cbirt
Genomics | Proteomics | Bioinformatics
Centre of Bioinformatics Research and Technology's (CBIRT) aim is to attain new heights in bioinformatics research. CBIRT acts as a catalyst to advance innovations in bioinformatics, chemoinformatics, nanoinformatics, neuroinformatics, immunoinformatics, artificial intelligence research, education and training for the benefit of society and the environment.
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Microscopy has revolutionized our understanding of the world, allowing us to peer into the intricate details of cells, tissues, and even viruses. However, obtaining precise measurements in these minute worlds is quite difficult. Just like fog can make distant objects look different from reality, so does the light treatment of samples in microscopes, which makes them compressed or elongated along the depth axis especially. For decades now, this problem, known as refractive index mismatch (RIM), has troubled researchers.
Recently, there was a breakthrough at Delft University of Technology. In their work published in Optica journal, they present an innovative approach that could be used to determine depth-dependent re-scaling factors, which are very important in correcting distortions caused by RIM. This blog post delves into the complexities of RIM, explores existing approaches to deal with it, and explains how this new method is changing the world of microscopy.
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When compared to other mental conditions, posttraumatic stress disorder (PTSD) has a lower discoverability rate. A meta-analysis encompassing many ancestries, including European, African, and Native American, revealed 95 relevant sites across the genome and 43 putative causative genes. These genes are categorized as developmental factors, immunological or endocrine regulators, neurotransmitter and ion channel synaptic modulators, and synaptic structure and function genes. These findings expand on our knowledge of the neural pathways pertinent to the pathophysiology of PTSD and provide new avenues for research, all of which contribute to a better understanding of the disorder.
After exposure to a traumatic event, some people may experience chronic symptoms of posttraumatic stress disorder, which include intrusive thoughts, hyperarousal, avoidance, and unfavorable changes in mood and cognition. The prevalence of PTSD among individuals who have experienced trauma is 5.6% globally; rates are higher in those who have experienced severe levels of trauma and specific forms of trauma, such as survivors of assault and combat. For many, PTSD is a chronic illness that has a significant negative impact on both the individual’s quality of life and the economy of the community.
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Think about peering into the intricate world of biomolecules, those complex assemblies that direct the symphony of life. Scientists have long relied on molecular dynamics (MD) simulations to watch them dance, but these often require costly quantum-mechanical calculations to get accurate results. However, a groundbreaking new technique called GEMS (general approach for constructing accurate machine-learned force fields for large-scale molecular simulations) developed by researchers from Google DeepMind, Germany, and collaborators may soon usher in a revolution in biomolecular research.
GEMS was designed with machine learning (ML), which gives it an unprecedentedly high level of accuracy when simulating huge biomolecules. This blog post delves into some of the nuances surrounding GEMS, its potential impact on understanding biomolecular dynamics, and its prospects for biological research and drug discovery going forward.
MD simulations are like a movie of the movements of biological molecules. It is necessary to have a set of rules known as force fields (FFs) that define how atoms interact with each other. Yet, traditional FFs often present simple approximations of these interactions at the cost of precision and speed. This inadequacy becomes more apparent when dealing with large and complex biomolecules such as proteins. In most cases, conventional FFs fail to capture the subtle intricacies in these delicate systems, leading to incorrect results that can be misleading.
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An epidemic of monkeypox occurred in May 2023 that led to a disease named mpox displaying symptoms such as fever, enlarged lymph nodes, and rash. This ailment is usually mild and self-limited, but severe cases can be harrowing and may cause lifetime scarring. In response to the outbreak, researchers from Mount Sinai and the Carlos III Health Institute (ICI) in Madrid, Spain, worked together to investigate the genetic makeup of the monkeypox virus (MPXV). They mainly studied subclade IIb strains of the virus, helping them to understand the convolutions in viral genes that influence virus behavior, thereby offering strategies for intervention.
The concept of “genomic accordion” refers to periodic expansions and contractions within the genome of monkeypox virus (MPXV), especially in low-complexity regions (LCRs). Adaptive evolution for this virus depends on these variants, which are drivers of gene expression changes or modifications, including short tandem repeats.
Contrarily, researchers believe that differences in LCRs rather than single-nucleotide polymorphisms (SNPs) may explain the distinct epidemiology of subclade IIb MPXV strains. MPXV’s genetic pathways that underlie its unique transmission dynamics and pathogenicity have been illuminated through precise LCR resolution and repeat length analysis.
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Single-cell transcriptomics has been generating large-scale information, improving our knowledge of cellular processes across different tissues, and facilitating medication discovery, diagnosis, and prognosis. But sorting through all of this data has proven to be an enormous undertaking that frequently takes weeks or months.
The vast amount of data generated—between hundreds of gigabytes and tens of terabytes—that necessitates a significant amount of time for analysis is the cause of this bottleneck. Biologists also have a challenging learning curve due to the complex set of stages involved in data processing, which needs a variety of software programs. Furthermore, because data analysis in this field is iterative, it takes a profound understanding of biology to develop pertinent questions, carry out analyses, evaluate findings, and more ideas.
In order to tackle these issues, scientists from the University of California introduced Bioinformatics Copilot 1.0, a software that utilizes a broad language model. With the help of an easy-to-use natural language interface, users may analyze data without needing to be proficient in programming languages like Python or R. It is designed to work on multiple operating systems, including Windows, Linux, and Mac. Significantly, it makes local data analysis easier and guarantees compliance with strict data management guidelines governing the use of patient samples in healthcare and research facilities.
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Just think about yourself as a physician examining an x-ray. You see an area that seems out of the ordinary, but you are unsure of exactly where it starts and ends. At times, there may be more to the story than what current AI models can provide by way of a single response. This is where Tyche comes in, a groundbreaking framework developed by a team at MIT and the Broad Institute to unravel the inherent indeterminacy in medical image segmentation.
Tyche differs from conventional AI systems that provide only one answer by generating a range of possible answers instead. It’s as if many expert consultants were whispering different versions into your ear to enable you to arrive at better decisions.
The Achilles’ Heel of Traditional Segmentation
Medical imaging analysis, ranging from X-rays to MRIs, usually requires segmentation, which is the identification and delineation of specific structures within an image, such as tumors or organs. This process traditionally has been done manually; it’s slow and error-prone. There was some hope in AI, though, promising automation and increased accuracy.
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Imagine a teeming city where proteins are the movers and shakers. Each protein intertwines with others in partnerships that are vital to every cellular process. Nevertheless, unraveling these interactions, which are called protein-protein interactions (PPIs), forms the basis for both biology and drug development. Detecting PPIs has been akin to overhearing hushed conversations in a crowded room.
A recent study by Harvard Medical School researchers makes significant strides toward understanding the landscape of protein interaction. In this research, SPOC, a powerful classifier, was introduced, which improves the highly accurate identification of true PPIs compared to predictions made by AlphaFold-Multimer (AF-M), an innovative protein structure prediction tool. Predictions generated by the SPOC can be accessed and evaluated on the Predictomes database (predictomes.org). It serves as a repository for protein-protein interaction predictions, allowing users to explore and score their own predictions using SPOC.
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The effective paradigm of molecular linkers in drug discovery is crucial for obtaining relevant candidate molecules in early-stage drug development. In this study, researchers present DiffLinker, a three-dimensional conditional diffusion model for molecular linker design that is E(3)-equivariant. A synthetically available model called DiffLinker generates molecules from disconnected fragments that include all of the original fragments. It can automatically count the number of atoms in the linker and its attachment locations to the input fragments. It can link an infinite number of fragments.
On benchmark datasets, the model performs better than other approaches, producing more varied and readable molecules. It can effectively generate legitimate linkers conditioned on target protein pockets, according to experimental testing conducted in practical applications.
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Understanding molecular mechanisms requires an understanding of protein interactions with nucleic acids. Researchers can query preprocessed and clustered structural data, analyze the data, and draw conclusions about protein interactions based on homology using the PPI3D web server. All interactions for proteins homologous to the query, interactions between two proteins or their homologs, and interactions within a particular PDB entry are the three interaction exploration options that the server provides.
Protein annotations, structures, interface residues, and contact surface regions are all included in the interactive study. All contact interfaces and binding sites from PDB are included in the weekly updated PPI3D database, which is grouped according to structural similarity and protein sequence. For proteins that are extensively investigated, this prevents repetitive information by producing non-redundant datasets without sacrificing different interaction types.
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Researchers from the Institute of Bioengineering, Lausanne, Switzerland, introduce GEMLI, a powerful computational tool that enables robust identification of cell lineages solely from scRNA-seq data. By leveraging gene expression memory, GEMLI unveils heritable patterns, cell fate decisions, and multicellular structures, shedding new light on processes like cancer invasiveness.
Introduction
What if you have to take a snapshot of a busy city during rush hour? Back and forth, vehicles move with their destinations. Can you tell which vehicles set off at the same time? It’s what scientists studying cell lineages have to face: the family trees of cells. In this case, traditional methods encompass marking individual cells, just like putting colored stickers on the vehicles. However, this can be technically difficult and restricts researchers to specific periods.
Notably, GEMLI (Gene Expression Memory-based Lineage Inference), a cutting-edge tool for such purposes, was invented by Dr. Almut Eisele et al., which is capable of tracking cellular ancestry only through monitoring their gene expression patterns – the particular sets of genes that are active in a cell at any given moment. By introducing the concept in their recent Nature Communications article, novel approaches negate extra experiments, allowing easy and keen study of lineage.
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The significance of comprehending gene expression regulation in tissue development is highlighted by the examination of disease progression through methods such as ChIP-seq and ATAC-seq. On the other hand, the growing volume of data poses computing difficulties, and the dearth of organized tools emphasizes the requirement for effective analysis platforms. Researchers from the Shanghai Institute of Nutrition and Health created the scalable cloud-based Epigenomic Analysis Platform (EAP, https://www.biosino.org/epigenetics) to solve these problems and analyze large-scale ChIP/ATAC-seq data sets effectively.
In order to extract biologically significant insights from heterogeneous datasets and automatically produce publication-ready figures and tabular results, EAP uses sophisticated computational algorithms. This allows for thorough epigenomic analysis and data mining in fields like cancer subtyping and therapeutic target discovery.
Understanding the regulation of gene expression in tissue development and disease progression is largely dependent on epigenome profiling. Cutting-edge deep sequencing methods like ATAC-seq and ChIP-seq have made it possible to analyze epigenetic variation in disease cohorts and developmental cells, offering important new insights into the processes governing gene expression and the course of disease. However, to explore these massive datasets, researchers need greater computing power as data collection grows in scope.
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Picture a world where computers can not only translate languages but also decipher biology’s convoluted language. This is the exciting frontier of Large Language Models (LLMs) that could transform our knowledge of genes and cells, which are the foundation of all life forms. Researchers from the Center, Chinese Academy of Sciences, China, explore this intriguing crossroad. Genes, which are passed down from one generation to another, hold the truths of our being. Cells, the tiny factories that keep us alive, execute these instructions coded in genes. Decoding how genes and cells interact helps to unravel health complications, diseases, and even mysteries regarding evolution.
Traditionally, scientists have used gene sequencing to study these intricate associations. But LLMs present an alternative way forward with immense promise. These models are trained using huge volumes of text data, enabling them to understand complicated patterns as well as mappings between them. Perhaps scientists can get a breakthrough by passing such datasets through LLMs.
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Are you aware that plenty of operational AI applications have emerged in the early stages of small-molecule drug discovery? Do you recognize that those packages regularly require a thorough grasp of software programs and hardware, as well as a specialization in an optimistic effort, inflicting boundaries for regular users, in fact, normalization and switching among them? Researchers at Zhejiang Shuren University and Hangzhou SanOmics Information Technology created MolProphet, a user-friendly software with an AI-based total interface to cope with this impediment. MolProphet offers a complete answer for small molecule drug development, together with AI-pushed target pocket prediction, hit discovery, lead optimization, compound concentration, and powerful analytics tools. Its design seeks to simplify the process, permitting novice users to navigate through the numerous tiers of drug research.
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The synergy among the Nuffield Department of Medicine and the Department of Statistics at the University of Oxford represents a blend of medical expertise with statistical rigor – “The MolSnapper,” built using deep learning, promptly exploring intricate molecular specificity for proteins in 3D conformations. Unlike previous approaches that rely on costly trial and error, Conditioning Diffusion uses deep learning to navigate the maze of molecular interactions with unprecedented efficiency to provide novel medical research solutions.
Their research bridges the gap by making it less complicated to evolve patterns learned from large molecular datasets for pocket-binding applications. MolSnapper employs a controlled and environmentally friendly producing approach to seamlessly combine 3-D structural insights with expert knowledge, revolutionizing the ligand era in pharmaceutical applications. MolSnapper enables researchers to generate molecules from large datasets by providing personalized instruction and enhanced selection. This differs from conventional structure-based drug design approaches, which are stereotypically proficient on restricted protein molecular data.
Precision is imperative in drug design and discovery. Therefore, MolSnapper authenticates this concept by serving to deliver personalized descriptions specific to the investigator’s requirements. With the potential for drug discovery employing deep learning, the path has been opened for personalized medicine intensive on molecular markers unique to particular diseases.
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Proteins are life’s molecular workhorses and play crucial roles in every biological process. Understandably, their complex shapes, also known as conformations, are the key that unlocks their secrets to new drug development. Proteins are not still statues but rather change into different conformations like ninjas to play different functions. This movement of protein has been a major challenge during drug discovery because traditional methods usually capture a single snapshot of a protein.
A glimmer of hope comes from a recent study published in Nature Communications by a team at Brown University. Their investigation introduces a brand new method that employs artificial intelligence (AI) to predict several shapes that proteins can adopt. If it is upheld, this advancement could alter our perception of protein functioning and lead to better medications.
As stated by the media release on the Brown University website, protein structures were conventionally identified using X-ray crystallography, among other techniques. Despite their value, however, these methods give a static image, just like a still photo of protein in one pose. Nonetheless, proteins are dynamic entities that change their shapes continuously to perform their function. This dynamic nature is important for understanding how drugs interact with proteins. A protein could be likened to a lock while the drug is seen as the key; if the protein changes shape, then the key may not fit any longer, and hence, this renders it useless for what it was meant for.
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Can you imagine that you can design proteins that have a particular function, and they are like small robots working inside our cells? This may be the reality pretty soon. Researchers from the University of California and Yale University came up with an innovative way of creating transmembrane proteins from scratch, thus leading to targeted treatment and a better understanding of cell biology. However, before we dive into this thrilling research, let us first look at what proteins and membranes are.
Picture your cells as something like busy factories. Proteins make sure these little factories keep running smoothly the entire time. They exist in a multitude of forms and sizes, each having its own work. Some function as enzymes, which are catalysts for chemical reactions, while others transport molecules across membranes, which enclose every cell as protective barriers.
There is a special kind of protein called Transmembrane proteins; it has a unique structure. It has got a hydrophobic section embedded within the cellular membrane, just like the screw goes into a cork bottle stopper. This part is known as transmembrane domain (TM domain). Depending on its purpose, the other part of the protein can stay in or outside the cell. These domains act as channels for molecule exchange between cells.
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Single-cell RNA sequencing (scRNA-seq), a rapidly developing field of RNA sequencing of single cells, has recently made a breakthrough that could revolutionize cell type annotation. Using GPT-4’s powerful language model, Columbia University Mailman School of Public Health and Duke University School of Medicine researchers have demonstrated that cell types can be accurately annotated based on marker gene information, greatly reducing the effort and expertise required for this critical step. The researchers additionally developed an R programming suite named GPTCelltype tailored for the automated annotation of cell types by GPT-4.
Although cell type annotation is a fundamental step in scRNA-seq analysis, it has traditionally been a long and laborious process. This analysis is typically done by a human expert by comparing highly expressed genes with canonical cell type markers. The task requires a lot of knowledge and experience.
Despite the development of automated cell-type annotation methods, manual annotation based on marker genes remains widely used, raising the need for more efficient and accurate solutions.
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