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Genetics and Genomics

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Full-Text Articles in Life Sciences

Dmk_Dissertation_11.19.18.Pdf, Dana King Dec 2018

Dmk_Dissertation_11.19.18.Pdf, Dana King

Dana King

No abstract provided.


Dmk_Dissertation_11.19.18.Pdf, Dana King Dec 2018

Dmk_Dissertation_11.19.18.Pdf, Dana King

Dana King

No abstract provided.


Rediscovery Of Red Wolf Ghost Alleles In Canid Population Along The American Gulf Coast, Elizabeth Heppenheimer, Kristin Brzeski, Ron Wooten, William Waddell, Linda Y. Rutledge, Michael J. Chamberlain, Et. Al. Dec 2018

Rediscovery Of Red Wolf Ghost Alleles In Canid Population Along The American Gulf Coast, Elizabeth Heppenheimer, Kristin Brzeski, Ron Wooten, William Waddell, Linda Y. Rutledge, Michael J. Chamberlain, Et. Al.

School of Forest Resources and Environmental Science Publications

Rediscovering species once thought to be extinct or on the edge of extinction is rare. Red wolves have been extinct along the American Gulf Coast since 1980, with their last populations found in coastal Louisiana and Texas. We report the rediscovery of red wolf ghost alleles in a canid population on Galveston Island, Texas. We analyzed over 7000 single nucleotide polymorphisms (SNPs) in 60 canid representatives from all legally recognized North American Canis species and two phenotypically ambiguous canids from Galveston Island. We found notably high Bayesian cluster assignments of the Galveston canids to captive red wolves with extensive sharing ...


Enabling Study Of Human Immune Dysfunction Using Yeast Gene 0st3/Ungi, Ariyanna Casey Dec 2018

Enabling Study Of Human Immune Dysfunction Using Yeast Gene 0st3/Ungi, Ariyanna Casey

Undergraduate Research Symposium (URS)

OST3 is a yeast gene for Obligosaccharyl transferase, a homolog of the Magnesium Transport 1 gene in humans. This human gene produce XMEN disease. XMEN disease is an X-Linked immune system deficiency where the amount of CD4+ T cells present in the body are reduced in function. XMEN is caused by a mutation in the MAGT1 gene. The MAGT1 gene produces a protein called magnesium transport. As shown in Magnesium transport is important because it activates CD4+ T cells, allowing for infections to be effectively detected. A mutation in the MAGT1 gene, reduces the function and effectivity of CD4+ T ...


Population Genomic Analysis Of North American Eastern Wolves (Canic Lycaon) Support Their Conservation Priority Status, Elizabeth Heppenheimer, Ryan Harrigan, Linda Rutledge, Klaus-Peter Koepfli, Alexandra L. Decandia, Kristin Brzeski, Et. Al. Dec 2018

Population Genomic Analysis Of North American Eastern Wolves (Canic Lycaon) Support Their Conservation Priority Status, Elizabeth Heppenheimer, Ryan Harrigan, Linda Rutledge, Klaus-Peter Koepfli, Alexandra L. Decandia, Kristin Brzeski, Et. Al.

School of Forest Resources and Environmental Science Publications

The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency ...


Genetic And Epigenetic Investigations On Pulmonary Hypertension Syndrome In Meat Type- Chickens, Khaloud Alzahrani Dec 2018

Genetic And Epigenetic Investigations On Pulmonary Hypertension Syndrome In Meat Type- Chickens, Khaloud Alzahrani

Theses and Dissertations

This dissertation presents a collection of studies that investigate the genetic and epigenetic associations to ascites phenotype in broiler chickens. Ascites is a significant metabolic disease associated with fast-growing meat-type chickens (broilers) and is a terminal result of pulmonary hypertension syndrome PHS. It is a multi-factorial syndrome caused by interactions between genetic, physiological, environmental, and managemental factors. It was estimated that ascites accounts for losses of about US$1 billion annually worldwide and for over 25% of broilers mortality. Although traditional and molecular genetic methods in the selection and in performance improvements, has greatly reduced ascites frequency, yet it has ...


Temperature And Polyunsaturated Fatty Acid’S Effect On Daphnia Magna Reproduction, Mark Albright Dec 2018

Temperature And Polyunsaturated Fatty Acid’S Effect On Daphnia Magna Reproduction, Mark Albright

Electronic Theses and Dissertations

Organisms adapt to their environments by adjusting their biochemistry and physiology; such adaptation is limited by resource availability and physiological constraints. The freshwater crustacean Daphnia magna inhabits a wide range of environments and must survive and reproduce within a range of temperatures. One limit to low-temperature adaptation is thought to be the availability of unsaturated fatty acids necessary to maintain proper fluidity of cellular membranes. D. magna maintained at 10 ºC on a diet poor in unsaturated fatty acids have been observed to produce clutches that fail to develop. However, this has not been observed on a diet rich in ...


Generation And Evaluation Of Modified Opaque-2 (O2) Popcorn Suggests A Route To Quality Protein Popcorn (Qpp), Ying Ren Dec 2018

Generation And Evaluation Of Modified Opaque-2 (O2) Popcorn Suggests A Route To Quality Protein Popcorn (Qpp), Ying Ren

Theses, Dissertations, and Student Research in Agronomy and Horticulture

I have been working on a Quality Protein Popcorn breeding project where QPM conversion is carried out simultaneously for several elite popcorn germplasms. During my study in the graduate program, I led the following aspects of the Quality Protein Popcorn Breeding Project:

1. Identified suitable QPMs as opaque-2 allele donors.

2.Examined the feasibility of quick introgression of the opaque-2 allele into popcorn lines via marker-assisted selection.

3. Monitored modification by SDS-PAGE zein profiling and light box phenotypic selection to make sure multiple modifier loci for opaque-2 were incorporated each time generation advancement was carried out.

4. Carried out high ...


Insights Into The Evolution Of The New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based On Genome Sequencing, Corrinne E. Grover, Mark A. Arick Ii, Adam Thrash, Justin L. Conover, William S. Sanders, Daniel G. Peterson, James E. Frelichowski, Jodi A. Scheffler, Brian E. Scheffler, Jonathan F. Wendel Nov 2018

Insights Into The Evolution Of The New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based On Genome Sequencing, Corrinne E. Grover, Mark A. Arick Ii, Adam Thrash, Justin L. Conover, William S. Sanders, Daniel G. Peterson, James E. Frelichowski, Jodi A. Scheffler, Brian E. Scheffler, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33X genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following trans-oceanic dispersal from Africa about 6.6 mya, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0.5-2.0 mya), with multiple long-distance dispersals required to account for range expansion to Arizona, the Galapagos Islands ...


Thinking Computationally About Forensics: Anthropological Perspectives On Advancements In Technologies, Data, And Algorithms, Bridget F.B. Algee-Hewitt, Jieun Kim, Cris E. Hughes Nov 2018

Thinking Computationally About Forensics: Anthropological Perspectives On Advancements In Technologies, Data, And Algorithms, Bridget F.B. Algee-Hewitt, Jieun Kim, Cris E. Hughes

Human Biology Open Access Pre-Prints

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New Approaches To Juvenile Age Estimation In Forensics: Application Of Transition Analysis Via The Shackelford Et Al. Method To A Diverse Modern Subadult Sample, Kelly R. Kamnikar, Nicholas P. Herrmann, Amber M. Plemons Nov 2018

New Approaches To Juvenile Age Estimation In Forensics: Application Of Transition Analysis Via The Shackelford Et Al. Method To A Diverse Modern Subadult Sample, Kelly R. Kamnikar, Nicholas P. Herrmann, Amber M. Plemons

Human Biology Open Access Pre-Prints

Dental development is one of the most widely utilized and accurate methods available for estimating age in subadult skeletal remains. The timing of tooth growth and development is regulated by genetics and less affected by external factors, allowing reliable estimates of chronological age. Traditional methodology focuses on comparing tooth developmental scores to corresponding age charts. Using the Moorrees, Fanning, and Hunt (MFH) developmental scores, Shackelford and colleagues embed the dental development method in a statistical framework based on transition analysis. They generated numerical parameters underlining each “stage” and age-at-death distribution and applied them to fossil hominins and Neanderthals with limited ...


Who Needs Data? I’Ve Got Experience!, Dawnie Wolfe Steadman Nov 2018

Who Needs Data? I’Ve Got Experience!, Dawnie Wolfe Steadman

Human Biology Open Access Pre-Prints

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Human Genetic Intervention: How Far Should We Go?, Lance Gregory A. Nunes Nov 2018

Human Genetic Intervention: How Far Should We Go?, Lance Gregory A. Nunes

Mānoa Horizons

Since the beginning of time, man has treated illness and disease with natural remedies. With the advancement in knowledge and technology, new kinds of treatments have entered the realm of medicine—namely genetic intervention. This paper aims to help determine where we should take our development of this technology. In each branch of genetic intervention—whether it be gene therapy, prevention, remediation, or enhancement—issues of ethics, socio-economics, and religion have casted a cloud over the technology, hindering its progression. In contrary, the power to improve the quality and save the lives of individuals affected by genetic diseases does not ...


Gene Therapy: An Overview Of Approaches And Issues, Tony Head Nov 2018

Gene Therapy: An Overview Of Approaches And Issues, Tony Head

Mānoa Horizons

For over 25 years, scientists have been researching and testing gene therapy techniques, but this work has only resulted in a single FDA-approved therapy: Kymriah™ from Novartis. Kymriah™ was approved in the U.S. in August 2017, and genetically modifies a patient’s own immune cells to seek out and destroy abnormal blood cells. Although clinical trials continue to test and refine different gene therapy approaches, understanding and evaluating the risks associated with treatment may be overwhelming to patients and caregivers alike. This article attempts to provide readers with an introduction to gene therapy so that anyone considering treatment or ...


Who Owns Our Genes?, Julia Fujisaka Nov 2018

Who Owns Our Genes?, Julia Fujisaka

Mānoa Horizons

In June of 2013, the United States Supreme Court ruled 9-0 in favor of the American Civil Liberties Union (ACLU) and others in a case arguing against the patentability of human genes. Critics of gene patenting had long suggested that instead of promoting innovation, human gene patents posed a significant roadblock to the development of important diagnostics and therapeutics, and had a negative impact on public health. Myriad Genetics, Inc., the opposing party, argued that the patenting of human genes encouraged researchers and scientists to try to find alternate paths to reach end goals. However, Myriad Genetics strictly defended patents ...


Exposure To Herbicide Is Linked To Elevated Homocysteine And Folic Acid Deficiency, Tony Head, Julia Fujisaka, Jasmine Padamada, Steffanie Sobitz Nov 2018

Exposure To Herbicide Is Linked To Elevated Homocysteine And Folic Acid Deficiency, Tony Head, Julia Fujisaka, Jasmine Padamada, Steffanie Sobitz

Mānoa Horizons

SciFiToxin (SFT) is the active ingredient in a popular non-selective herbicide, RoundUpTM. Introduced in 2020, SFT obtained regulatory approval for general use and has since become the leading residential and agricultural herbicide, especially among farmers of genetically modified (GM) crops. Results from two recent studies indicate a rise in the average homocysteine level in humans worldwide and implicate SFT as a possible cause for this phenomenon as well as folic acid deficiency, due to SFT’s effect on key enzymes in the body. Elevated homocysteine levels in the blood may lead to a number of life-threatening conditions, and folic acid ...


The Right To Know: Should Gmo Labeling Be Mandatory In The U.S.?, Steffanie Sobitz Nov 2018

The Right To Know: Should Gmo Labeling Be Mandatory In The U.S.?, Steffanie Sobitz

Mānoa Horizons

From the commercial release of the first successful genetically modified food to the current debate about the safety of GM foods, one issue has stayed on the forefront of consumers’ minds: the right to know what is in our food. While the history of genetically modified products is easy to follow, the arguments surrounding these high-tech consumables have become convoluted at best. One of the most prominent issues regarding GM foods is the argument that companies who produce, grow, market and sell genetically modified foodstuffs should be required to label them as such. Some iterate the right to know what ...


Speciation And Hybridization In Jamaican-Endemic Streamertail Hummingbirds (Trochilus Polytmus And T. Scitulus), Caroline D. Judy Nov 2018

Speciation And Hybridization In Jamaican-Endemic Streamertail Hummingbirds (Trochilus Polytmus And T. Scitulus), Caroline D. Judy

LSU Doctoral Dissertations

Streamertails hummingbirds (Trochilus polytmus and T. scitulus) are recently diverged sister taxa that appear to have speciated in situ on the island of Jamaica. They are distinguished by male bill color, a secondary sexual trait that is coral red in T. polytmus and jet black in T. scitulus. They hybridize in a narrow zone where their ranges meet in eastern Jamaica. In Chapter 2, I performed a formal population survey of T. scitulus to determine the size of the population, which was unknown. I determined that the total population contains well over 100,000 individuals despite its limited geographic range ...


How Does Antibiotic Resistance Spread In Tuberculosis?, Julie A. Spencer Nov 2018

How Does Antibiotic Resistance Spread In Tuberculosis?, Julie A. Spencer

Shared Knowledge Conference

The ancient bacterial disease of tuberculosis (TB) is curable with antibiotics, but according to the World Health Organization, in 2016 over 10 million people became infected with the disease. 600,000 of these cases were resistant to antibiotics, yet the worldwide treatment success rate for drug resistant TB is only 54%. Furthermore, strains exist now that are resistant to all known antibiotics. In the current environment of global travel, this poses a risk for emergent epidemics of drug resistant TB. In this study, I asked: after an antibiotic resistant strain has evolved in someone’s lungs, how does it spread ...


Mechanisms For The Spread Of Antibiotic Resistance In Tuberculosis, Julie Allison Spencer Nov 2018

Mechanisms For The Spread Of Antibiotic Resistance In Tuberculosis, Julie Allison Spencer

Shared Knowledge Conference

Tuberculosis (TB) is currently the ninth leading cause of death for humans worldwide, causing 10.4 million new infections in 2016. According to the World Health Organization, of these infections, 600,000 were antibiotic resistant. However, the treatment success rate for resistant TB was only 54%. The potential for emergent epidemics of drug resistant TB highlights the need to understand the mechanisms for the spread of resistance. Mycobacterium tuberculosis, the bacterium that causes TB, evolves resistant strains within individuals who are being treated with antibiotics. It has been assumed previously that the resistant characteristics of these strains are spread primarily ...


Cystic Fibrosis Gene Therapy: Looking Back, Looking Forward, Ashley L. Cooney, Paul B. Mccray, Patrick L. Sinn Nov 2018

Cystic Fibrosis Gene Therapy: Looking Back, Looking Forward, Ashley L. Cooney, Paul B. Mccray, Patrick L. Sinn

Stead Family Department of Pediatrics Publications

Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that encodes a cAMP-regulated anion channel. Although CF is a multi-organ system disease, most people with CF die of progressive lung disease that begins early in childhood and is characterized by chronic bacterial infection and inflammation. Nearly 90% of people with CF have at least one copy of the ΔF508 mutation, but there are hundreds of CFTR mutations that result in a range of disease severities. A CFTR gene replacement approach would be efficacious regardless of the disease-causing mutation. After ...


28 - Terminal Die-Back, The Result Of A New Neofusicoccum Species, Courtney Cameron Nov 2018

28 - Terminal Die-Back, The Result Of A New Neofusicoccum Species, Courtney Cameron

Georgia Undergraduate Research Conference (GURC)

Neofusicoccum, a member of the Botryosphaeriaceae family, is a fungal pathogen of woody hosts. It is a threat to pecans (Carya illinoinensis) throughout the South as it damages the above ground parts of plants. Terminal die-back is the most common symptom, resulting in dying or browning of terminal leaflets, and eventually entire compound leaves, scattered throughout a tree. The pathogen often remains dormant until the host's immune response is suppressed by environmental factors such as drought. Some orchards in Georgia have begun displaying terminal die-back. The causal fungus has been identified as a member of the genus Neofusicoccum, but ...


20 - Putative Targets Of The Pp2a Serine/Threonine Phosphatase Complex In Regulating Dendritic Morphology, Andre Golshir, Shatabdi Bhattacharjee, Daniel N. Cox Nov 2018

20 - Putative Targets Of The Pp2a Serine/Threonine Phosphatase Complex In Regulating Dendritic Morphology, Andre Golshir, Shatabdi Bhattacharjee, Daniel N. Cox

Georgia Undergraduate Research Conference (GURC)

Proper dendritic development is essential for functional neuronal networks. Elucidating the molecular mechanisms that regulate dendritic diversification is therefore essential to understanding the formation and modulation of functional neural circuitry. PP2A is a serine/threonine phosphatase that is evolutionarily conserved from yeast to mammals. In Drosophila, the PP2A complex is composed of a catalytic subunit encoded by microtubule star (mts), a scaffolding subunit encoded by PP2A-29B and one of four alternate regulatory subunits encoded by widerborst (wdb), twins, PP2A-B’ and CG4733. Previous studies in the lab showed that specific RNAi-mediated knockdown of various PP2A subunits in CIV neurons severely impaired ...


33 - Identification Of Proteins That Regulate Crispr Dna Uptake Of Pyrococcus Furiosus, Landon Clark Nov 2018

33 - Identification Of Proteins That Regulate Crispr Dna Uptake Of Pyrococcus Furiosus, Landon Clark

Georgia Undergraduate Research Conference (GURC)

The CRISPR-Cas (Clustered Regularly Interspace Short Palindromic Repeats-CRISPR associated) system is a prokaryotic, adaptive immune system used by bacterial and archaeal organism to fight infections by viruses and other harmful invasive DNAs. These prokaryotic CRISPR-Cas immune systems have been exploited as powerful genome editing tools that work many different organisms and cells including humans. The newly developed CRISPR-based technologies are transforming medicine and science and have been used in research applications for developing cures for certain cancers, HIV, hemophilia, etc. The function of the CRISPR-Cas systems follow three basis steps: (1) adaptation (invading DNA is integrated into the host genome ...


Identification Of New Genes In Congenital Heart Defects, Naomi Siddiquee Nov 2018

Identification Of New Genes In Congenital Heart Defects, Naomi Siddiquee

Georgia Undergraduate Research Conference (GURC)

Tetralogy of Fallot (TOF) is the most common form of cyanotic congenital heart disease, occurring in 1 in 3000 live births. TOF is a combination of four heart defects that affect normal blood flow. Shone’s Syndrome is another rare congenital heart disease consisting of left-sided obstructive heart lesions. Although the diagnosis of both diseases is confirmed by clinical evaluation and physical examination, their pathogenesis is unknown. This research aimed to identify and characterize new genetic variants in hereditary cardiac diseases, specifically Tetralogy of Fallot and Shone’s Syndrome. Exome sequencing identified 20 nucleotide variants in different genes among TOF ...


Alternative Genes For Exploring Ranavirus Phylogenetics: Four Core Genes Compared To The Major Capsid Protein And The Whole Genome., Abigale Garner Nov 2018

Alternative Genes For Exploring Ranavirus Phylogenetics: Four Core Genes Compared To The Major Capsid Protein And The Whole Genome., Abigale Garner

Georgia Undergraduate Research Conference (GURC)

The Iridoviridae is a family of virus that infects invertebrates and poikilothermic vertebrates such as amphibians, reptiles, and fish. Ranavirus is one of the five genera within the Iridoviridae. Ranavirus infections have been seen on every continent. The ranaviruses have 26 core genes, but our study focuses on the utility of: an immediate early protein ICP-46 [open reading frame (ORF) 91R in Frog virus 3 (FV3)]; a transcription elongation factor TIIS (ORF 81R in FV3); Evrl/Air family protein (ORF 88R in FV3); and a hypothetical/putative protein of unknown function (ORF 94R in FV3) as alternative genes for phylogenetic ...


Robust Genome Editing With Short Single-Stranded And Long, Partially Single-Stranded Dna Donors In Caenorhabditis Elegans, Gregoriy A. Dokshin, Krishna S. Ghanta, Katherine M. Piscopo, Craig C. Mello Nov 2018

Robust Genome Editing With Short Single-Stranded And Long, Partially Single-Stranded Dna Donors In Caenorhabditis Elegans, Gregoriy A. Dokshin, Krishna S. Ghanta, Katherine M. Piscopo, Craig C. Mello

Open Access Articles

CRISPR-based genome editing using ribonucleoprotein complexes and synthetic single-stranded oligodeoxynucleotide (ssODN) donors can be highly effective. However, reproducibility can vary, and precise, targeted integration of longer constructs-such as green fluorescent protein tags remains challenging in many systems. Here, we describe a streamlined and optimized editing protocol for the nematode Caenorhabditis elegans We demonstrate its efficacy, flexibility, and cost-effectiveness by affinity-tagging 14 Argonaute proteins in C. elegans using ssODN donors. In addition, we describe a novel PCR-based, partially single-stranded, "hybrid" donor design that yields high efficiency editing with large (kilobase-scale) constructs. We use these hybrid donors to introduce fluorescent protein tags ...


Genetic Variants In The Sirt6 Transcriptional Regulatory Region Affect Gene Activity And Carcass Quality Traits In Indigenous Chinese Beef Cattle (Bos Taurus), Lin-Sheng Gui, Sayed Haidar Abbas Raza, Matthew Garcia, Yong-Gang Sun, Irfan Ullah, Yin-Cang Han Nov 2018

Genetic Variants In The Sirt6 Transcriptional Regulatory Region Affect Gene Activity And Carcass Quality Traits In Indigenous Chinese Beef Cattle (Bos Taurus), Lin-Sheng Gui, Sayed Haidar Abbas Raza, Matthew Garcia, Yong-Gang Sun, Irfan Ullah, Yin-Cang Han

Animal, Dairy, and Veterinary Science Faculty Publications

Background: The aim of this study was to analyze potential influences of polymorphisms within the regulatory region of the bovine SIRT6 gene on carcass quality traits. Expression analyses suggested that SIRT6 gene is predominately expressed in kidney, compared with other tissues. In 535 indigenous Chinese beef cattle, two novel single nucleotide polymorphisms (SNPs) were identified within the promoter region of the SIRT6 gene.

Results: Association analysis indicated that G allele of the c.-1100 A > G had a positive effect on fat deposition, and the Hap4/4 diplotype had more favourable results than other dipoltypes with respect to the evaluation ...


Rare Gene Fusion Rearrangement Sptnb1-Pdgfrb In An Atypical Myeloproliferative Neoplasm, Vanessa Fiorini Furtado, Neeraj Y. Saini, William V. Walsh, Venu G. Bathini, Patricia M. Miron Oct 2018

Rare Gene Fusion Rearrangement Sptnb1-Pdgfrb In An Atypical Myeloproliferative Neoplasm, Vanessa Fiorini Furtado, Neeraj Y. Saini, William V. Walsh, Venu G. Bathini, Patricia M. Miron

Open Access Articles

The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia recognizes a distinct class of myeloid and lymphoid tumors with eosinophilia-related proliferations associated with specific gene rearrangements, one of which involves rearrangements of platelet-derived growth factor receptor B (PDGFRB) gene. We report a case of a rare PDGFRB rearrangement with SPTNB1 (spectrin beta, nonerythrocytic 1) that presented as atypical myeloproliferative neoplasm.


Stochastic Difference Model For Evolutional Dynamics Of Large Antigen Repertoires In African Trypanosomes, Fan Yu Oct 2018

Stochastic Difference Model For Evolutional Dynamics Of Large Antigen Repertoires In African Trypanosomes, Fan Yu

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.