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Statistical Inference Of Adaptation At Multiple Genomic Scales Using Supervised Classification And A Hidden Markov Model, Lauren A. Sugden 2020 Duquesne University

Statistical Inference Of Adaptation At Multiple Genomic Scales Using Supervised Classification And A Hidden Markov Model, Lauren A. Sugden

Biology and Medicine Through Mathematics Conference

No abstract provided.


Identification Of Clinically-Relevant Sequence Variants Within The Human Reference Genome, Lisa A. Lansdon 2020 Children's Mercy Kansas City

Identification Of Clinically-Relevant Sequence Variants Within The Human Reference Genome, Lisa A. Lansdon

Research Days

No abstract provided.


Performance Analysis Of Three Bioinformatic Variant Callers Using A Somatic Reference Standard, Binu Porath, Binu Porath 2020 Children's Mercy Kansas City

Performance Analysis Of Three Bioinformatic Variant Callers Using A Somatic Reference Standard, Binu Porath, Binu Porath

Research Days

No abstract provided.


Use Of Embark Database And An Active Learning Protocol In A High School Classroom, Landon Goodreau 2020 University of Mississippi

Use Of Embark Database And An Active Learning Protocol In A High School Classroom, Landon Goodreau

Honors Theses

With advances in technology, personal genome sequencing has become more affordable than ever before. With this wealth of genetic information come new individualized approaches to medicine and pharmacology, along with moral, legal, and ethical issues to carefully consider. Yet studies suggest that most members of the general public do not have the genetic literacy required to understand the implications of genomic data. It is important that today’s students are able to grasp concepts relating to their own genome to make informed medical decisions in the future. Here I describe an active learning-based activity designed to enhance high school students ...


Transcriptomic Profiling Reveals Extraordinary Diversity Of Venom Peptides In Unexplored Predatory Gastropods Of The Genus Clavus, Aiping Lu, Maren Watkins, Qing Li, Samuel D. Robinson, Gisela P. Concepcion, Mark Yandell, Zhiping Weng, Baldomero M. Olivera, Helena Safavi-Hemami, Alexander E. Fedosov 2020 Tongji University

Transcriptomic Profiling Reveals Extraordinary Diversity Of Venom Peptides In Unexplored Predatory Gastropods Of The Genus Clavus, Aiping Lu, Maren Watkins, Qing Li, Samuel D. Robinson, Gisela P. Concepcion, Mark Yandell, Zhiping Weng, Baldomero M. Olivera, Helena Safavi-Hemami, Alexander E. Fedosov

Open Access Articles

Predatory gastropods of the superfamily Conoidea number over 12,000 living species. The evolutionary success of this lineage can be explained by the ability of conoideans to produce complex venoms for hunting, defense and competitive interactions. Whereas venoms of cone snails (family Conidae) have become increasingly well studied, the venoms of most other conoidean lineages remain largely uncharacterized. In the present study we present the venom gland transcriptomes of two species of the genus Clavus that belong to the family Drilliidae. Venom gland transcriptomes of two specimens of Clavus canalicularis, and two specimens of Cv. davidgilmouri were analyzed, leading to ...


Genetic Studies Of Wildlife, Brittaney L. Buchanan 2020 University of Nebraska-Lincoln

Genetic Studies Of Wildlife, Brittaney L. Buchanan

Dissertations & Theses in Natural Resources

Genetic techniques are being more frequently used to understand the biology and management of wildlife species. The wild turkey is one species of genetic interest because the correct identification of individuals to the subspecies level is difficult using traditional methods. Currently phenotypic differences in plumage, especially the upper tail coverts, are used to assign individuals to subspecies. To hunters wanting to complete a “grand slam,” identification of birds’ subspecies is important. This study focuses on the five extant subspecies: Eastern (M. g. silvestris), Osceola (M. g. osceola), Rio Grande (M. g. intermedia), Merriam’s (M. g. merriami), and Gould’s ...


Dolphinnext: A Distributed Data Processing Platform For High Throughput Genomics, Onur Yukselen, Osman Turkyilmaz, Ahmet R. Ozturk, Manuel Garber, Alper Kucukural 2020 University of Massachusetts Medical School

Dolphinnext: A Distributed Data Processing Platform For High Throughput Genomics, Onur Yukselen, Osman Turkyilmaz, Ahmet R. Ozturk, Manuel Garber, Alper Kucukural

Open Access Articles

BACKGROUND: The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of data, the variety and continuous change of data processing tools, algorithms and databases make analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for highly parallel, flexible, portable, and reproducible data processing frameworks. Several platforms currently ...


Broad Host Range Of Sars-Cov-2 Predicted By Comparative And Structural Analysis Of Ace2 In Vertebrates, Joana Damas, Elinor K. Karlsson, Harris A. Lewin 2020 University of California, Davis

Broad Host Range Of Sars-Cov-2 Predicted By Comparative And Structural Analysis Of Ace2 In Vertebrates, Joana Damas, Elinor K. Karlsson, Harris A. Lewin

University of Massachusetts Medical School Faculty Publications

The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of 410 vertebrates, including 252 mammals, to study cross-species conservation of ACE2 and its likelihood to function as a SARS-CoV-2 receptor. We designed a five-category ranking score based on the conservation properties of 25 amino acids important for the binding between receptor and virus, classifying all species from very high to very low. Only mammals fell ...


Single-Cell Analysis Of Upper Airway Cells Reveals Host-Viral Dynamics In Influenza Infected Adults, Yuming Cao, Zhiru Guo, Pranitha Vangala, Elisa Donnard, Ping Liu, Patrick McDonel, Jose Ordovas Montanes, Alex K. Shalek, Robert W. Finberg, Jennifer P. Wang, Manuel Garber 2020 University of Massachusetts Medical School

Single-Cell Analysis Of Upper Airway Cells Reveals Host-Viral Dynamics In Influenza Infected Adults, Yuming Cao, Zhiru Guo, Pranitha Vangala, Elisa Donnard, Ping Liu, Patrick Mcdonel, Jose Ordovas Montanes, Alex K. Shalek, Robert W. Finberg, Jennifer P. Wang, Manuel Garber

University of Massachusetts Medical School Faculty Publications

Influenza virus infections are major causes of morbidity and mortality. Research using cultured cells, bulk tissue, and animal models cannot fully capture human disease dynamics. Many aspects of virus-host interactions in a natural setting remain unclear, including the specific cell types that are infected and how they and neighboring bystander cells contribute to the overall antiviral response. To address these questions, we performed single-cell RNA sequencing (scRNA-Seq) on cells from freshly collected nasal washes from healthy human donors and donors diagnosed with acute influenza during the 2017-18 season. We describe a previously uncharacterized goblet cell population, specific to infected individuals ...


Whole Genome Sequencing For Mutation Discovery In A Single Case Of Lysosomal Storage Disease (Mps Type 1) In The Dog, Tamer A. Mansour, Kevin D. Woolard, Karen L. Vernau, Devin M. Ancona, Sara M. Thomasy, Lionel Sebbag, Bret A. Moore, Marguerite F. Knipe, Haitham A. Seada, Tina M. Cowan, Miriam Aguilar, C. Titus Brown, Danika L. Bannasch 2020 University of California, Davis and Mansoura University

Whole Genome Sequencing For Mutation Discovery In A Single Case Of Lysosomal Storage Disease (Mps Type 1) In The Dog, Tamer A. Mansour, Kevin D. Woolard, Karen L. Vernau, Devin M. Ancona, Sara M. Thomasy, Lionel Sebbag, Bret A. Moore, Marguerite F. Knipe, Haitham A. Seada, Tina M. Cowan, Miriam Aguilar, C. Titus Brown, Danika L. Bannasch

Veterinary Clinical Sciences Publications

Mucopolysaccharidosis (MPS) is a metabolic storage disorder caused by the deficiency of any lysosomal enzyme required for the breakdown of glycosaminoglycans. A 15-month-old Boston Terrier presented with clinical signs consistent with lysosomal storage disease including corneal opacities, multifocal central nervous system disease and progressively worsening clinical course. Diagnosis was confirmed at necropsy based on histopathologic evaluation of multiple organs demonstrating accumulation of mucopolysaccharides. Whole genome sequencing was used to uncover a frame-shift insertion affecting the alpha-L-iduronidase (IDUA) gene (c.19_20insCGGCCCCC), a mutation confirmed in another Boston Terrier presented 2 years later with a similar clinical picture. Both dogs were homozygous ...


Evolutionary Ecology Of Host-Parasite Relationships: Role Of Host Ecology, Phylogeny, And Demographics In Shaping Parasite Evolution, Erika Taylor Gendron 2020 University of New Mexico

Evolutionary Ecology Of Host-Parasite Relationships: Role Of Host Ecology, Phylogeny, And Demographics In Shaping Parasite Evolution, Erika Taylor Gendron

Biology ETDs

Host-parasite systems exist across complex and ecologically heterogeneous landscapes, and may occur across taxonomically and ecologically disparate host species. Under these conditions, mechanisms underlying microevolutionary processes (i.e. gene flow, genetic drift) are not always clear, and may be mediated by numerous co-occurring factors specific to individual hosts. Host traits such as host immunology, demographics, phylogeny and ecology may act in concert to shape host-parasite relationships, and ultimately evolutionary processes. The research described herein used phylogeographic, phylogenomic, and population genetic methods to further understanding of how host traits impact the evolutionary ecology of trematode systems, using avian schistosomes (Digenea: Schistosomatidae ...


Content And Performance Of The Minimuga Genotyping Array, A New Tool To Improve Rigor And Reproducibility In Mouse Research, John Sebastian Sigmon, Christopher M. Sassetti, Martin T. Ferris, Leonard McMillan, Fernando Pardo-Manuel de Villena 2020 University of North Carolina

Content And Performance Of The Minimuga Genotyping Array, A New Tool To Improve Rigor And Reproducibility In Mouse Research, John Sebastian Sigmon, Christopher M. Sassetti, Martin T. Ferris, Leonard Mcmillan, Fernando Pardo-Manuel De Villena

University of Massachusetts Medical School Faculty Publications

The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well annotated genome, wealth of genetic resources and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost effective, informative and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole genome sequencing. Here we describe the content and performance of a new Mouse Universal Genotyping Array (MUGA). MiniMUGA, an ...


Detecting Chromatin Interactions Along And Between Sister Chromatids With Sisterc, Marlies E. Oomen, Adam K. Hedger, Jonathan K. Watts, Job Dekker 2020 University of Massachusetts Medical School

Detecting Chromatin Interactions Along And Between Sister Chromatids With Sisterc, Marlies E. Oomen, Adam K. Hedger, Jonathan K. Watts, Job Dekker

University of Massachusetts Medical School Faculty Publications

Accurate chromosome segregation requires chromosome compaction with concordant disentanglement of the two sister chromatids. This process has been studied extensively by microscopy but has remained a challenge for genomic methods, such as Hi-C, because sister chromatids have identical DNA sequences. Here we describe SisterC, a chromosome conformation capture assay that can distinguish interactions between and within sister chromatids. The assay is based on BrdU incorporation during S-phase, which labels the newly replicated strands of the sister chromatids. This is followed by Hi-C, e.g. during different stages of mitosis, and the selective destruction of BrdU containing strands by UV/Hoechst ...


Evaluation Of Pre-Processing On The Meta-Analysis Of Dna Methylation Data From The Illumina Humanmethylation450 Beadchip Platform, Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, Christine Nardini 2020 University of Bologna

Evaluation Of Pre-Processing On The Meta-Analysis Of Dna Methylation Data From The Illumina Humanmethylation450 Beadchip Platform, Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, Christine Nardini

Open Access Articles

INTRODUCTION: Meta-analysis is a powerful means for leveraging the hundreds of experiments being run worldwide into more statistically powerful analyses. This is also true for the analysis of omic data, including genome-wide DNA methylation. In particular, thousands of DNA methylation profiles generated using the Illumina 450k are stored in the publicly accessible Gene Expression Omnibus (GEO) repository. Often, however, the intensity values produced by the BeadChip (raw data) are not deposited, therefore only pre-processed values -obtained after computational manipulation- are available. Pre-processing is possibly different among studies and may then affect meta-analysis by introducing non-biological sources of variability.

MATERIAL AND ...


Adaptive Evolution Targets A Pirna Precursor Transcription Network, Swapnil Parhad, Tianxiong Yu, Gen Zhang, Nicholas P. Rice, Zhiping Weng, William E. Theurkauf 2020 University of Massachusetts Medical School

Adaptive Evolution Targets A Pirna Precursor Transcription Network, Swapnil Parhad, Tianxiong Yu, Gen Zhang, Nicholas P. Rice, Zhiping Weng, William E. Theurkauf

Open Access Articles

In Drosophila, transposon-silencing piRNAs are derived from heterochromatic clusters and a subset of euchromatic transposon insertions, which are bound by the Rhino-Deadlock-Cutoff complex. The HP1 homolog Rhino binds to Deadlock, which recruits TRF2 to promote non-canonical transcription from both genomic strands. Cuff function is less well understood, but this Rai1 homolog shows hallmarks of adaptive evolution, which can remodel functional interactions within host defense systems. Supporting this hypothesis, Drosophila simulans Cutoff is a dominant-negative allele when expressed in Drosophila melanogaster, in which it traps Deadlock, TRF2, and the conserved transcriptional co-repressor CtBP in stable complexes. Cutoff functions with Rhino and ...


Stride-A Fluorescence Method For Direct, Specific In Situ Detection Of Individual Single- Or Double-Strand Dna Breaks In Fixed Cells, Magdalena M. Kordon, Miroslaw Zarebski, Kamil Solarczyk, Hanhui Ma, Thoru Pederson, Jurek W. Dobrucki 2020 Jagiellonian University

Stride-A Fluorescence Method For Direct, Specific In Situ Detection Of Individual Single- Or Double-Strand Dna Breaks In Fixed Cells, Magdalena M. Kordon, Miroslaw Zarebski, Kamil Solarczyk, Hanhui Ma, Thoru Pederson, Jurek W. Dobrucki

Open Access Articles

We here describe a technique termed STRIDE (SensiTive Recognition of Individual DNA Ends), which enables highly sensitive, specific, direct in situ detection of single- or double-strand DNA breaks (sSTRIDE or dSTRIDE), in nuclei of single cells, using fluorescence microscopy. The sensitivity of STRIDE was tested using a specially developed CRISPR/Cas9 DNA damage induction system, capable of inducing small clusters or individual single- or double-strand breaks. STRIDE exhibits significantly higher sensitivity and specificity of detection of DNA breaks than the commonly used terminal deoxynucleotidyl transferase dUTP nick-end labeling assay or methods based on monitoring of recruitment of repair proteins or ...


Urine As A High-Quality Source Of Host Genomic Dna From Wild Populations, Andrew T. Ozga, Timothy H. Webster, Ian C. Gilby, Melissa A. Wilson, Rebecca Nockerts, Michael L. Wilson, Anne Pusey, Yingying Li, Beatrice H. Hahn, Anne C. Stone 2020 Arizona State University; Nova Southeastern University

Urine As A High-Quality Source Of Host Genomic Dna From Wild Populations, Andrew T. Ozga, Timothy H. Webster, Ian C. Gilby, Melissa A. Wilson, Rebecca Nockerts, Michael L. Wilson, Anne Pusey, Yingying Li, Beatrice H. Hahn, Anne C. Stone

Biology Faculty Articles

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbors ...


A Chromosomal Connectome For Psychiatric And Metabolic Risk Variants In Adult Dopaminergic Neurons, Sergio Espeso-Gil, Tyler M. Borrman, Zhiping Weng, Schahram Akbarian 2020 Icahn School of Medicine at Mount Sinai

A Chromosomal Connectome For Psychiatric And Metabolic Risk Variants In Adult Dopaminergic Neurons, Sergio Espeso-Gil, Tyler M. Borrman, Zhiping Weng, Schahram Akbarian

Open Access Articles

BACKGROUND: Midbrain dopaminergic neurons (MDN) represent 0.0005% of the brain's neuronal population and mediate cognition, food intake, and metabolism. MDN are also posited to underlay the neurobiological dysfunction of schizophrenia (SCZ), a severe neuropsychiatric disorder that is characterized by psychosis as well as multifactorial medical co-morbidities, including metabolic disease, contributing to markedly increased morbidity and mortality. Paradoxically, however, the genetic risk sequences of psychosis and traits associated with metabolic disease, such as body mass, show very limited overlap.

METHODS: We investigated the genomic interaction of SCZ with medical conditions and traits, including body mass index (BMI), by exploring ...


Hiv-1 Did Not Contribute To The 2019-Ncov Genome, Chuan Xiao, Xiaojun Li, Shuying Liu, Yongming Sang, Shou-Jiang Gao, Feng Gao 2020 University of Texas at El Paso

Hiv-1 Did Not Contribute To The 2019-Ncov Genome, Chuan Xiao, Xiaojun Li, Shuying Liu, Yongming Sang, Shou-Jiang Gao, Feng Gao

Coronavirus COVID-19 Publications by UMMS Authors

When a new pathogen that causes a global epidemic in humans, one key question is where it comes from. This is especially important for a zoonotic infectious disease that jumps from animals to humans. Knowing the origin of such a pathogen is critical to develop means to block further transmission and to develop vaccines. Discovery of the origin of a newly human pathogen is a sophisticated process that requires extensive and vigorous scientific validations and generally takes many years, such as the cases for HIV-1, SARS and MERS. Unfortunately, before the natural sources of new pathogens are clearly defined, conspiracy ...


Frequent Mutation Of Hypoxia-Related Genes In Persistent Pulmonary Hypertension Of The Newborn, Mingbang Wang, Deyi Zhuang, Mei Mei, Haiyan Ma, Zixiu Li, Fusheng He, Guoqiang Cheng, Guang Lin, Wenhao Zhou 2020 Children's Hospital of Fudan University

Frequent Mutation Of Hypoxia-Related Genes In Persistent Pulmonary Hypertension Of The Newborn, Mingbang Wang, Deyi Zhuang, Mei Mei, Haiyan Ma, Zixiu Li, Fusheng He, Guoqiang Cheng, Guang Lin, Wenhao Zhou

Open Access Articles

AIMS: Persistent pulmonary hypertension of the newborn (PPHN) is characterized by sustained high levels of pulmonary vascular resistance after birth with etiology unclear; Arterial blood oxygen saturation of Tibetan newborns at high latitudes is higher than that of Han newborns at low latitudes, suggesting that genetic adaptation may allow sufficient oxygen to confer Tibetan populations with resistance to pulmonary hypertension; We have previously identified genetic factors related to PPHN through candidate gene sequencing; In this study, we first performed whole exome sequencing in PPHN patients to screen for genetic-related factors.

METHODS AND RESULTS: In this two-phase genetic study, we first ...


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