Open Access. Powered by Scholars. Published by Universities.®

Bioinformatics Commons

Open Access. Powered by Scholars. Published by Universities.®

3,518 Full-Text Articles 5,735 Authors 451,550 Downloads 136 Institutions

All Articles in Bioinformatics

Faceted Search

3,518 full-text articles. Page 4 of 135.

Tal Effector-Nucleotide Targeter (Tale-Nt) 2.0: Tools For Tal Effector Design And Target Prediction, Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. VanDyk, Adam J. Bogdanove 2019 Iowa State University

Tal Effector-Nucleotide Targeter (Tale-Nt) 2.0: Tools For Tal Effector Design And Target Prediction, Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. Vandyk, Adam J. Bogdanove

Nicholas J. Booher

Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the DNA target, with some degeneracy. A TAL effector-nucleotide binding code that links repeat type to specified nucleotide enables prediction of genomic binding sites for TAL effectors and customization of TAL effectors for use in DNA targeting, in particular as custom transcription factors for engineered gene regulation and as site-specific nucleases for genome editing. We have developed a suite of web-based tools called TAL Effector-Nucleotide Targeter 2.0 (TALE-NT 2.0;https://boglab.plp ...


Molecular Phylogeny Implemented In An Introductory Plant Classification Course, Chao Cai, Jo Ann Banks 2019 Purdue University

Molecular Phylogeny Implemented In An Introductory Plant Classification Course, Chao Cai, Jo Ann Banks

Libraries Faculty and Staff Presentations

Plant classification is one of the core components in undergraduate programs related to plant sciences. Traditionally plant classification courses primarily introduce morphology-based taxonomy because of practical needs in the field. However, the publication of new plant classification systems by Angiosperm Phylogeny Group (APG) using molecular phylogeny methods leads to the trends of using molecular evidence (DNA barcode) for plant identification. In our introductory plant classification course, we included a two-week module (lectures and labs) to introduce key concepts and fundamental skills in molecular phylogeny. Week 1 included concepts of evolutionary tree thinking, data mining in NCBI using BLAST search, and ...


Sdrap: An Annotation Pipeline For Highly Scrambled Genomes, Jasper Braun 2019 Illinois State University

Sdrap: An Annotation Pipeline For Highly Scrambled Genomes, Jasper Braun

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Network Reconstruction Using Computational Algebra And Gene Knockouts, Matthew Macauley 2019 Illinois State University

Network Reconstruction Using Computational Algebra And Gene Knockouts, Matthew Macauley

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Loop Homology Of Bi-Secondary Structures, Andrei Bura 2019 Illinois State University

Loop Homology Of Bi-Secondary Structures, Andrei Bura

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


The Energy-Spectrum Of Bicompatible Sequences, Wenda Huang 2019 Illinois State University

The Energy-Spectrum Of Bicompatible Sequences, Wenda Huang

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


On An Enhancement Of Rna Probing Data Using Information Theory, Thomas J.X. Li, Christian M. Reidys 2019 University of Virginia

On An Enhancement Of Rna Probing Data Using Information Theory, Thomas J.X. Li, Christian M. Reidys

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Common Nodes Of Virus-Host Interaction Revealed Through An Integrated Network Analysis, Korbinian Bosl, Richard K. Kandasamy 2019 Norwegian University of Science and Technology

Common Nodes Of Virus-Host Interaction Revealed Through An Integrated Network Analysis, Korbinian Bosl, Richard K. Kandasamy

Open Access Articles

Viruses are one of the major causes of acute and chronic infectious diseases and thus a major contributor to the global burden of disease. Several studies have shown how viruses have evolved to hijack basic cellular pathways and evade innate immune response by modulating key host factors and signaling pathways. A collective view of these multiple studies could advance our understanding of virus-host interactions and provide new therapeutic perspectives for the treatment of viral diseases. Here, we performed an integrative meta-analysis to elucidate the 17 different host-virus interactomes. Network and bioinformatics analyses showed how viruses with small genomes efficiently achieve ...


Highly Structured Homolog Pairing Reflects Functional Organization Of The Drosophila Genome, Jumana AlHaj Abed, Jelena Erceg, Anton Goloborodko, Son C. Nguyen, Ruth B. McCole, Wren Saylor, Geoffrey Fudenberg, Bryan R. Lajoie, Job Dekker, Leonid A. Mirny, C-Ting Wu 2019 Harvard Medical School

Highly Structured Homolog Pairing Reflects Functional Organization Of The Drosophila Genome, Jumana Alhaj Abed, Jelena Erceg, Anton Goloborodko, Son C. Nguyen, Ruth B. Mccole, Wren Saylor, Geoffrey Fudenberg, Bryan R. Lajoie, Job Dekker, Leonid A. Mirny, C-Ting Wu

Program in Systems Biology Publications

Trans-homolog interactions have been studied extensively in Drosophila, where homologs are paired in somatic cells and transvection is prevalent. Nevertheless, the detailed structure of pairing and its functional impact have not been thoroughly investigated. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, showing that homologs pair with varying precision genome-wide, in addition to establishing trans-homolog domains and compartments. We also elucidate the structure of pairing with unprecedented detail, observing significant variation across the genome and revealing at least two forms of pairing: tight pairing, spanning contiguous small domains, and loose pairing, consisting of single ...


The Genome-Wide Multi-Layered Architecture Of Chromosome Pairing In Early Drosophila Embryos, Jelena Erceg, Jumana AlHaj Abed, Anton Goloborodko, Bryan R. Lajoie, Geoffrey Fudenberg, Nezar Abdennur, Maxim Imakaev, Ruth B. McCole, Son C. Nguyen, Wren Saylor, Eric F. Joyce, T. Niroshini Senaratne, Mohammed A. Hannan, Guy Nir, Job Dekker, Leonid A. Mirny, C-Ting Wu 2019 Harvard Medical School

The Genome-Wide Multi-Layered Architecture Of Chromosome Pairing In Early Drosophila Embryos, Jelena Erceg, Jumana Alhaj Abed, Anton Goloborodko, Bryan R. Lajoie, Geoffrey Fudenberg, Nezar Abdennur, Maxim Imakaev, Ruth B. Mccole, Son C. Nguyen, Wren Saylor, Eric F. Joyce, T. Niroshini Senaratne, Mohammed A. Hannan, Guy Nir, Job Dekker, Leonid A. Mirny, C-Ting Wu

Program in Systems Biology Publications

Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a ...


Evidence For Adaptive Introgression Of Exons Across A Hybrid Swarm In Deer, Emily Latch, Margaret Haines, Gordon Luikart, Stephen Amish, Seth Smith 2019 University of Wisconsin - Milwaukee

Evidence For Adaptive Introgression Of Exons Across A Hybrid Swarm In Deer, Emily Latch, Margaret Haines, Gordon Luikart, Stephen Amish, Seth Smith

Biological Sciences Faculty Articles

Background: Secondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study ...


Activity, Distribution, And Density Of Brown Rats (Rattus Norvegicus) On Misali Island, Pemba Island, Tanzania, Raegan Hasselbring 2019 SIT Study Abroad

Activity, Distribution, And Density Of Brown Rats (Rattus Norvegicus) On Misali Island, Pemba Island, Tanzania, Raegan Hasselbring

Independent Study Project (ISP) Collection

This project investigated the activity, distribution, and density of brown rats (R. norvegicus) on Misali Island, Pemba. These factors were studied through field observations conducted over a 21-day observation period. Brown rats were highest in density around areas of human activity, attracted to the detritus, an ample food source. Although highest in density in these areas, a greater total population of brown rats was distributed in the coastal forest due to its proportion of area on the overall island. In the forest, the rats were most active along the coastal sections for unknown and unexplored reasons – possibly due to regular ...


Leopards Are Good To Think With: Spotting The Zanzibar Leopard In Jozani Forest, Andrew Weier 2019 SIT Study Abroad

Leopards Are Good To Think With: Spotting The Zanzibar Leopard In Jozani Forest, Andrew Weier

Independent Study Project (ISP) Collection

In this project, the modern narrative of the Zanzibar leopard was studied in Jozani-Chwaka Bay National Park. Game cameras were installed and various locations around the national park to try and gather primary evidence that supported the existence of a leopard population in the forest. In addition, local community members were interviewed about recent leopard related activities. No biological evidence was gathered that supported the existence of the Zanzibar leopard and information collected from interviews indicated a potential shift in which other organisms are considered leopards. Recommendations were made for future research to be able to better understand the complex ...


Genome-Wide Discovery Of Missing Genes In Biological Pathways Of Prokaryotes., Yong Chen, Fenglou Mao, Guojun Li, Ying Xu 2019 Rowan University

Genome-Wide Discovery Of Missing Genes In Biological Pathways Of Prokaryotes., Yong Chen, Fenglou Mao, Guojun Li, Ying Xu

Yong Chen

BACKGROUND: Reconstruction of biological pathways is typically done through mapping well-characterized pathways of model organisms to a target genome, through orthologous gene mapping. A limitation of such pathway-mapping approaches is that the mapped pathway models are constrained by the composition of the template pathways, e.g., some genes in a target pathway may not have corresponding genes in the template pathways, the so-called "missing gene" problem.

METHODS: We present a novel pathway-expansion method for identifying additional genes that are possibly involved in a target pathway after pathway mapping, to fill holes caused by missing genes as well as to expand ...


Investigating The Dispersal Of Antibiotic Resistance Associated Genes From Manure Application To Soil And Drainage Waters In Simulated Agricultural Farmland Systems, Schuyler D. Smith, Phillip Colgan, Fan Yang, Elizabeth L. Rieke, Michelle L. Soupir, Thomas B. Moorman, Heather K. Allen, Adina Howe 2019 Iowa State University

Investigating The Dispersal Of Antibiotic Resistance Associated Genes From Manure Application To Soil And Drainage Waters In Simulated Agricultural Farmland Systems, Schuyler D. Smith, Phillip Colgan, Fan Yang, Elizabeth L. Rieke, Michelle L. Soupir, Thomas B. Moorman, Heather K. Allen, Adina Howe

Agricultural and Biosystems Engineering Publications

Manure from animals that have been treated with antibiotics is often used to fertilize agricultural soils and its application has previously been shown to enrich for genes associated with antibiotic resistance in agroecosystems. To investigate the magnitude of this effect, we designed a column experiment simulating manure-treated agricultural soil that utilizes artificial subsurface drainage to determine the duration and extent which this type of manure fertilization impacts the set of genes associated with antibiotic resistance in drainage water. We classified ARGs in manure-treated drainage effluent water by its source of origin. Overall, we found that 61% and 7% of the ...


Chromatin Digestion By The Chemotherapeutic Agent Bleomycin Produces Nucleosome And Transcription Factor Footprinting Patterns Similar To Micrococcal Nuclease, Joshua Michael Stolz 2019 Rowan University

Chromatin Digestion By The Chemotherapeutic Agent Bleomycin Produces Nucleosome And Transcription Factor Footprinting Patterns Similar To Micrococcal Nuclease, Joshua Michael Stolz

Theses and Dissertations

Bleomycin (BLM), a glycopeptide antibiotic commonly used in chemotherapeutic treatments, has been shown to produce single and double stranded DNA breaks. Subsequent analysis of DNA fragmentation patterns has demonstrated preferential digestion of chromatin in the TSS of active genes and the ability to produce nucleosome-sized fragments within intact chromatin. Nucleosome positioning plays a critical role in the regulation of gene activation. Currently, micrococcal nuclease (MNase) is used as the standard for mapping the position of nucleosomes in the genome. In order to identify whether BLM can be used as an effective nucleosome-mapping agent, BLM was used to digest chromatin in ...


Clinical Molecular Marker Testing Data Capture To Promote Precision Medicine Research Within The Cancer Research Network, Andrea N. Burnett-Hartman, Mara M. Epstein 2019 Kaiser Permanente Colorado

Clinical Molecular Marker Testing Data Capture To Promote Precision Medicine Research Within The Cancer Research Network, Andrea N. Burnett-Hartman, Mara M. Epstein

Open Access Articles

PURPOSE: To evaluate health care systems for the availability of population-level data on the frequency of use and results of clinical molecular marker tests to inform precision cancer care.

METHODS: We assessed cancer-related molecular marker test data availability across 12 US health care systems in the Cancer Research Network. Overall, these systems provide care to a diverse population of more than 12 million people in the United States. We performed qualitative analyses of test data availability for five blood-based protein, nine germline, and 14 tissue-based tumor marker tests in each health care system's electronic health record and tumor registry ...


Diverse Repertoire Of Human Adipocyte Subtypes Develops From Transcriptionally Distinct Mesenchymal Progenitor Cells, So Yun Min, Anand Desai, Zinger Yang, Agastya Sharma, Tiffany DeSouza, Ryan Genga, Alper Kucukural, Lawrence M. Lifshitz, Soren Nielsen, Camilla Scheele, Rene Maehr, Manuel Garber, Silvia Corvera 2019 University of Massachusetts Medical School

Diverse Repertoire Of Human Adipocyte Subtypes Develops From Transcriptionally Distinct Mesenchymal Progenitor Cells, So Yun Min, Anand Desai, Zinger Yang, Agastya Sharma, Tiffany Desouza, Ryan Genga, Alper Kucukural, Lawrence M. Lifshitz, Soren Nielsen, Camilla Scheele, Rene Maehr, Manuel Garber, Silvia Corvera

Open Access Articles

Single-cell sequencing technologies have revealed an unexpectedly broad repertoire of cells required to mediate complex functions in multicellular organisms. Despite the multiple roles of adipose tissue in maintaining systemic metabolic homeostasis, adipocytes are thought to be largely homogenous with only 2 major subtypes recognized in humans so far. Here we report the existence and characteristics of 4 distinct human adipocyte subtypes, and of their respective mesenchymal progenitors. The phenotypes of these distinct adipocyte subtypes are differentially associated with key adipose tissue functions, including thermogenesis, lipid storage, and adipokine secretion. The transcriptomic signature of "brite/beige" thermogenic adipocytes reveals mechanisms for ...


Genome-Wide Analysis Of Polymerase Iii-Transcribed Alu Elements Suggests Cell-Type-Specific Enhancer Function, Xiao-Ou Zhang, Thomas R. Gingeras, Zhiping Weng 2019 University of Massachusetts Medical School

Genome-Wide Analysis Of Polymerase Iii-Transcribed Alu Elements Suggests Cell-Type-Specific Enhancer Function, Xiao-Ou Zhang, Thomas R. Gingeras, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications

Alu elements are one of the most successful families of transposons in the human genome. A portion of Alu elements is transcribed by RNA Pol III, whereas the remaining ones are part of Pol II transcripts. Because Alu elements are highly repetitive, it has been difficult to identify the Pol III-transcribed elements and quantify their expression levels. In this study, we generated high-resolution, long-genomic-span RAMPAGE data in 155 biosamples all with matching RNA-seq data and built an atlas of 17,249 Pol III-transcribed Alu elements. We further performed an integrative analysis on the ChIP-seq data of 10 histone marks and ...


From Single Cells To Human Disease: High-Resolution Phenotyping Of Male Infertility Models Using Single-Cell Rna Sequencing, Min Jung 2019 Washington University in St. Louis

From Single Cells To Human Disease: High-Resolution Phenotyping Of Male Infertility Models Using Single-Cell Rna Sequencing, Min Jung

Arts & Sciences Electronic Theses and Dissertations

Male infertility is a complex disease that can result in significant emotional distress and treatment costs. Globally, male infertility affects 7% of males, and while its incidence is rising, its etiology remains elusive. In order to improve patient care, it is critical to identify the nature of spermatogenic failure in as many men as possible. The extensive cellular heterogeneity of testis has limited the application of bulk expression measurements to capture crucial information to dissect molecular mechanisms of defects in the infertile patients. Thus, the application of single-cell RNA-sequencing on male germ cells provides an amazing new set of scientific ...


Digital Commons powered by bepress