcysteine in Chronic Pain Management
The Mechanism and Inflammatory Markers Involved in the Potential Use of N-acetylcysteine in Chronic Pain Management Open
N-acetylcysteine (NAC) has established use as an antidote for acetaminophen overdose and treatment for pulmonary conditions and nephropathy. It plays a role in regulating oxidative stress and interacting with various cytokines including IL…
View article: TB and HIV induced immunosenescence: where do vaccines play a role?
TB and HIV induced immunosenescence: where do vaccines play a role? Open
This paper tackles the complex interplay between Human Immunodeficiency virus (HIV-1) and Mycobacterium tuberculosis ( M . tuberculosis ) infections, particularly their contribution to immunosenescence, the age-related decline in immune fu…
View article: Computational Methods for Predicting Key Interactions in T Cell–Mediated Adaptive Immunity
Computational Methods for Predicting Key Interactions in T Cell–Mediated Adaptive Immunity Open
The adaptive immune system recognizes pathogen- and cancer-specific features and is endowed with memory, enabling it to respond quickly and efficiently to repeated encounters with the same antigens. T cells play a central role in the adapt…
View article: A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening
A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening Open
Prime editing installs precise edits into the genome with minimal unwanted byproducts, but low and variable editing efficiencies have complicated application of the approach to high-throughput functional genomics. Leveraging several recent…
View article: From Gut to Hormones: Unraveling the Role of Gut Microbiota in (Phyto)Estrogen Modulation in Health and Disease
From Gut to Hormones: Unraveling the Role of Gut Microbiota in (Phyto)Estrogen Modulation in Health and Disease Open
The human gut microbiota regulates estrogen metabolism through the “estrobolome,” the collection of bacterial genes that encode enzymes like β‐glucuronidases and β‐glucosidases. These enzymes deconjugate and reactivate estrogen, influencin…
View article: Towards Equitable MHC Binding Predictions: Computational Strategies to Assess and Reduce Data Bias
Towards Equitable MHC Binding Predictions: Computational Strategies to Assess and Reduce Data Bias Open
Deep learning tools that predict peptide binding by major histocompatibility complex (MHC) proteins play an essential role in developing personalized cancer immunotherapies and vaccines. In order to ensure equitable health outcomes from th…
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: A Reappraisal of the Antiviral Properties of and Immune Regulation through Dietary Phytochemicals
A Reappraisal of the Antiviral Properties of and Immune Regulation through Dietary Phytochemicals Open
In the present era of the COVID-19 pandemic, viral infections remain a major cause of morbidity and mortality worldwide. In this day and age, viral infections are rampant and spreading rapidly. Among the most aggressive viral infections ar…
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: Leveraging protein language models for accurate multiple sequence alignments
Leveraging protein language models for accurate multiple sequence alignments Open
Multiple sequence alignment (MSA) is a critical step in the study of protein sequence and function. Typically, MSA algorithms progressively align pairs of sequences and combine these alignments with the aid of a guide tree. These alignment…
View article: Monkeypox virus: phylogenomics, host–pathogen interactome and mutational cascade
Monkeypox virus: phylogenomics, host–pathogen interactome and mutational cascade Open
While the world is still recovering from the Covid-19 pandemic, monkeypox virus (MPXV) awaits to cause another global outbreak as a challenge to all of mankind. However, the Covid-19 pandemic has taught us a lesson to speed up the pace of …
View article: Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers
Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers Open
Despite the vast phenotypic differences observed across primates, their protein products are largely similar to each other at the sequence level. We hypothesized that, since proteins accomplish all their functions via interactions with oth…
View article: Network-augmented compartmental models to track asymptomatic disease spread
Network-augmented compartmental models to track asymptomatic disease spread Open
Summary A major challenge in understanding the spread of certain newly emerging viruses is the presence of asymptomatic cases. Their prevalence is hard to measure in the absence of testing tools, and yet the information is critical for tra…
View article: Vector-clustering Multiple Sequence Alignment: Aligning into the twilight zone of protein sequence similarity with protein language models
Vector-clustering Multiple Sequence Alignment: Aligning into the twilight zone of protein sequence similarity with protein language models Open
Multiple sequence alignment is a critical step in the study of protein sequence and function. Typically, multiple sequence alignment algorithms progressively align pairs of sequences and combine these alignments with the aid of a guide tre…
View article: Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings
Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings Open
Knowledge of how proteins interact with DNA is essential for understanding gene regulation. Although DNA-binding specificities for thousands of transcription factors (TFs) have been determined, the specific amino acid–base interactions com…
View article: Monkey Pox Virus (MPXV): Phylogenomics, Host-Pathogen Interactome, and Mutational Cascade
Monkey Pox Virus (MPXV): Phylogenomics, Host-Pathogen Interactome, and Mutational Cascade Open
While the world is still managing to recover from Covid-19 pandemic, Monkeypox awaits to bring in another global outbreak as a challenge to the entire mankind. However, Covid-19 pandemic have taught us lessons to move fast in viral genomic…
View article: Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings
Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings Open
Knowledge of how proteins interact with DNA is essential for understanding gene regulation. While DNA-binding specificities for thousands of transcription factors (TFs) have been determined, the specific amino acid-base interactions compri…
View article: Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate
Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate Open
Significance The protovertebrate Ciona intestinalis is an ideal system to investigate both gene regulatory networks that underlie cell-type specification and how cell types have evolved. In this study, we use single-cell technology, experi…
View article: Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections
Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections Open
Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts …
View article: Improved inference of tandem domain duplications
Improved inference of tandem domain duplications Open
Motivation Protein domain duplications are a major contributor to the functional diversification of protein families. These duplications can occur one at a time through single domain duplications, or as tandem duplications where several co…