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At least 19 recordsLinked to original sources
PubMed2026

The Saccharomyces Genome Database-a history of ideas and accomplishments, 1994-2026.

The Saccharomyces Genome Database (SGD) is one of the longest-running and most consequential biological databases in the world. Founded in the early 1990s at Stanford University under the visionary leadership of David Botstein and developed under the long-term technical direction of J. Michael Cherry, SGD has served for more than three decades not only as the authoritative knowledge center for the budding yeast Saccharomyces cerevisiae, but also as the source for much of the fundamentals of eukaryotic biology. This history traces the arc of a remarkable intellectual and scientific project: beginning with the challenge of building the very first integrated eukaryotic genome database and evolving across 30 years into a global knowledge hub for genetics, functional genomics, and human disease research. The history is organized chronologically, with each section highlighting the central ideas, technical developments, and concrete accomplishments of that period.

Databases, Genetic↗
PubMed2025

The Use of Next-Generation Sequencing in Personalized Medicine.

The revolutionary progress in development of next-generation sequencing (NGS) technologies has made it possible to deliver accurate genomic information in a timely manner. Over the past several years, NGS has transformed biomedical and clinical research and found its application in the field of personalized medicine. Here we discuss the rise of personalized medicine and the history of NGS. We discuss current applications and uses of NGS in medicine, including infectious diseases, oncology, genomic medicine, and dermatology. We provide a brief discussion of selected studies where NGS was used to respond to wide variety of questions in biomedical research and clinical medicine. Finally, we discuss the challenges of implementing NGS into routine clinical use.

Humans↗
PubMed2025

The Elements of Life, Photosynthesis and Genomics.

I am a Professor of Biochemistry, Biophysics and Structural Biology and Plant and Microbial Biology at the University of California in Berkeley. I was born and raised in India, emigrated to the United States to attend university, earning a B.S. in Molecular Biology and a Ph.D. in Biochemistry at the University of Wisconsin in Madison. Following post-doctoral studies with Lawrence Bogorad at Harvard University where I became interested in genetic control of trace element quotas, I joined the department of Chemistry and Biochemistry at UCLA. One of the first to appreciate essential trace metals as potential regulators of gene expression, I articulated the details of the nutritional Cu regulon in Chlamydomonas. In parallel, I used genetic approaches to discover the genes governing missing steps in tetrapyrrole metabolism, including the attachment of heme to apocytochromes in the thylakoid lumen and the factors catalyzing the formation of ring V in chlorophyll. After biochemistry and classical genetics, I embraced genomics, taking a leadership role on the Joint Genome Institute's efforts on the Chlamydomonas genome and more recently, contributing to high quality assemblies of several genomes in the green algal radiation, and large transcriptomic and proteomic datasets - focusing on the diel metabolic cycle in synchronized cultures and acclimation to key environmental and nutritional stressors - that are well-used and appreciated by the community. A new venture in Berkeley is the promotion of Auxenochlorella protothecoides as the true "green yeast" and as a platform for engineering algae to produce useful bioproducts.

Photosynthesis↗
PubMed2025

Peering into the Bacterial Cell: From Transcription to Functional Genomics.

I started my faculty career in 1981 at the UW-Madison in the Department of Bacteriology and moved to the University of California, San Francisco in 1993, where I am a Professor in the Departments of Microbiology and Immunology and Cell and Tissue Biology. In this article, I first review my contributions to understanding the molecular biology of the bacterial transcriptional apparatus and the global role of alternative sigmas (σs), a major pillar of bacterial transcriptional control. I then discuss my role in spearheading the development of bacterial systems biology, specifically to the genome-wide phenotyping approaches necessary for rapid understanding of gene function and the molecular basis of pathway connections across the bacterial universe.

Genomics↗
PubMed2025

Historical review: more than two decades understanding the genetic architecture of hemostasis and thrombosis.

From the beginning of the millennium and the development of genome-wide analyses, the technical advances and remarkable increase in research sample sizes have led to an escalating number of discoveries revealing genetic determinants of levels of the main factors regulating hemostasis and thrombosis and demonstrating a clear polygenic complex regulation of most coagulation factors. These discoveries have been useful to understand the biology underlying hemostasis regulation and to understand risk of associated thrombotic disease, such as venous thromboembolism, coronary artery disease, and ischemic stroke. In this historical review, we outline the main discoveries in genetic studies of coagulation factors (fibrinogen and its alternatively spliced γ' isoform, D-dimer, factor [F]V, FVII, FVIII, von Willebrand factor, and FXI), the main natural anticoagulants (protein C, protein S, and antithrombin), components of fibrinolysis (tissue plasminogen activator and plasminogen activator inhibitor-1), and global coagulation tests (prothrombin time and activated partial thromboplastin time). We explore the clinical implications of these discoveries and suggest new avenues for future investigation.

Humans↗
PubMed2024

Innovations Toward Immunopeptidomics.

Over the past 30 years, immunopeptidomics has grown alongside improvements in mass spectrometry technology, genomics, transcriptomics, T cell receptor sequencing, and immunological assays to identify and characterize the targets of activated T cells. Together, multiple research groups with expertise in immunology, biochemistry, chemistry, and peptide mass spectrometry have come together to enable the isolation and sequence identification of endogenous major histocompatibility complex (MHC)-bound peptides. The idea to apply highly sensitive mass spectrometry techniques to study the landscape of peptide antigens presented by cell surface MHCs was innovative and continues to be successfully used and improved upon to deepen our understanding of how peptide antigens are processed and presented to T cells. Multiple research groups were involved in this bringing immunopeptidomics to the forefront of translational research, and we will highlight the contributions of one of the earliest developers, Professor Donald F. Hunt, and his research group at the University of Virginia. The Hunt laboratory applied cutting edge mass spectroscopy-based immunopeptidomics to study cancer, autoimmunity, transplant rejection, and infectious diseases. Across these diverse research areas, the Hunt laboratory and collaborators would characterize previously unknown MHC peptide-binding motifs and identify immunologically active antigens using ultra sensitive mass spectrometry techniques. Amazingly, many of the MHC-bound peptide antigens discovered in collaborations with the Hunt laboratory were sequenced by mass spectrometry before the completion of the human genome using manual de novo sequencing. In this perspective article, we will chronicle the work of the Hunt laboratory and their many collaborators that would be a major part of the foundation for mass spectrometry-based immunopeptidomics and its application to immunology research.

Animals↗
PubMed2024

A Donald F. Hunt Story (John's Version).

A personal narrative of my time in the Hunt laboratory and beyond is provided. The impact of the Hunt laboratory on the analysis of peptides and proteins by tandem mass spectrometry is described in the context of the time.

History, 20th Century↗
PubMed2026

Pouria Salehi Nowbandegani.

Dr. Laura Zahn asked Dr. Pouria Salehi Nowbandegani about their study, "Defining and cataloging variants in pangenome graphs," and how they came to study this aspect of genomics.

Humans↗
PubMed2025

A century of research on the Planctomycetota bacterial phylum, previously known as Planctomycetes.

One hundred years after planctomycetes were discovered and 50 years since the first isolate was successfully cultured, this bacterial phylum remains enigmatic in many ways. In the last few decades, a significant effort to characterize new isolates has resulted in >150 described species, allowing a more comprehensive analysis of their features. However, metagenomic studies reveal that a diverse group of planctomycetes has yet to be cultured and characterized, and that many biological surprises are yet to be revealed. This is the case for the recently discovered phagotrophic Candidatus Uabimicrobium, which challenges our understanding of the distinction between prokaryotes and eukaryotes. The unique biology of planctomycete cells, such as their ability to divide without the FtsZ protein, their complex structure and characteristic morphology, their relatively large genomes containing many genes with unknown function, and their variable metabolic capabilities, imposes significant barriers for researchers. Although ubiquitous, the precise ecological roles of planctomycetes in various environments are still not fully understood. However, their distinctive metabolism opens the door to a large number of potential biotechnological applications, which are beginning to be unveiled. In this article, we first review the historical milestones in planctomycetes research and describe the pioneers of the field. We then describe the controversies and their resolutions, we highlight the past discoveries and current interrogations related to planctomycetes, and discuss the ongoing challenges that hinder a comprehensive understanding of their biology. We end up with directions for exploring the biology and ecological roles of these fascinating organisms.

Bacteria↗
PubMed2026

The Genomics and Genetics of Rare Disease Illuminate Human Biology.

Richard Gibbs interviews James (Jim) Lupski about his training in New York and work in Houston to elucidate the role of complex genomic rearrangements in human genetic diseases. The challenges and excitement of developing human personalized genomics and the advantages of clinical translation of genome methods for both patients and researchers are discussed.

Humans↗
PubMed2019

Recombinant Adeno-Associated Virus Gene Therapy in Light of Luxturna (and Zolgensma and Glybera): Where Are We, and How Did We Get Here?

The recent market approvals of recombinant adeno-associated virus (rAAV) gene therapies in Europe and the United States are landmark achievements in the history of modern science. These approvals are also anticipated to herald the emergence of a new class of therapies for monogenic disorders, which had hitherto been considered untreatable. These events can be viewed as stemming from the convergence of several important historical trends: the study of basic virology, the development of genomic technologies, the imperative for translational impact of National Institutes of Health-funded research, and the development of economic models for commercialization of rare disease therapies. In this review, these historical trends are described and the key developments that have enabled clinical rAAV gene therapies are discussed, along with an overview of the current state of the field and future directions.

Animals↗
PubMed2025

History and clinical epidemiology of NF2-related schwannomatosis.

NF2-related schwanomatosis (NF2-SWN) (previously Neurofibromatosis 2) as characterised by bilateral vestibular schwannomas (VS) was first described in 1822. However, due to the erroneous conflation of individuals with bilateral eighth nerve tumours with von Recklinghausen disease (currently Neurofibromatosis 1, NF1) in 1917 the literature was confusing for much of the 20th century. Even when the conditions were separated officially in 1987 (with separate localisation of the genes), NF2-SWN remained classified as a neurofibromatosis despite the tumours pathognomonic for NF1, neurofibromas, not being a feature of NF2-schwannomatosis. It is only in 2022 that NF2-SWN was correctly delineated as a schwannomatosis. The epidemiology of NF2-SWN has only been possible to delineate after the separation of NF2-SWN from the much more frequent nerve sheath predisposing tumour condition NF1. Two research groups have published on the birth prevalence and population prevalence of NF2-SWN in the UK and Finland. The most highly ascertained assessment of NF2-SWN cases from the Manchester region of England (population 4.8 million) gave a diagnostic prevalence of 1 in 50,500 and calculated birth prevalences of 1 in 27,956 respectively. However, an updated prevalence across England in 2024 (population 55 million) gave a prevalence of at least 1 in 58,000. NF2-SWN usually presents with bilateral vestibular schwannoma, but can present with meningioma or spinal tumour or ophthalmic features before a VS diagnosis or with a unilateral VS and other tumours and rarely with a unilateral VS alone. Molecular testing is now extremely helpful in confirming the diagnosis of mosaic (present in up to 50% of de novo cases) versus germline NF2 and distinguishing from other tumour predisposition conditions especially in childhood or cases with less common presentation. This chapter summarises the clinical epidemiology of NF2-SWN differentiating the condition from the overlapping non NF2-SWN.

Humans↗
PubMed2025

100+ years of phase variation: the premier bacterial bet-hedging phenomenon.

Stochastic, reversible switches in the expression of Salmonella flagella variants were first described by Andrewes in 1922. Termed phase variation (PV), subsequent research found that this phenomenon was widespread among bacterial species and controlled expression of major determinants of bacterial-host interactions. Underlying mechanisms were not discovered until the 1970s/1980s but were found to encompass intrinsic aspects of DNA processes (i.e. DNA slippage and recombination) and DNA modifications (i.e. DNA methylation). Despite this long history, discoveries are ongoing with expansions of the phase-variable repertoire into new organisms and novel insights into the functions of known loci and switching mechanisms. Some of these discoveries are somewhat controversial as the term 'PV' is being applied without addressing key aspects of the phenomenon such as whether mutations or epigenetic changes are reversible and generated prior to selection. Another 'missing' aspect of PV research is the impact of these adaptive switches in real-world situations. This review provides a perspective on the historical timeline of the discovery of PV, the current state-of-the-art, controversial aspects of classifying phase-variable loci and possible 'missing' real-world effects of this phenomenon.

Gene Expression Regulation, Bacterial↗
PubMed2026

Syndemics, violence and injury: exploring historical relationships between infectious disease epidemics and violent crime in South Africa.

This paper explores historical and contemporary intersections between mass-mortality epidemics and violent crime in South Africa, focusing on four major epidemics - Spanish Flu, tuberculosis, HIV, and Covid-19. The study integrates epidemiological data and contextual historical information such as crime statistics, archival records, and secondary scholarship to explore whether epidemic-driven mortality crises are associated with subsequent changes in violence and injury profiles. With the possible exception of gendered violence, the study finds little evidence that earlier epidemics directly contributed to rapid or sustained increases in violent crime, despite causing substantial adult mortality and long-term social and economic disruption. A comparison between epidemic and socio-economic profiles strongly suggests that the significant increases in violent crime recorded after the Covid-19 pandemic are highly localised, and may be more strongly related to lockdown responses, including alcohol restrictions, rather than the effects of disease itself.

Humans↗
PubMed2026

The first 25 years of the NICHD structural birth defects initiative.

Initiated by NICHD and crafted with clinicians and laboratory scientists, the Structural Birth Defects (SBD) Initiative has supported research into the clinical, genetic, biochemical, mechanistic, developmental, and environmental basis of human disorders with structural anomalies for 25 years. The SBD Initiative has supported and continues to fund research teams studying a broad spectrum of single gene (Mendelian) disorders along with defining loci and susceptibility genes in oligogenic phenotypes, including genetic and environmental risk modifiers. The Initiative required and currently convenes biennial meetings of SBD investigators to share data, exchange ideas and initiate collaborations. In alternate years, online trainee symposia provide a platform for medical fellows, postdoctoral fellows and graduate students to present their data, with the goal of attracting and retaining this future generation of investigators in SBD research. In addition to determining their etiology, the SBD Initiative has supported remarkable progress in developing a fundamental mechanistic understanding of this diverse group of phenotypes. Together, scientific progress has led to translational benefits that include 1) widespread diagnostic testing for families with these disorders, both within the United States and across the world, and 2) pharmacological treatments for affected individuals. This progress has fulfilled the promise of the vision of the architects of the program, which is reviewed in this article, and continues to drive the field forward.

Animals↗
PubMed2026

Invasive Wickerhamomyces anomalus Infections among Injecting Drug Users, France, 2012-20241.

Wickerhamomyces anomalus is a yeast rarely involved in human invasive fungal diseases (IFD). We retrospectively analyzed 44 episodes of W. anomalus IFD in France during 2012-2024. Injecting drug use (IDU) was the main risk factor among 26/35 (74.3%) incident cases. Most infections were community acquired; overall 3-month mortality rate was 1/30 (3.3%). Short tandem repeat (STR) genotyping and whole-genome sequencing analyses revealed substantial genetic diversity among isolates. However, 1 STR genotype was shared by 2 IDU patients, suggesting common exposure. In addition, 1 isolate obtained from a cotton filter used for drug preparation was identical by STR genotyping to the bloodstream isolate from the same patient, indicating direct inoculation via contaminated material or poor injection practices. Our findings highlight the increased risk for W. anomalus IFD among IDU patients and emphasize the importance of targeted preventive measures within that population.

Humans↗