Jeremy Johnson
A5078963968- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- Biosensors and Analytical Detection
- SARS-CoV-2 detection and testing
- Marine animal studies overview
- RNA Research and Splicing
- Wildlife Ecology and Conservation
- SARS-CoV-2 and COVID-19 Research
- Advanced biosensing and bioanalysis techniques
- Sarcoma Diagnosis and Treatment
- Bat Biology and Ecology Studies
- Evolution and Paleontology Studies
- Genetic and phenotypic traits in livestock
- Virology and Viral Diseases
- Obsessive-Compulsive Spectrum Disorders
- Virus-based gene therapy research
- Epigenetics and DNA Methylation
- Palliative Care and End-of-Life Issues
- Veterinary Oncology Research
- Evolution and Genetic Dynamics
- Fish Biology and Ecology Studies
- Cancer Genomics and Diagnostics
- Autism Spectrum Disorder Research
Concordia University
2023-2024
Broad Institute
2014-2023
Icahn School of Medicine at Mount Sinai
2023
Texas Tech University
2023
Massachusetts Institute of Technology
2014-2022
Harvard University
2014-2022
University of Vienna
2022
Beth Israel Deaconess Medical Center
2021
Concord Consortium
2020
Howard Hughes Medical Institute
2020
Marine stickleback fish have colonized and adapted to thousands of streams lakes formed since the last ice age, providing an exceptional opportunity characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing genomes twenty additional individuals from global set marine freshwater populations, identify genome-wide loci that are consistently associated with...
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand molecular mechanisms underlying cichlid phenotypic diversity, we sequenced genomes transcriptomes five lineages African cichlids: Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; four members lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent Malawi), Pundamilia nyererei (very recent...
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage lobe-finned fish thought to have become extinct 70 million years ago. modern looks remarkably similar many its ancient relatives, and evolutionary proximity our own ancestors provides glimpse the that first walked on land. Here we report genome sequence African coelacanth, Latimeria chalumnae. Through phylogenomic analysis, conclude lungfish, not is closest relative tetrapods. Coelacanth protein-coding...
The evolution of the amniotic egg was one great evolutionary innovations in history life, freeing vertebrates from an obligatory connection to water and thus permitting conquest terrestrial environments. Among amniotes, genome sequences are available for mammals birds, but not non-avian reptiles. Here we report sequence North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes highly syntenic with chicken microchromosomes, yet do exhibit high GC...
Ingo Braasch, John Postlethwait and colleagues report the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before duplication. Their data provide insights into evolution genes involved in immunity, mineralization development facilitate comparison cis-regulatory elements between humans. To connect human biology to fish biomedical models, we sequenced teleost duplication (TGD). The slowly evolving has conserved content size many entire chromosomes bony...
Abstract New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements third-generation technologies 1–3 . For example, the number of vertebrate currently NCBI (National Center for Biotechnology Information) database 4 increased by more than 50% 1,485 year from July 2018 2019. In addition this influx different species, new human de novo 5 are being produced, which enable analysis not only small polymorphisms, but also complex,...
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify different classes RNAs among plethora reconstructed transcripts, particularly those that will be translated (mRNAs) from class long non-coding (lncRNAs). Here, we present FEELnc (FlExible Extraction LncRNAs), an alignment-free program accurately annotates lncRNAs based on Random Forest model trained with general features...
The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for rabbit and compared it to resequencing data from populations wild domestic rabbits. identified more than 100 selective sweeps specific rabbits but only relatively small number fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) derived alleles. SNPs with marked allele frequency differences between were enriched conserved noncoding...
The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions genome, negatively impacting annotation study candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB novel now covers 99.8% euchromatic portion genome. We also multiple RNA-Sequencing data sets from 10 different canine tissues to catalog...
The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays detecting severe acute respiratory syndrome 2 (SARS-CoV-2) other viruses their emerging variants. Here, we present cost-effective virus variant detection platform, called microfluidic Combinatorial Arrayed Reactions Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics microfluidics with streamlined workflow clinical use. We...
Significance Elephantids were once among the most widespread megafaunal families. However, only three species of this family exist today. To reconstruct their evolutionary history, we generated 14 genomes from living and extinct elephantids American mastodon. While previous studies examined simple bifurcating relationships, found that gene flow between elephantid was common in past. Straight-tusked elephants descend a mixture ancestral populations related to ancestor African elephants,...
Behavioral genetics in dogs has focused on modern breeds, which are isolated subgroups with distinctive physical and, purportedly, behavioral characteristics. We interrogated breed stereotypes by surveying owners of 18,385 purebred and mixed-breed genotyping 2155 dogs. Most traits heritable [heritability ( h 2 ) > 25%], admixture patterns reveal propensities. Breed explains just 9% variation individuals. Genome-wide association analyses identify 11 loci that significantly associated...
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...
Abstract The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in nucleus impact their disruption disease biology. We present 4DN Data Portal ( https://data.4dnucleome.org/ ), a repository for datasets generated network relevant external datasets. Datasets were with wide range experiments, including chromosome conformation capture assays such as Hi-C other innovative sequencing microscopy-based probing architecture. All together, data portal...
Annotating coding genes and inferring orthologs are two classical challenges in genomics evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method integrates structural gene annotation orthology inference. implements different paradigm orthologous loci, improves ortholog detection of conserved compared with state-of-the-art methods, handles even highly fragmented assemblies. scales...
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis genetic variation across an alignment 241 mammal genome assemblies, addressing prior concerns regarding limited genomic sampling species. compared neutral genome-wide phylogenomic signals using concatenation coalescent-based approaches, interrogated chromosomes, analyzed extensive catalogs structural variants. Interordinal...
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,...
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. found that although mammals resemble one another total and diversity, they show substantial differences with regard recent accumulation. This includes multiple expansion quiescence events across mammalian tree. Young TEs, particularly long interspersed elements, drive increases size, whereas DNA transposons are associated smaller genomes....
Human accelerated regions (HARs) are conserved genomic loci that evolved at an rate in the human lineage and may underlie human-specific traits. We generated HARs chimpanzee with automated pipeline alignment of 241 mammalian genomes. Combining deep learning chromatin capture experiments neural progenitor cells, we discovered a significant enrichment topologically associating domains containing variants change three-dimensional (3D) genome organization. Differential gene expression between...
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 (
Understanding the regulatory landscape of human genome is a long-standing objective modern biology. Using reference-free alignment across 241 mammalian genomes produced by Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million candidate cis-regulatory elements (cCREs) and 15.6 transcription factor binding sites (TFBSs). We identified 439,461 cCREs 2,024,062 TFBSs under constraint. Genes near constrained perform fundamental cellular processes, whereas genes...
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent functionally conserved despite low sequence conservation. We developed Tissue-Aware Conservation Inference Toolkit (TACIT) associate candidate with species' using predictions from machine learning...
Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) are enriched for brain functions across genetic, epigenomic, transcriptomic datasets. Using massively parallel reporter assays six cell types, we discovered 800 hCONDELs conferring significant differences regulatory activity, half of which enhance rather than disrupt function....