David Botstein
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View article: Geographic distribution of genetic diversity of <i>Heterocephalus glaber</i> analyzed using whole genome sequencing and a chromosome-scale genome assembly
Geographic distribution of genetic diversity of <i>Heterocephalus glaber</i> analyzed using whole genome sequencing and a chromosome-scale genome assembly Open
Naked mole-rats ( Heterocephalus glaber ) are a species of rodent endemic to the Horn of Africa, notable among mammals for their long lifespans, resistances to a variety of stresses, and eusocial mating behavior. Though their natural range…
View article: Regulators of health and lifespan extension in genetically diverse mice on dietary restriction
Regulators of health and lifespan extension in genetically diverse mice on dietary restriction Open
Caloric restriction (CR) delays aging and extends healthy lifespan in multiple species. Alternative forms of dietary restriction (DR) such as intermittent fasting (IF) have drawn significant interest as a more sustainable regimen, but the …
View article: Interactions between the gut microbiome, dietary restriction, and aging in genetically diverse mice
Interactions between the gut microbiome, dietary restriction, and aging in genetically diverse mice Open
Summary The intestinal microbiome changes with age, but the causes and consequences of microbiome aging remain unclear. Furthermore, the gut microbiome has been proposed to mediate the benefit of lifespan- extending interventions such as d…
View article: Regulators of health and lifespan extension in genetically diverse mice on dietary restriction
Regulators of health and lifespan extension in genetically diverse mice on dietary restriction Open
Summary Caloric restriction (CR) delays aging and extends healthy lifespan in multiple species. Alternative forms of dietary restriction (DR) such as intermittent fasting (IF) have drawn significant interest as a more sustainable regimen, …
View article: Global analysis of the yeast knockout phenome
Global analysis of the yeast knockout phenome Open
Genome-wide phenotypic screens in the budding yeast Saccharomyces cerevisiae , enabled by its knockout collection, have produced the largest, richest, and most systematic phenotypic description of any organism. However, integrative analyse…
View article: Supplementary Table S1 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
Supplementary Table S1 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer Open
Supplementary Table S1 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
View article: Supplementary Information from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
Supplementary Information from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer Open
Supplementary Information from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
View article: Supplementary Table S1 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
Supplementary Table S1 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer Open
Supplementary Table S1 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
View article: Data from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
Data from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer Open
Neoadjuvant treatment offers an opportunity to correlate molecular variables to treatment response and to explore mechanisms of drug resistance in vivo. Here, we present a statistical analysis of large-scale gene expression patterns and th…
View article: Data from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
Data from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer Open
Neoadjuvant treatment offers an opportunity to correlate molecular variables to treatment response and to explore mechanisms of drug resistance in vivo. Here, we present a statistical analysis of large-scale gene expression patterns and th…
View article: Supplementary Table S2 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
Supplementary Table S2 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer Open
Supplementary Table S2 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
View article: Supplementary Table S2 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
Supplementary Table S2 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer Open
Supplementary Table S2 from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
View article: Supplementary Information from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
Supplementary Information from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer Open
Supplementary Information from Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
View article: Global analysis of the yeast knock-out phenome
Global analysis of the yeast knock-out phenome Open
Genome-wide phenotypic screens in the budding yeast Saccharomyces cerevisiae have produced the largest, richest and most systematic phenotypic description of any organism. Such an achievement was enabled by the development of highly scalab…
View article: Author response: Novel insights from a multiomics dissection of the Hayflick limit
Author response: Novel insights from a multiomics dissection of the Hayflick limit Open
Article Figures and data Abstract Editor's evaluation Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract The process wherein di…
View article: RERG Is a Novel ras -related, Estrogen-regulated and Growth-inhibitory Gene in Breast Cancer
RERG Is a Novel ras -related, Estrogen-regulated and Growth-inhibitory Gene in Breast Cancer Open
Using microarray analysis, we identified a unique ras superfamily gene, termed RERG (ras-related and estrogen-regulated growth inhibitor), whose expression was decreased or lost in a significant percentage of primary human breast tumors th…
View article: Revisiting the Hayflick Limit: Insights from an Integrated Analysis of Changing Transcripts, Proteins, Metabolites and Chromatin
Revisiting the Hayflick Limit: Insights from an Integrated Analysis of Changing Transcripts, Proteins, Metabolites and Chromatin Open
The process wherein dividing cells exhaust proliferative capacity and enter into replicative senescence has become a prominent model for cellular aging in vitro . Despite decades of study, this cellular state is not fully understood in cul…
View article: A genome-scale yeast library with inducible expression of individual genes
A genome-scale yeast library with inducible expression of individual genes Open
The ability to switch a gene from off to on and monitor dynamic changes provides a powerful approach for probing gene function and elucidating causal regulatory relationships, including instances of feedback control. Here, we developed and…
View article: Expression of Cytokeratins 17 and 5 Identifies a Group of Breast Carcinomas with Poor Clinical Outcome
Expression of Cytokeratins 17 and 5 Identifies a Group of Breast Carcinomas with Poor Clinical Outcome Open
While several prognostic factors have been identified in breast carcinoma, the clinical outcome remains hard to predict for individual patients. Better predictive markers are needed to help guide difficult treatment decisions. In a previou…
View article: Repeated observation of breast tumor subtypes in independent gene expression data sets
Repeated observation of breast tumor subtypes in independent gene expression data sets Open
Characteristic patterns of gene expression measured by DNA microarrays have been used to classify tumors into clinically relevant subgroups. In this study, we have refined the previously defined subtypes of breast tumors that could be dist…
View article: Suppression of yeast geranylgeranyl transferase I defect by alternative prenylation of two target GTPases, Rho1p and Cdc42p.
Suppression of yeast geranylgeranyl transferase I defect by alternative prenylation of two target GTPases, Rho1p and Cdc42p. Open
Geranylgeranyl transferase I (GGTase I), which modifies proteins containing the sequence Cys-Ali-Ali-Leu (Ali: aliphatic) at their C-termini, is indispensable for growth in the budding yeast Saccharomyces cerevisiae. We report here that GG…
View article: Aip3p/Bud6p, a yeast actin-interacting protein that is involved in morphogenesis and the selection of bipolar budding sites.
Aip3p/Bud6p, a yeast actin-interacting protein that is involved in morphogenesis and the selection of bipolar budding sites. Open
A search for Saccharomyces cerevisiae proteins that interact with actin in the two-hybrid system and a screen for mutants that affect the bipolar budding pattern identified the same gene, AIP3/BUD6. This gene is not essential for mitotic g…
View article: Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors
Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors Open
The genome-wide program of gene expression during the cell division cycle in a human cancer cell line (HeLa) was characterized using cDNA microarrays. Transcripts of >850 genes showed periodic variation during the cell cycle. Hierarchical …
View article: Perspective: Linkage Maps, Communities of Geneticists, and Genome Databases
Perspective: Linkage Maps, Communities of Geneticists, and Genome Databases Open
The Thomas Hunt Morgan Medal recognizes lifetime contributions to the field of genetics. The 2020 recipient is David Botstein of Calico Labs and Princeton University, recognizing his multiple contributions to genetics, including the collab…
View article: Fully Phased Sequence of a Diploid Human Genome Determined <i>de Novo</i> from the DNA of a Single Individual
Fully Phased Sequence of a Diploid Human Genome Determined <i>de Novo</i> from the DNA of a Single Individual Open
In recent years, improved sequencing technology and computational tools have made de novo genome assembly more accessible. Many approaches, however, generate either an unphased or only partially resolved representation of a diploid genome,…
View article: A tps1Δ persister-like state in Saccharomyces cerevisiae is regulated by MKT1
A tps1Δ persister-like state in Saccharomyces cerevisiae is regulated by MKT1 Open
Trehalose metabolism in yeast has been linked to a variety of phenotypes, including heat resistance, desiccation tolerance, carbon-source utilization, and sporulation. The relationships among the several phenotypes of mutants unable to syn…
View article: Universal Reference RNA as a standard for microarray experiments
Universal Reference RNA as a standard for microarray experiments Open
Background Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation a…