Susan J. Birren
A5028406457- Nerve injury and regeneration
- Neurogenesis and neuroplasticity mechanisms
- Mosquito-borne diseases and control
- Malaria Research and Control
- Neuropeptides and Animal Physiology
- Trace Elements in Health
- Tuberculosis Research and Epidemiology
- Mycobacterium research and diagnosis
- Viral Infections and Vectors
- Receptor Mechanisms and Signaling
- Congenital heart defects research
- Insect symbiosis and bacterial influences
- Axon Guidance and Neuronal Signaling
- Neuroscience and Neural Engineering
- Iron Metabolism and Disorders
- RNA Research and Splicing
- Heavy Metal Exposure and Toxicity
- vaccines and immunoinformatics approaches
- Ion channel regulation and function
- Congenital gastrointestinal and neural anomalies
- TGF-β signaling in diseases
- Neuroscience and Neuropharmacology Research
- RNA regulation and disease
- Fibroblast Growth Factor Research
- Plant Pathogens and Fungal Diseases
Brandeis University
2011-2024
Broad Institute
2010-2023
Massachusetts Institute of Technology
2003-2012
Harvard University
2010
Howard Hughes Medical Institute
1992-1994
California Institute of Technology
1990-1994
University of California, Los Angeles
1983-1987
Oklahoma State University Center for Health Sciences
1983
The goal of the International HapMap Project is to determine common patterns DNA sequence variation in human genome and make this information freely available public domain. An international consortium developing a map these across by determining genotypes one million or more variants, their frequencies degree association between them, samples from populations with ancestry parts Africa, Asia Europe. will allow discovery variants that affect disease, facilitate development diagnostic tools,...
In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 genomes from 78 patients in Leone to ~2000× coverage. observed a rapid accumulation of interhost intrahost genetic variation, allowing us characterize patterns viral transmission over the initial weeks epidemic. This West African variant likely diverged central lineages around 2004, crossed Guinea May 2014, has exhibited sustained human-to-human subsequently, with no...
The rapid spread of dengue is a worldwide public health problem. In two clinical studies in Managua, Nicaragua, we observed an abrupt increase disease severity across several epidemic seasons virus serotype 2 (DENV-2) transmission. Waning DENV-1 immunity appeared to the risk severe subsequent DENV-2 infections after period cross-protection. coincided with replacement Asian/American NI-1 clade new clade, NI-2B. vitro analyses viral isolates from clades and analysis viremia patient blood...
The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on resolution technology used samples studied. Isolates Escherichia coli O104:H4 from centered in Germany May-July 2011, much smaller southwest France June were indistinguishable by standard tests. We report a epidemiological analysis using multiplatform whole-genome sequencing multiple isolates German French outbreaks. showed remarkably little diversity, with...
Background The continued advance of antibiotic resistance threatens the treatment and control many infectious diseases. This is exemplified by largest global outbreak extensively drug-resistant (XDR) tuberculosis (TB) identified in Tugela Ferry, KwaZulu-Natal, South Africa, 2005 that continues today. It unclear whether emergence XDR-TB KwaZulu-Natal was due to recent inadequacies TB conjunction with HIV or other factors. Understanding origins drug this fatal XDR will inform prevention...
ABSTRACT The major cause of athlete’s foot is Trichophyton rubrum , a dermatophyte or fungal pathogen human skin. To facilitate molecular analyses the dermatophytes, we sequenced T. and four related species, tonsurans equinum Microsporum canis gypseum . These species differ in host range, mating, disease progression. genomes are highly colinear yet contain gene family expansions not found other human-associated fungi. Dermatophyte enriched for families containing LysM domain, which binds...
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes 240 species, we identify bases that, when mutated, are likely affect fitness and alter disease risk. At least 332 million (~10.7%) in human genome unusually conserved across species (evolutionarily constrained) relative neutrally evolving repeats, 4552 ultraconserved elements nearly perfectly conserved. Of 101 significantly constrained single bases, 80% outside protein-coding exons half...
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability discern which positions functionally important. Evolutionary constraint is a powerful predictor function, agnostic cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% the genome as significantly constrained and likely functional. We compared annotation, association studies, copy-number variation,...
Species persistence can be influenced by the amount, type, and distribution of diversity across genome, suggesting a potential relationship between historical demography resilience. In this study, we surveyed genetic variation single genomes 240 mammals that compose Zoonomia alignment to evaluate how effective population size (
Sympathetic neurons require NGF for survival, but it is not known when these cells first become dependent on neurotrophic factors. We have examined in vitro mitotically active sympathetic neuroblasts immuno-isolated from different embryonic stages, and correlated this functional data with the expression of neurotrophin receptor mRNAs vivo. Cells E14.5 ganglia are supported by neurotrophin-3 (NT-3) a serum-free medium, NGF; NT-3 acts as bona fide survival factor simply mitogen. By birth,...
Thomas Nutman and colleagues report the draft genome of filarial pathogen Loa loa, African eyeworm. They also coverage two other pathogens, Wuchereria bancrofti Onchocerca volvulus. Unlike most filariae, L. loa lacks an obligate intracellular Wolbachia endosymbiont, comparative genomic analyses suggest that does not contain new metabolic synthesis or transport pathways compared to filariae. eyeworm, is a major humans. endosymbiont. We describe 91.4-Mb related parasite predict 14,907 genes on...
A better description of the extent and structure genetic diversity in dengue virus (DENV) endemic settings is central to its eventual control. To this end we determined complete coding region sequence 187 DENV-2 genomes 68 E genes from viruses sampled Vietnamese patients between 1995 2009. Strikingly, an episode genotype replacement was observed, with Asian 1 lineage entirely displacing previously dominant Asian/American viruses. This event also seems have occurred within Thailand Cambodia,...
Understanding the fine-structure molecular architecture of bacterial epidemics has been a long-sought goal infectious disease research. We used short-read-length DNA sequencing coupled with mass spectroscopy analysis SNPs to study pathogenomics three successive invasive infections involving 344 serotype M3 group A Streptococcus in Ontario, Canada. Sequencing genome 95 strains from epidemics, 280 biallelic all strains, revealed an unexpectedly complex population structure composed dynamic...
Carbapenem-resistant Enterobacteriaceae (CRE) are among the most severe threats to antibiotic era. Multiple different species can exhibit resistance due many mechanisms, and mobile elements capable of transferring between lineages. We prospectively sampled CRE from hospitalized patients three Boston-area hospitals, together with a collection single California hospital, define frequency characteristics outbreaks determine whether there is evidence for transfer strains within hospitals which...
Artemisinin-based combination therapies are the first line of treatment for Plasmodium falciparum infections worldwide, but artemisinin resistance has risen rapidly in Southeast Asia over past decade. Mutations kelch13 gene have been implicated this resistance. We used longitudinal genomic surveillance to detect signals and other loci that contribute or partner drug retrospectively sequenced genomes 194 P. isolates from five sites Northwest Thailand, period a rapid increase emergence...
The genome sequence of the ferret, a model human respiratory disease, enables research on influenza and cystic fibrosis. domestic ferret (Mustela putorius furo) is an important animal for multiple diseases. It considered 'gold standard' modeling virus infection transmission1,2,3,4. Here we describe 2.41 Gb draft assembly constituting 2.28 plus gaps. We annotated 19,910 protein-coding genes this using RNA-seq data from 21 tissues. characterized host response to two infections by analysis 42...
ABSTRACT Dengue is a pantropic public health problem. In children, dengue shock syndrome (DSS) the most common life-threatening complication. The ability to predict which patients may develop DSS improve triage and treatment. To this end, we conducted nested case-control comparison of early host transcriptional features in 24 56 sex-, age-, virus serotype-matched uncomplicated (UC) patients. first instance, defined “early dengue” profile. signature acute rather than convalescent samples (≤72...
Abstract This paper updates and builds on a previous White Paper in this journal that some of us contributed to concerning the molecular cellular basis cardiac neurobiology heart disease. Here we focus recent findings underpin autonomic development, novel intracellular pathways neuroplasticity. Throughout highlight unanswered questions areas controversy. Whilst neurochemical are already demonstrating prognostic viability patients with failure, also discuss opportunity better understand...