How can bioinformatics transfer in biotechnology?

Horizontal Gene Transfer. N. Yutin, in Brenner’s Encyclopedia of Genetics (Second Edition), 2022.

  • Introduction
  • Horizontal Gene Transfer
  • Abstract
  • Lateral Gene Transfer
  • Focus on Relevant Research
  • Conceptual questions
  • Discussion points

Horizontal Gene TransferN. Yutin, in Brenner’s Encyclopedia of Genetics (Second Edition), 2013IntroductionHorizontal, or lateral, gene transfer is generally defined as exchange of genetic information between contemporary organisms. Horizontal transfer is distinct from vertical transfer by which genetic information is passed from parent to offspring. A special case of the horizontal transfer involves the transfer of DNA between chloroplast or mitochondrial and nuclear genomes. In addition to entire genes, parts of genes, such as exons or introns, may also be transferred in this way. Although horizontal transfer is more likely to be successful between closely related than distantly related species, it does occur between species as divergent as those found in different domains of life. Read full chapterURL: sciencedirect. com/science/article/pii/B978012374984000735XGenome Evolution’s Role in Developmental EvolutionN. Rohner, in Encyclopedia of Evolutionary Biology, 2016Horizontal Gene TransferHorizontal gene transfer also known as lateral gene transfer is the process by which an organism incorporates genetic material from another organism without mating.


Video advice: How to Use the NCBI’s Bioinformatics Tools and Databases

This video tutorial provides a quick overview of the NCBI website. We walk you through how to search for nucleotide and protein sequences using NCBI’s databases and explain what information is provided with each sequence. We also give you tips on how to interpret gene data and guide you through the process of assessing gene variants and mutations using NCBI’s Variation Viewer. With the information provided in this video, you should be well equipped to start your own bioinformatics or genomics adventure!


Career change to bioinformatics/biotech? – Hello everyone. This post goes under the “I don’t know what I don’t know” category, so I’m looking to broaden my horizons a bit here. I’m…

I’ve seen the Bioinformatics specialization on Coursera and have been curious if that alone would warrant enough to change into the field (my assumption is no since a lot of people have MS/PHD in the field?) but it certainly cannot hurt from a just gaining a background. Again, just looking for enlightenment on how to go about a change.

Detecting horizontal gene transfer by mapping sequencing reads across species boundaries

AbstractMotivation. Horizontal gene transfer (HGT) is a fundamental mechanism that enables organisms such as bacteria to directly transfer genetic material betw.

Shiga contaminant-encoding bacteriophages–genomes moving. Int. J. Mediterranean. Microbiol., 294, 115–121. Holtgrewe M. Mason – a read simulator for second generation sequencing data. Technical Report TR-B-10-06. Institut fr Mathematik und Informatik, Freie Universitt Berlin. Hormozdiari F. et al.

  1. 1 Datasets
  2. 2 Assembly approach
  3. 2 KO11FL
  4. 3 EHEC
  5. Funding

MotivationHorizontal gene transfer (HGT) is a fundamental mechanism that enables organisms such as bacteria to directly transfer genetic material between distant species. This way, bacteria can acquire new traits such as antibiotic resistance or pathogenic toxins. Current bioinformatics approaches focus on the detection of past HGT events by exploring phylogenetic trees or genome composition inconsistencies. However, these techniques normally require the availability of finished and fully annotated genomes and of sufficiently large deviations that allow detection and are thus not widely applicable. Especially in outbreak scenarios with HGT-mediated emergence of new pathogens, like the enterohemorrhagic Escherichia coli outbreak in Germany 2011, there is need for fast and precise HGT detection. Next-generation sequencing (NGS) technologies facilitate rapid analysis of unknown pathogens but, to the best of our knowledge, so far no approach detects HGTs directly from NGS reads. ResultsWe present Daisy, a novel mapping-based tool for HGT detection.

Applications of Bioinformatics in Biotechnology

Bioinformatics has got so many applications in biotechnology field. Some of the important ones include automatic genome sequencing, automatic identification of genes, identification of functions of gens, predicting the 3D structure modelling and pair-wise compairism of genes.

Small fragments of genome could be amplified using polymerase squence of events or microbial artificial chromosome. Amplified fragments are affected from nucleotide studying errors, repeats these consequently generate multiple copies of the identical genome fragments. These repeats are removed right before the ultimate set up of genome fragments via mathematical models.

After the identification of functioning of a particular gene, bioinformatics is also used for pair-wise genome comparisons. Pair-wise comparison of a genome with itself is done to get the details of paralogous genes or duplicated genes that have the same base sequence with some functional variations. Also pair-wise genome comparison is also done against other genome to get information such as orthologous genes. These genes are equivalent genes present in two different genomes due to speciation. This technique is also used to identify different types of gene-groups and adjacent genes that occur in the close proximity as they are involved in common higher level function, and also lateral-gene transfer that is transfer of genes from a microorganism that is evolutionary distant. Bioinformatics technique is also used to analyse gene-fusion or gene-fission, gene-group duplication and much more.

A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data

The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such “bioprospecting” requires a suite of sophisticated bioinformatics tools to make sense of the data. This review summarizes the most commonly used bioinformatics tools for the assembly and annotation of metagenomic sequence data with the aim of discovering novel genes.

Bowe, A., Onodera, T., Sadakane, K., and Shibuya, T. . “Succinct de bruijn graphs,” in Proceedings from the twelfth Worldwide Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012: Algorithms in Bioinformatics, eds B. Raphael and J. Tang (Berlin: Springer), 225–235. doi: 10. 1007/978-3-642-33122-_18.


Video advice: NCBI Minute: A Beginner’s Guide to Genes and Sequences at NCBI

Presented September 11, 2019.


Sequencing Technologies for Whole Genome Shotgun Metagenomics

The term microbiome refers to the entire community of micro-organisms that exist within any particular ecosystem, and includes bacteria, archaea, viruses, phages, fungi, and protozoa; though the majority of microbiome studies focus only on the bacteria and archaea. There are two main methods for studying the microbiome using high-throughput sequencing: marker-gene studies and whole-genome-shotgun (WGS) metagenomics. In marker-gene studies, generic primers are designed to PCR amplify a particular gene (e. g., 16S rRNA for bacteria/archaea, 18S for fungi) from all genomes present in a sample, and the resulting product is sequenced. The sequences are clustered into operational-taxonomic-units (OTUs) and these are compared across samples. Whilst fast and cheap, this method does not reveal anything else about the hundreds of thousands of genes encoded in the parts of the (meta) genomes that remained unsequenced.

Bioinformatics and Computational Biology

Faculty & Affiliate Faculty – We are developing algorithms with improved accuracy for large-scale and complex estimation problems in phylogenomics (genome-scale phylogeny estimation), multiple sequence alignment, and metagenomics. We are exploring gene regulation—developing advanced techniques to predict the diverse function of noncoding parts of DNA and to relate interspecies and interpersonal differences in DNA to differences in the organism’s form and function. We work broadly in the development of machine learning techniques for computational biology, with research spanning the areas of molecular and structural biology; networks and systems biology; and molecular mechanisms of human disease.

Major in Biology, Concentration in Bioinformatics

Requirements for a Major in Biology, Concentration in Bioinformatics – The purpose of this interdisciplinary concentration is to prepare students to enter the computer-intensive fields of bioinformatics, computational biology, computational chemistry, and molecular modeling including genomics and proteomics. With the ever increasing number of fully sequenced genomes, including the human genome, databases such as GenBank and EMBL have grown at such a rate that storing, organizing, indexing, and ultimately mining the data have become key to answering biological questions. Questions of gene expression have led to computational biology, the process of analyzing genomic sequences and to the field of proteomics, the understanding of protein structure and function. The information obtained by computational biology and computational chemistry is used in the design of new drugs to treat a variety of diseases. Major drug and biotechnology companies are seeking people trained in bioinformatics.

Admission and Application Requirements – Prerequisites Bachelor’s degree from an accredited college or university in the biological sciences or in engineering. Programs require a minimum GPA of 3.0 on a 4.0 scale. Meeting the minimum GPA requirement does not guarantee admission. All the prerequisites listed below can be taken from the existing Master of Science in Computer Science or the…

Official transcripts: JHU AAP accepts official transcripts that are electronically sent directly from the granting institution and emailed to aapadmissions@jhu. edu. If your institution does not provide electronic transcripts, request that your institution send an official transcript directly to:

Online Biotechnology Master’s Degree

Gain a specialty in bioinformatics in the online biotechnology graduate program at University of Maryland Global Campus. Formerly UMUC.

You have to conserve a GPA of three. or greater whatsoever occasions. All degree needs should be satisfied within five consecutive years. Any transfer credits should have been earned inside the five-year time period to become applied toward a graduate degree. Please review our summary of overall master’s degree needs for further factors.

  • What You’ll Learn
  • Coursework Examples
  • Master’s – specialization Courses
  • Initial Requirement
  • Core Courses
  • Specialization Courses
  • Capstone Course
  • Course Rules and Program Progression
  • Other Requirements

Biotechnology Master’s Degree with Bioinformatics Specialization Requirements

This is our recommended course sequence to progress through this program. This sequence incorporates course prerequisites and program requirements but does not list course alternatives that may be available. We recommend you take a maximum of 6 credits per term. You cannot take a prerequisite with its subsequent course during the same session. Your plan will be unique and dependent on multiple factors, including the number of credits you transfer to this program. Contact an advisor if you any questions about this plan, course alternatives, or your course load limit.

UCSC General Catalog

The Bachelor of Arts in Biotechnology is intended for students who plan to be involved in the biotechnology industry as writers, artists, ethicists, executives, sales force, regulators, lawyers, politicians, and other roles that require an understanding of the technology, but not the intensive training needed for technicians, research scientists, engineers, and bioinformaticians. (For those more technical roles, the biomolecular engineering and bioinformatics major or the molecular, cell, and developmental biology major is recommended.)

Students who’re informed that they’re not qualified to declare may appeal this decision by submitting instructions towards the BSOE Undergraduate Counseling Office. Within 15 times of delivery of the appeal, the Undergraduate Counseling office will inform a student, the school, and also the Office from the Registrar from the decision.

  1. Academic Advising for the Program
  2. Getting Started in the Major
  3. Program Learning Outcomes
  4. Major Qualification Policy and Declaration Process
  5. Major Qualification
  6. Appeal Process
  7. How to Declare a Major
  8. Transfer Information and Policy
  9. Transfer Admission Screening Policy
  10. Getting Started at UCSC as a Transfer Student
  11. Letter Grade Policy

Requirements and Planners

The Bachelor of Arts in Biotechnology is intended for students who plan to be involved in the biotechnology industry as writers, artists, ethicists, executives, sales force, regulators, lawyers, politicians, and other roles that require an understanding of the technology, but not the intensive training needed for technicians, research scientists, engineers, and bioinformaticians. (For those more technical roles, the biomolecular engineering and bioinformatics major or the molecular, cell, and developmental biology major is recommended.

Bioinformatics, P.S.M. Temple University

COLLEGE OF SCIENCE AND TECHNOLOGY.

Full-Time/Part-Time Status: The amount program could be completed on the full- or part-time basis. The majority of the courses are offered within the nights or on weekends to allow full-time working professionals to become signed up for this program. International students are needed to join up as full-time students.

  • Plan of Study Grid
  • Department Contacts:

Contacts

Interdisciplinary Study: Students in the Temple University Bioinformatics master’s degree program benefit from an advanced curriculum developed by leading Temple faculty in the Departments of Biology, Chemistry, and Computer and Information Sciences. The program has been designed to provide students with extensive skills in computer programming as well as deep knowledge in genomics and structural biology. All three areas are required in this challenging and exciting field.

Howard Community College

An Arts and Sciences Area of Study.

1. Understand fundamental biological processes at organism, cellular, and molecular levels. 2. Understand computer-programming methodology and then apply software programs for biological data analysis. 3. Identify, understand, evaluate, and apply ethical reasoning to problems, dilemmas, and issues in bioinformatics.

Bioinformatics – A.A. Degree (Transfer)

This curriculum is designed for students planning to transfer to a four-year institution to complete a bachelor’s degree in Bioinformatics. Bioinformatics blends biological sciences and technology so that the discovery, manipulation, storage, and extension of data can be accomplished. The program includes coursework in biology and computer science and emphasizes the use and handling of data. Technical courses provide basic knowledge of programming languages, databases and the Internet. The program prepares graduates for careers in pharmaceutical and biotechnology industries. Students should be familiar with the curriculum requirements of the institution to which they intend to transfer.

Biotechnology

  1. Major Requirements
  2. Careers
  3. Graduate Study
  4. Alumni Employers

Are you interested in the mechanics of life and improving human and animal health, food safety, energy production and environmental quality? Biotechnology is a multidisciplinary major that has an impact on almost every aspect of modern human life. Students develop a strong background in the biological sciences with an emphasis on the basic principles of genetics, molecular biology and cell biology. Students focus their studies into one of four areas to gain a more in-depth understanding of these topics: microbial biotechnology, animal biotechnology, plant biotechnology or bioinformatics.


Video advice: Genome bioinformatics: can you build expertise from scratch?

Have you ever wondered about the best way to build expertise from scratch? During the last years, Lilit and her colleagues have been pondering over this question. The pieces of the puzzle have come together, and now being one of the founders of the Armenian Bioinformatics Institute, Lilit and the team seem to have developed just the right model. Lilit has more than 10 years of experience in the field of bioinformatics and genomics. She holds an MS degree in biotechnology and MS in Computer Science. She was the first one in Armenia awarded with a PhD in computational biology and genomics from the Institute of Molecular Biology NAS Armenia and Leipzig University Germany. Afterwards, Lilit has conducted postdoctoral studies in computational biology at the Karolinska Institute in Sweden. In 2021 she became the founding director of the Armenian Bioinformatics Institute. Lilit has been the principal investigator of 3 research grants, an author of 20 peer-reviewed publications, and has won several fellowships in life sciences, including the Marie-Curie Individual Fellowship, the European Molecular Biology Organization (EMBO), the DAAD German Academic Research Service; has twice been nominated among “the most productive scientists of the year” by the Science Committee of Armenia. This talk was given at a TEDx event using the TED conference format but independently organized by a local community. Learn more at https://www.ted.com/tedx


Erwin van den Burg

Stress and anxiety researcher at CHUV2014–present
Ph.D. from Radboud University NijmegenGraduated 2002
Lives in Lausanne, Switzerland2013–present

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