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A Note From The Editor, Daphne Fauber 2020 Purdue University

A Note From The Editor, Daphne Fauber

Ideas: Exhibit Catalog for the Honors College Visiting Scholars Series

This piece is a letter from Daphne Fauber, the editor of this issue of Ideas. In the letter, the editor introduces the work of Dr. Paschalis Gkoupidenis as well as the moment in time in which his Visiting Scholars talk occurs.


Pathway-Extended Gene Expression Signatures Integrate Novel Biomarkers That Improve Predictions Of Patient Responses To Kinase Inhibitors, Ashis Jem Bagchee-Clark, Eliseos J. Mucaki, Tyson Whitehead, Peter Rogan 2020 Western University

Pathway-Extended Gene Expression Signatures Integrate Novel Biomarkers That Improve Predictions Of Patient Responses To Kinase Inhibitors, Ashis Jem Bagchee-Clark, Eliseos J. Mucaki, Tyson Whitehead, Peter Rogan

Biochemistry Publications

No abstract provided.


Stochastic Modeling Of Ovarian Follicle Growth In Adult Female Rats, Zhaozhi Li 2020 Illinois State University

Stochastic Modeling Of Ovarian Follicle Growth In Adult Female Rats, Zhaozhi Li

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Measuring Stability Of 3d Chromatin Conformations And Identifying Neuron Specific Chromatin Loops Associated With Schizophrenia Risk, Tyler M. Borrman 2020 University of Massachusetts Medical School

Measuring Stability Of 3d Chromatin Conformations And Identifying Neuron Specific Chromatin Loops Associated With Schizophrenia Risk, Tyler M. Borrman

GSBS Dissertations and Theses

The 23 pairs of chromosomes comprising the human genome are intricately folded within the nucleus of each cell in a manner that promotes efficient gene regulation and cell function. Consequently, active gene rich regions are compartmentally segregated from inactive gene poor regions of the genome. To better understand the mechanisms driving compartmentalization we investigated what would occur if this system was disrupted. By digesting the genome to varying sizes and analyzing the fragmented 3D structure over time, our work revealed essential laws governing nuclear compartmentalization.

At a finer resolution within compartments, chromatin forms loop structures capable of regulating gene expression ...


Discrete Models And Algorithms For Analyzing Dna Rearrangements, Jasper Braun 2020 University of South Florida

Discrete Models And Algorithms For Analyzing Dna Rearrangements, Jasper Braun

Graduate Theses and Dissertations

In this work, language and tools are introduced, which model many-to-many mappings that comprise DNA rearrangements in nature. Existing theoretical models and data processing methods depend on the premise that DNA segments in the rearrangement precursor are in a clear one-to-one correspondence with their destinations in the recombined product. However, ambiguities in the rearrangement maps obtained from the ciliate species Oxytricha trifallax violate this assumption demonstrating a necessity for the adaptation of theory and practice.

In order to take into account the ambiguities in the rearrangement maps, generalizations of existing recombination models are proposed. Edges in an ordered graph model ...


Progressive Cactus Is A Multiple-Genome Aligner For The Thousand-Genome Era, Joel Armstrong, Elinor K. Karlsson, Guojie Zhang, Benedict Paten 2020 University of California, Santa Cruz

Progressive Cactus Is A Multiple-Genome Aligner For The Thousand-Genome Era, Joel Armstrong, Elinor K. Karlsson, Guojie Zhang, Benedict Paten

University of Massachusetts Medical School Faculty Publications

New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies(1-3). For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database(4) increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies(5) are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes ...


Daglogo: An R/Bioconductor Package For Identifying And Visualizing Differential Amino Acid Group Usage In Proteomics Data, Jianhong Ou, Haibo Liu, Niraj K. Nirala, Alexey Stukalov, Usha Acharya, Michael R. Green, Lihua Julie Zhu 2020 University of Massachusetts Medical School

Daglogo: An R/Bioconductor Package For Identifying And Visualizing Differential Amino Acid Group Usage In Proteomics Data, Jianhong Ou, Haibo Liu, Niraj K. Nirala, Alexey Stukalov, Usha Acharya, Michael R. Green, Lihua Julie Zhu

Open Access Publications by UMMS Authors

Sequence logos have been widely used as graphical representations of conserved nucleic acid and protein motifs. Due to the complexity of the amino acid (AA) alphabet, rich post-translational modification, and diverse subcellular localization of proteins, few versatile tools are available for effective identification and visualization of protein motifs. In addition, various reduced AA alphabets based on physicochemical, structural, or functional properties have been valuable in the study of protein alignment, folding, structure prediction, and evolution. However, there is lack of tools for applying reduced AA alphabets to the identification and visualization of statistically significant motifs. To fill this gap, we ...


The Meadow Jumping Mouse Genome And Transcriptome Suggest Mechanisms Of Hibernation [Preprint], Qian Cong, Ethan A. Brem, Jing Zhang, Jessica Alfoldi, Jeremy Johnson, Elinor K. Karlsson, Kerstin Lindblad-Toh, Jason L. Malaney, William J. Israelsen 2020 University of Texas Southwestern Medical Center

The Meadow Jumping Mouse Genome And Transcriptome Suggest Mechanisms Of Hibernation [Preprint], Qian Cong, Ethan A. Brem, Jing Zhang, Jessica Alfoldi, Jeremy Johnson, Elinor K. Karlsson, Kerstin Lindblad-Toh, Jason L. Malaney, William J. Israelsen

University of Massachusetts Medical School Faculty Publications

Hibernating mammals exhibit medically relevant phenotypes, but the genetic basis of hibernation remains poorly understood. Using the meadow jumping mouse (Zapus hudsonius), we investigated the genetic underpinnings of hibernation by uniting experimental and comparative genomic approaches. We assembled a Z. hudsonius genome and identified widespread expression changes during hibernation in genes important for circadian rhythm, membrane fluidity, and cell cycle arrest. Tissue-specific gene expression changes during torpor encompassed Wnt signaling in the brain and structural and transport functions in the kidney brush border. Using genomes from the closely related Zapus oregonus (previously classified as Z. princeps) and leveraging a panel ...


Genetic And Epigenetic Features Of Promoters With Ubiquitous Chromatin Accessibility Support Ubiquitous Transcription Of Cell-Essential Genes [Preprint], Kaili Fan, Jill E. Moore, Xiao-Ou Zhang, Zhiping Weng 2020 University of Massachusetts Medical School

Genetic And Epigenetic Features Of Promoters With Ubiquitous Chromatin Accessibility Support Ubiquitous Transcription Of Cell-Essential Genes [Preprint], Kaili Fan, Jill E. Moore, Xiao-Ou Zhang, Zhiping Weng

University of Massachusetts Medical School Faculty Publications

Gene expression is controlled by regulatory elements with accessible chromatin. Although the majority of regulatory elements are cell type-specific, being in the open chromatin state in only one or a few cell types, approximately 16,000 regions in the human genome and 13,000 regions in the mouse genome are in the open chromatin state in nearly all of the 517 human and 94 mouse cell and tissue types assayed by the ENCODE consortium, respectively. We performed a systematic analysis on the subset of 9,000 human and 8,000 mouse ubiquitously (ubi) open chromatin regions that were also classified ...


Deepfrag-K: A Fragment-Based Deep Learning Approach For Protein Fold Recognition, Wessam Elhefnawy, Min Li, Jianxin Wang, Yaohang Li 2020 Old Dominion University

Deepfrag-K: A Fragment-Based Deep Learning Approach For Protein Fold Recognition, Wessam Elhefnawy, Min Li, Jianxin Wang, Yaohang Li

Computer Science Faculty Publications

Background: One of the most essential problems in structural bioinformatics is protein fold recognition. In this paper, we design a novel deep learning architecture, so-called DeepFrag-k, which identifies fold discriminative features at fragment level to improve the accuracy of protein fold recognition. DeepFrag-k is composed of two stages: the first stage employs a multi-modal Deep Belief Network (DBN) to predict the potential structural fragments given a sequence, represented as a fragment vector, and then the second stage uses a deep convolutional neural network (CNN) to classify the fragment vector into the corresponding fold.

Results: Our results show that DeepFrag-k yields ...


Oran: A Meta-Modeling Platform To Drive Real-Life And Online Outbreak Simulations, Andres Colubri 2020 University of Massachusetts Medical School

Oran: A Meta-Modeling Platform To Drive Real-Life And Online Outbreak Simulations, Andres Colubri

University of Massachusetts Medical School Publications

Presented virtually during the "New Faculty Talks" session at the 25th Annual University of Massachusetts Medical School Research Retreat 2020 on October 27, 2020.


Metabolic Interactions In Microbial Communities, Elizabeth A. Shank 2020 University of Massachusetts Medical School

Metabolic Interactions In Microbial Communities, Elizabeth A. Shank

University of Massachusetts Medical School Publications

The Shank laboratory studies the chemical and physical interactions of microbes with each other and their hosts. Microbes live everywhere, and their activities can have profound impacts on their hosts as well as on ecosystem‐level processes. How microbes interact within these communities, however, remains largely unknown. We are fascinated by the idea that microbes are able to generate and secrete chemical cues (known as specialized or secondary metabolites) that can act as interspecies signals to influence the physiology and metabolism of their microbial neighbors, and thus contribute to the stability and functioning of complex microbial communities. Our research dissects ...


Pan-Cancer Analysis Of Telomerase Reverse Transcriptase (Tert) Isoforms, Mathushan Subasri 2020 The University of Western Ontario

Pan-Cancer Analysis Of Telomerase Reverse Transcriptase (Tert) Isoforms, Mathushan Subasri

Electronic Thesis and Dissertation Repository

Reactivation of the multi-subunit ribonucleoprotein telomerase is the primary telomere maintenance mechanism in cancer, but it is rate-limited by the enzymatic component, telomerase reverse transcriptase (TERT). While regulatory in nature, TERT alternative splice variant/isoform regulation and functions are not fully elucidated and are further complicated by their highly diverse expression. In this thesis, I characterized TERT expression across normal and neoplastic tissues using TCGA and GTEx RNA-sequencing data. In doing so, I demonstrated the global overexpression and splicing shift towards full-length TERT in neoplastic tissue. Furthermore, my studies identified tumour subtype expression differences possibly regulated by subtype-specific characteristics, detailed ...


Genome-Wide Dna Methylation Profiling In Human Breast Tissue By Illumina Truseq Methyl Capture Epic Sequencing And Infinium Methylationepic Beadchip Microarray, Nan Lin, Jinpeng Liu, James Castle, Jun Wan, Aditi Shendre, Yunlong Liu, Chi Wang, Chunyan He 2020 University of Kentucky

Genome-Wide Dna Methylation Profiling In Human Breast Tissue By Illumina Truseq Methyl Capture Epic Sequencing And Infinium Methylationepic Beadchip Microarray, Nan Lin, Jinpeng Liu, James Castle, Jun Wan, Aditi Shendre, Yunlong Liu, Chi Wang, Chunyan He

Markey Cancer Center Faculty Publications

A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing. We empirically examined the performance of TruSeq EPIC and EPIC-array in assessing genome-wide DNA methylation in breast tissue samples. TruSeq EPIC provided data with a much higher density in the regions when compared to EPIC-array (~2.74 million CpGs with at least 10X coverage vs ~752 K CpGs, respectively). Approximately 398 K CpGs were common and measured across the two platforms in every sample. Overall ...


Engineering Essential Genes With A "Jump Board" Strategy Using Crispr/Cas9, Ye Duan, Sungwook Choi, Charles Nelson, Victor R. Ambros 2020 University of Massachusetts Medical School

Engineering Essential Genes With A "Jump Board" Strategy Using Crispr/Cas9, Ye Duan, Sungwook Choi, Charles Nelson, Victor R. Ambros

University of Massachusetts Medical School Faculty Publications

Here, we describe a platformed “jump board” strategy and its application in systematically engineering the essential microRNA let-7 (Fig. 1A-E) and protein coding gene lin-28 (Fig. 1F) in C. elegans. We chose the jump board protospacer sequence (INPP4A) which is (1) comprised of a PAM site and a protospacer antisense to a crRNA with experimentally confirmed high editing efficiency (INPP4A-crRNA), and (2) non-homologous to C. elegans genome, including the genetic balancer we used (mnDp1). Notably, the jump board protospacer contains an EcoRV restriction site, which can be utilized for rapid large-scale genotyping by which HDR events can be identified in ...


Estimating Partial Body Ionizing Radiation Exposure By Automated Cytogenetic Biodosimetry, Ben Shirley, Peter Rogan 2020 Cytognomix

Estimating Partial Body Ionizing Radiation Exposure By Automated Cytogenetic Biodosimetry, Ben Shirley, Peter Rogan

Biochemistry Publications

Purpose: Inhomogeneous exposures to ionizing radiation can be detected and quantified with the dicentric chromosome assay (DCA) of metaphase cells. Complete automation of interpretation of the DCA for whole-body irradiation has significantly improved throughput without compromising accuracy, however, low levels of residual false positive dicentric chromosomes (DCs) have confounded its application for partial-body exposure determination.

Materials and methods: We describe a method of estimating and correcting for false positive DCs in digitally processed images of metaphase cells. Nearly all DCs detected in unirradiated calibration samples are introduced by digital image processing. DC frequencies of irradiated calibration samples and those exposed ...


Onestoprnaseq: A Web Application For Comprehensive And Efficient Analyses Of Rna-Seq Data, Rui Li, Kai Hu, Haibo Liu, Michael R. Green, Lihua Julie Zhu 2020 University of Massachusetts Medical School

Onestoprnaseq: A Web Application For Comprehensive And Efficient Analyses Of Rna-Seq Data, Rui Li, Kai Hu, Haibo Liu, Michael R. Green, Lihua Julie Zhu

Open Access Publications by UMMS Authors

Over the past decade, a large amount of RNA sequencing (RNA-seq) data were deposited in public repositories, and more are being produced at an unprecedented rate. However, there are few open source tools with point-and-click interfaces that are versatile and offer streamlined comprehensive analysis of RNA-seq datasets. To maximize the capitalization of these vast public resources and facilitate the analysis of RNA-seq data by biologists, we developed a web application called OneStopRNAseq for the one-stop analysis of RNA-seq data. OneStopRNAseq has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, such as comprehensive data-quality control, differential analysis ...


Comparison Of Cpu And Parabricks Gpu Enabled Bioinformatics Software For High Throughput Clinical Genomic Applications, Stefano Rosati 2020 Marquette University

Comparison Of Cpu And Parabricks Gpu Enabled Bioinformatics Software For High Throughput Clinical Genomic Applications, Stefano Rosati

Master's Theses (2009 -)

In recent years, high performance computing (HPC) has begun to revolutionize the architecture of software and servers to meet the ever-increasing demand for speed & efficiency. One of the ways this change is manifesting is the adoption of graphics processor units (GPUs). Used correctly, GPUS can increase throughput and decrease compute time for certain computational problems. Bioinformatics, an HPC dependent discipline, is no exception. As bioinformatics continues advance clinical care by sequencing patient’s DNA and RNA for diagnosis of diseases, there is an ever-increasing demand for faster data processing to improve clinical sequencing turnaround time. Parabricks, a GPU enabled bioinformatics ...


Integrated Multiparametric Radiomics And Informatics System For Characterizing Breast Tumor Characteristics With The Oncotypedx Gene Assay, Michael A. Jacobs, Christopher B. Umbricht, Vishwa S. Parekh, Riham H. El Khouli, Leslie Cope, Katarzyna J. Macura, Susan Harvey, Antonio C. Wolff 2020 Johns Hopkins University

Integrated Multiparametric Radiomics And Informatics System For Characterizing Breast Tumor Characteristics With The Oncotypedx Gene Assay, Michael A. Jacobs, Christopher B. Umbricht, Vishwa S. Parekh, Riham H. El Khouli, Leslie Cope, Katarzyna J. Macura, Susan Harvey, Antonio C. Wolff

Radiology Faculty Publications

Optimal use of multiparametric magnetic resonance imaging (mpMRI) can identify key MRI parameters and provide unique tissue signatures defining phenotypes of breast cancer. We have developed and implemented a new machine-learning informatic system, termed Informatics Radiomics Integration System (IRIS) that integrates clinical variables, derived from imaging and electronic medical health records (EHR) with multiparametric radiomics (mpRad) for identifying potential risk of local or systemic recurrence in breast cancer patients. We tested the model in patients (n = 80) who had Estrogen Receptor positive disease and underwent OncotypeDX gene testing, radiomic analysis, and breast mpMRI. The IRIS method was trained using the ...


Feature Selection Via Random Subsets Of Uncorrelated Features, Long Kim Dang 2020 University of South Florida

Feature Selection Via Random Subsets Of Uncorrelated Features, Long Kim Dang

Graduate Theses and Dissertations

The role of feature selection is crucial in many applications. A few of these include computational biology, image classification and risk management. In biology, gene expression micro array data sets have been used extensively in many areas of research. These data sets typically suffer from an important problem: the ratio between the number of features over the number of examples is very high. This problem mainly affects prediction accuracy because it is best to collect more labeled examples than features. A correlation based random subspace ensemble feature selector (CCC_RSM) was proposed to handle this problem [5]. In this approach, first ...


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