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    BACKGROUND

    A two-year Postdoc position is available in the bioinformatics group (ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), (rth.dk) at Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences at University of Copenhagen. The Postdoc position in Bioinformatic and transcriptomic analysis and detection of non-coding RNA in bacteria is available from 2 January 2019 or as soon as possible thereafter.

    Information about the department can be found at ivh.ku.dk/english/.

    RESPONSIBILITIES

    As a team player working with great excitement you will be a key person in the project. The Postdoc position is part of the NextProd project (nextprod.dk), which aims to discover non-coding and structured RNA (ncRNA) that can affect the yield of cell factories. The NextProd project is supported by Innovation Fund Denmark.

    Background:
    Cell factories are based on organisms, which have been carefully optimised to produce protein-based products such as enzymes and pharmaceutical proteins with the highest possible yield. However, current technology is saturated with respect to yield improvement although the theoretical maximum has not yet been reached. Within the NextProd project, the goal is to improve the yield by manipulating ncRNAs.

    Job description:
    Transcriptomic data sets from relevant strains of the model cell-factory Bacillus subtilis will be used as outset for identification of ncRNAs, their expression, RNA structure and potential RNA-RNA interactions. An integrated workflow will be established including both known tools and tools developed on demand when relevant. The work involves interfacing and updating a genome browser framework with transcriptomics data, visualization results and gene associations. The work will be combined with further experimental analysis of candidates from the project collaborators.

    REQUIREMENTS

    Required qualifications and selection criteria:
    The applicant should hold the professional as well as personal skills and qualifications as stated below:
    • A completed PhD degree in bioinformatics, systems biology, computer science or in a similar area
    • General background knowledge of biological areas of genome structure and transcriptomes
    • Solid experience with transcriptome analysis
    • Experience with gene network and pathway analysis
    • Algorithmic insight broad and for RNA 2D structure and RNA-RNA interactions
    • Strong experience with script languages such as Perl or Python (or similar)
    • Strong experience with the Linux/Unix environment, command lines and shell scripting
    • Familiarity or experience in at least one of the following programming languages: C, C++ or Java
    • Good interpersonal skills
    • Excellent in English both in writing and speech

    PREFERENCES

    Candidates fulfilling one or more of the following qualifications will be prioritised:
    • Experience with transcriptomic data in bacteria
    • Strong experience in at least one of the following programming languages: C, C++ or Java
    It is recommended that the applicant address the qualification requirements one by one in the cover letter.

    TERMS & COMPENSATION

    Salary and other terms and conditions of appointment are set in accordance with the Agreement between the Ministry of Finance and AC (Danish Confederation of Professional Associations) or other relevant professional organisations. The position is covered by the "Memorandum on Job Structure for Academic Staff at the Universities" of June 28, 2013.

    The gross basic salary range for Postdoctoral Fellows is DKK 33,224 to DKK 34,980 per month (level 6 to 8). To the basic salary, a supplement could be negotiated, dependent on the candidate's experience and qualifications. An additional 17.1 % monthly contribution to pension will be paid by the employer. Non-Danish and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark for the last 10 years.

    The position is limited to a two-year period.

    LOCALE

    RTH is located on the Frederiksberg Campus; however, as part of the NextProd project research visits with project partners or collaborators will be a part of the Postdoc employment. Our research environment is highly international and stimulating. We frequently organise seminars, workshops, PhD summer schools with international speakers and have retreats with our international collaborators.

    ABOUT US

    Part of the International Alliance of Research Universities (IARU), and among Europe's top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.

    HOW TO APPLY

    Apply by clicking the "APPLY NOW" link below. Please note that only online applications will be accepted.

    Applications – in English – must include:
    • Cover letter detailing your motivation and background for applying for the specific Postdoc project
    • CV
    • Diploma and detailed transcripts of records
    • Other information for consideration, e.g. list of publications, peer reviewed and other
    • Personal Recommendations (if any)
    • A maximum of 3 relevant scientific works which the applicant wishes to be included in the assessment
    Questions:
    For further information about the scientific content of the position please contact Professor Jan Gorodkin, email gorodkin[at]sund.ku.dk, phone +45 2337 5667 [Ring op: +45 2337 5667] or for application procedure and formalities please contact HR, email sund-hr-ivh[at]sund.ku.dk.

    Deadline:
    The deadline for applications is 2 December 2018. Any applications received after this time or incomplete will not be considered.

    Receipts of the applications will be acknowledged, and the applicant will be kept continuously informed of the progress of the application.

    The further process:
    Shortlist: After the expiry of the deadline for applications, the authorised recruitment manager selects applicants for assessment on the advice of the Appointments Committee. All applicants are then immediately notified whether their application has been passed for assessment by an expert assessment committee. Selected applicants are notified of the composition of the committee and each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself. You can read about the recruitment process at employment.ku.dk.

    Assessment: The selected applications will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities and the University of Copenhagen's guidelines 2013. The Assessment Committee makes a non-prioritised assessment of the academic qualifications and experience with respect to the mentioned area of research, techniques, skills and other requirements listed in the advertisement.

    Please note that the applicant will be contacted if the assessment committee requires further documentation.

    APPLY NOW: candidate.hr-manager.net/Appl[...]=true

    POLICY

    The University of Copenhagen wishes to reflect the diversity of society and welcomes applications from all qualified candidates regardless of personal background.

    BACKGROUND

    Job Summary/Basic Function: The Oklahoma Medical Research Foundation (OMRF) is an independent, not-for-profit, biomedical research institute adjacent to the campus of the University of Oklahoma Health Sciences Center (OUHSC) located in Oklahoma City. Our Autoimmune Disease Institute houses Centers of Excellence and specialty research clinics for Rheumatic Diseases (focusing on Lupus, Rheumatoid Arthritis, UCTD, and Sjogren's) and for Multiple Sclerosis and related diseases. In addition to following over 4,000 patients with these conditions, teams of basic and clinical investigators conduct extensive clinical, translational and mechanistic research using samples obtained from these large clinical programs. Large clinical research databases, partnered with extensive clinical and experimental datasets, provide unique opportunities for data analyses and making clinically important observations.

    RESPONSIBILITIES

    This unique opportunity seeks a self-motivated, team player to provide critical research design, data management and analytic support to patient-oriented investigation. Ample opportunities exist for scientific writing and clinical impact. This position will apply strong knowledge of epidemiology, biostatistics, translational science, and/or clinical medicine to:

    1. Query and data mine electronic medical records, health information exchanges, and research databases to compile targeted population health information.
    2. Analyze data to identify risk factors, biomarkers, gene expression signatures and genetic polymorphisms/pathways which impact autoimmune disease.
    3. Perform literature searches, gather and synthesize data, and organize data into tables and scholarly reports.
    4. Assist with publication of research by preparing and authoring abstracts and manuscripts.
    5. Facilitate interactions between biostatisticians, bioinformaticians and epidemiologists with clinical and basic science faculty.

    REQUIREMENTS

    Minimum Qualifications: Bachelor's degree in Psychology, Business, Bioinformatics, Math, Statistics, Biostatistics or relevant field and 2 years relevant experience or a combination of relevant experience and education.

    Strong project management, organizational, analytic, and verbal and written communication skills required. Must have strong attention to detail and comply with confidentiality patient-protection regulations.

    Minimum Degree Required: Bachelors Degree

    Preferred Qualifications: Master's in Public Health or Master's of Science in Biostatistics, Epidemiology, Clinical Informatics, Clinical & Translational Science or related field.

    Ability to analyze data with R package, SAS or STATA. Clinical exposure and experience with data visualization programs, like SpotFire, Cytobank, etc., a plus.

    Physical Demands: Regularly moves about the work environment, talks, hears and listens. Occasionally lifts or moves up to 10 pounds. Requires the ability to see. The noise level and typical work conditions are consistent with an office environment.

    TERMS

    Status: Full-Time

    HOW TO APPLY

    Application Type Accepted:
    • General Application
    Required Applicant Documents:
    • Resume/Curriculum Vitae
    • Transcript 1
    Optional Applicant Documents:
    • Cover Letter
    • Transcript 2
    • Transcript 3
    Quicklink for Posting: apptrkr.com/1334039

    Posting Number: 0001204
    Classification: Ongoing
    Department: Arthritis & Clinical Immunology - James

    Submitter

    BACKGROUND

    This is a very interesting post for a Senior Scientific Manager to lead an established team delivering software to support the cellular and genomics operational facilities of the organisation.

    This post holder will be responsible for student, junior and senior software developers and will be a part of the scientific management team, reporting into the Production Software Manager.

    RESPONSIBILITIES

    Core Accountabilities Include:
    • Use a recognised software development life cycle (SDLC) process to manage the predictable delivery of software into production.
    • Gain and maintain a broad and where necessary detailed understanding of the operational process to model with the development team support process, interactions and data that adds value to the organisation.
    • Identify, champion and support process improvement of chosen SDLC in collaboration with development team and customers.
    • Mentor & coach developers (Senior, Junior & Industry placement students) identifying learning opportunities to sustainably increase the capability and capacity of the development team in line utilising available budgets.
    • Support and improve maintainability of software applications through understanding and influencing the selection and implementation of technologies, tooling and techniques in collaboration with development team.
    • Support line manager and senior managers in setting and influencing the technology strategy for core informatics.
    • Investing in personal professional development gaining and maintaining technical and managerial skills to support software development projects, people and process.
    • Transparently report progress and impediments towards the stated strategic aims of the organisation learning from failure and success.

    REQUIREMENTS

    Skills and Experience Required:
    • Experience with Agile development methods
    • Experience modelling complex domains
    • Experience with facilitating teams to identify process improvement and celebrate great team working
    • Experience of managing a team and coaching and developing staff
    • A technical background in software development
    • You will have experience with XP practices.
    • Ability and confidence to gain practical knowledge in new technologies
    • Ability to quickly and effectively forge relationships with senior internal and external stakeholders
    • Some experience with system thinking tools to engage with more complex situations

    HOW TO APPLY

    Please do not hesitate to contact Harvey Uppal at huppal[at]pararecruit.com or call (+44) 121 616 3407 to discuss this opportunity further.

    Keywords: Senior, Scientific, Software, Manager, Leader, Bioinformatics, Genomics, SDLC, Agile, Python, Technology, Cambridge.

    BACKGROUND

    Cal Poly's Computer Science and Software Engineering Department offers Bachelor's Degrees in Computer Science and Software Engineering, and Master's Degrees in Computer Science. Also, the Computer Science and the Electrical Engineering departments jointly offer a B.S. degree in Computer Engineering. U.S. News & World Report ranks the Computer Science Department among the top primarily undergraduate public programs in the nation. For further information about the department, visit csc.calpoly.edu.

    RESPONSIBILITIES

    ASSISTANT/ASSOCIATE PROFESSOR IN COMPUTER SCIENCE AND SOFTWARE ENGINEERING: The Computer Science and Software Engineering Department within the College of Engineering at Cal Poly State University, San Luis Obispo, CA invites applications for one full-time, academic year, tenure-track Computer Science and Software Engineering faculty position in the area of bioinformatics, at a rank and salary commensurate with the applicant's background and experience. The anticipated start date is September, 2019, or possibly January, 2020. Duties include teaching undergraduate and master's level courses, supporting and expanding curricular development in Computer Science and Software Engineering, curriculum development in support of the emerging cross-disciplinary program in bioinformatics, pursuing research in one's area of expertise, and providing service to the department, the university, and the community. Strategic priorities of the department for this position include bioinformatics, computational biology and related areas of study.

    An earned doctorate (Ph.D.) in Computer Science, Software Engineering, or a closely related field from an accredited institution or international equivalent is required for appointment.

    REQUIREMENTS

    An earned doctorate (Ph.D.) in Computer Science, Software Engineering, or a closely related field from an accredited institution or international equivalent is required for appointment. Candidates nearing completion of the doctorate (ABD) will be considered, but must provide proof that the doctorate was completed prior to the start of the appointment.

    Candidates must have a strong commitment to teaching excellence and laboratory-based instruction, dedication to continued professional development and scholarship, and a broad-based knowledge of computer science/software engineering, in addition to an established track record of research and/or teaching in the area of bioinformatics, computational biology or a related area of study. Demonstrated ability in written and oral use of the English language is required.

    The successful candidate must have the ability to work effectively with students, staff and faculty from diverse ethnic, cultural, and socioeconomic backgrounds. Cal Poly is committed to the teacher-scholar model. As teachers, faculty are expected to exhibit strong pedagogic skills and to remain proficient and current in their disciplines. As scholars, faculty should be engaged in scholarly work that is of very high quality as evidenced by external peer review. As colleagues, it is appropriate for faculty to perform service activities at all levels of the University.

    PREFERENCES

    Preference will be given to candidates with a demonstrated excellence in university level teaching and research (commensurate with time since degree), experience with laboratory-based instruction and industry experience. Past experience and a willingness to teach in multiple areas of the undergraduate curriculum in a collaborative setting is preferred. Candidates with industry experience are encouraged to apply.

    TERMS

    2 year appointment

    LOCALE

    San Luis Obispo, CA

    COMPENSATION

    Based on qualifications and experience

    ABOUT US

    Cal Poly emphasizes Learn by Doing, which involves extensive lab work and projects in support of theoretical knowledge. The CSSE department is collaborating with a number of other programs on campus to establish a unique Cross-Disciplinary Studies Minor in Bioinformatics. Successful candidate will have an opportunity to take a leadership role in both the curriculum development and administration of the program, as well as in the emerging strategic research collaborations between the CSSE department and the life sciences programs on campus.

    HOW TO APPLY

    For full details, qualifications and application instructions (online faculty application required), visit WWW.CALPOLYJOBS.ORG and apply to Requisition #104993.

    DEADLINE

    Open until filled. Review begins Dec. 1, 2018

    POLICY

    EEO. Cal Poly strongly values diversity and inclusion, especially in the classroom and among its areas of study. This Instructional Faculty search will occur at the same time as a university‐wide cluster of searches designed to increase curricular coverage of areas related to diversity and inclusion, as well as to promote inclusive teaching strategies across the university. If the successful Instructional Faculty AY candidate's research overlaps with the area of diversity and inclusion, there will be an opportunity to join and support these university efforts.
    Opportunity: Postdoctoral Fellowships @ University of Idaho -- Moscow, ID (US)
    Submitted by Ryan V; posted on Tuesday, November 13, 2018

    DESCRIPTION

    Two postdoctoral fellowships are available at the University of Idaho in the group of Dr. Benjamin Ridenhour. Both positions are focused on the analysis and modeling of microbiome data. One position is focused on developing and analyzing novel models for the evolution and ecology of microbial dynamics. The other position is focused on the bioinformatic analyses of gut microbiome data. A solid foundation in working with the analyses of complex systems is needed for either position, as well as a working knowledge of the R programming language. For the fellowship working with microbial dynamics, experience with eco-evolutionary models and a strong mathematical/quantitative skillset are desired. For the fellowship working on the gut microbiome data, experience performing bioinformatic analyses of microbiome data and a strong statistical background are desired.

    ABOUT US

    The Palouse region offers a vibrant research community that includes world-class researchers who focus on microbiomes. Dr. Ridenhour is part of the Department of Mathematics, but UI has numerous interdisciplinary programs such as Bioinformatics and Computational Biology (BCB), the Center for Modeling Complex Interactions (CMCI), and the Institute for Bioinformatics and Evolutionary Studies (IBEST). Additionally, Washington State University is located only 7 miles from UI (connected by a bike path) and has numerous similar programs. The Palouse is a stunning landscape that offers numerous opportunities for outdoor activities such as mountain biking, hiking, fishing, skiing, climbing, and whitewater all within 2-3 hours drive.

    HOW TO APPLY

    To apply for either position, visit the UI's HR website (apptrkr.com/1333817) and fill out the necessary forms; see position numbers uidaho.peopleadmin.com/postings/22986 (microbial dynamics) and uidaho.peopleadmin.com/postings/23138 (bioinformatics). A cover letter, a current CV, and a list of references are required to apply. Review of applications will begin 9 December; the positions will remain open until filled.

    For questions or more information regarding the positions and their requirements, or about the Moscow and the Palouse area, contact Ben Ridenhour (bridenhour[at]uidaho.edu).

    BACKGROUND

    About the role:
    We are currently looking for a Senior Computational Biologist within the Clinical and Experimental Pharmacology Group (CEP) and the newly established Manchester Centre for Cancer Biomarker Sciences (MCCBS). One aspect of this team's role will be to evaluate data from DNA and/or RNA derived from patient blood samples to derive robust classifiers. Pivotal goals of the Centre are to develop biomarker signatures to improve cancer detection, to aid prognosis and to predict patient response to therapy with an overall goal to facilitate the personalised medicine approach. The flagship project of the MCBBS is TARGET, a clinical protocol in which Phase I clinical trial patients provide a blood sample at baseline. We are asking whether analysis of their ctDNA can assist in selection of the best clinical trial available for each patient. Bioinformatics analysis of TARGET derived clinical samples will be the first priority for this post holder.

    RESPONSIBILITIES

    The aim of this post is to contribute to the success of translational research aimed at next generation sequencing (NGS) of nucleic acids obtained from patient blood samples. The overall goal of this project is to identify information that can be used to optimise cancer patient treatment selection.

    REQUIREMENTS

    About you:
    You should have a degree in computational biology, mathematics or related discipline (or equivalent) plus significant relevant experience analysing genomics data or a relevant postgraduate degree. Additionally you should have substantial experience writing complex code in at least one of the following: Perl, Python, R, Matlab, C, or C++.

    TERMS

    Duration of role: Fixed term until 31st March 2022

    COMPENSATION

    Salary in the range of £24,776 – £36,000 per annum (dependent upon experience)

    ABOUT US

    Why choose Cancer Research UK Manchester Institute?
    The Cancer Research UK Manchester Institute (www.cruk.manchester.ac.uk), an Institute of The University of Manchester (www.manchester.ac.uk), is a world-leading centre for excellence in cancer research. The Institute is core funded by Cancer Research UK (www.cancerresearchuk.org), the largest independent cancer research organisation in the world. We are currently situated at the internationally-renowned life sciences campus at Alderley Park in Cheshire England, 15 miles from Manchester, a vibrant and dynamic city surrounded by beautiful countryside.

    We are partnered with The Christie NHS Foundation Trust (adjacent to the CRUK MI Paterson Building) in South Manchester (www.christie.nhs.uk), one of the largest cancer treatment centres in Europe. These factors combine to provide an exceptional environment in which to pursue basic, translational and clinical research programmes.

    HOW TO APPLY

    To apply for this position please visit our website: www.cruk.manchester.ac.uk/Oppo[...]-Home

    For any informal enquiries about this position please contact Dr Ged Brady via email: ged.brady[at]cruk.manchester.ac.uk.

    Job Ref: MI/18/87

    DEADLINE

    Closing date: Sunday 9 December 2018.

    DESCRIPTION

    The "Genomics of Long Non-Coding RNAs in Disease" Laboratory (GOLD Lab) at the University of Bern has an opportunity for a Bioinformatics Postdoc.

    The Project: Understanding how long noncoding RNA (lncRNA) functions are encoded in their sequence is a great challenge in biology. Our goal is to discover, classify and characterise lncRNA functional elements by means of an integrative bioinformatic / experimental approach. You will lead the bioinformatic component to develop novel methods for identifying lncRNA elements and predicting their functions. In collaboration our experimental team, you will have ample opportunities for experimental validation of in silico-generated hypotheses.

    The Group: We are an international and interdisciplinary group of researchers with a passion for lncRNA research. We foster an open and collaborative working environment. Our work is funded by the Swiss National Center for Competence in Research (NCCR) "RNA & Disease" (nccr-rna-and-disease.ch), and we participate in the GENCODE project and International Cancer Genome Consortium (ICGC). We also have excellent biomedical links at the University Hospital of Bern. For more information about us: gold-lab.org / twitter.com/goldlab_bern

    The City: Bern, the capital of Switzerland, has a vibrant international community, numerous outdoors and cultural activities, and ranks among the best cities worldwide for quality of life (tinyurl.com/y9vrtb7d).

    The Person: We seek a dedicated and dynamic colleague to integrate into our diverse team. You should have strong background in bioinformatics or computer science, and specifically some/all of: Unix environment, R, Perl/Python, analysis of NGS data, webservers/databases. Experience in lncRNAs, CRISPR-Cas9 is a plus.

    Details: Ideal start date will be Q1 of 2019. Project is fully funded for 4 years. Salary is according to (generous) University of Bern scales.

    Recent Publications:
    Carlevaro-Fita et al. Biorxiv www.biorxiv.org/cont[...]89753
    Uszczynska-Ratajczak B et al. Nat Rev Genet. 2018 Sep;19(9):535-548. www.doi.org/10.1[...]017-y.
    Lagarde J et al. Nat Genet. 2017 Dec;49(12):1731-1740. www.doi.org/10.1038/ng.3988.

    HOW TO APPLY

    Please send a motivation letter, publications list, list of references, and CV to rory.johnson[at]dbmr.unibe.ch with subject title: "Job application Bioinformatics Postdoc". Informal enquiries are also welcome.

    BACKGROUND

    The Pennington Biomedical Research Center is seeking to fill a Research Associate position in Bioinformatics and Computational Biology. Pennington Biomedical, a campus of the Louisiana State University System located in Baton Rouge, Louisiana, is one of the largest academically based nutrition research centers in the world. The position is available in the COBRE Laboratory for Bioinformatics under the direction of Prof. Sujoy Ghosh. Dr. Ghosh's research applies computational systems biology approaches to understand the genetic and genomic architecture underlying metabolic disease. Additionally, the laboratory collaborates extensively with national and international investigators in cardiovascular and cancer-related disorders.

    RESPONSIBILITIES

    The Research Associate will have the opportunity to apply computational biology and bioinformatics methodologies on traditional transcriptomics, next generation sequencing approaches including bulk- as well as single-cell RNA-Seq, ChIP-Seq and ATAC-Seq, genome-wide association studies, and microbiome analyses that will add significant value to multiple signature research programs at PBRC.

    The position provides opportunities for the development and application of innovative, cutting-edge data analytic tools and approaches to enhance the research capabilities of multiple investigators in a highly collaborative framework. Independent thinking and excellent communication skills are essential.

    REQUIREMENTS

    We are seeking a motivated candidate with a high level of research dedication and skill, who can quickly integrate into the research team and make productive contributions to the exciting field of high-dimensional data analysis. A Master's degree in any of the following disciplines – Bioinformatics, Statistics, Biostatistics, or Computer Science – is required.

    The candidate must be familiar with handling and manipulation of large, multidimensional data sets. Skills in the use of the R statistical analysis tool as well as Python are critical, as is familiarity with a LINUX environment and multi-core computing. Expertise in publication-grade data visualization is required, and experience with additional applications (e.g. Perl, SAS, or Matlab), is highly desirable.

    COMPENSATION

    Salary and benefits will be commensurate with educational qualification and working experience.

    HOW TO APPLY

    Please visit lsu.wd1.myworkdayjobs.com/en-U[...]29094

    BACKGROUND

    A postdoctoral position and PhD positions are available in the lab of Mira Han at University of Nevada, Las Vegas and Nevada Institute of Personalized Medicine.

    Research will focus on integrating heterogeneous omics data to predict the tissue origin for metastatic cancer tissues. We are especially interested in integrating RNA and methylation data of non-coding elements and repeat elements.

    Other projects involve investigating the potential regulatory role of repeat elements, through analysis of existing ChIP-seq, eCLIP, RNA-seq and genetic datasets.

    Nevada Institute of Personalized Medicine was just awarded a $11.4M, 5 year Center of Biomedical Research Excellence P20 Grant from NIH in personalized Medicine.

    The position will involve collaboration with other computational biologists and molecular biologists in the Nevada Institute of Personalized Medicine and School of Life Sciences.

    It will also involve assisting in the supervision of graduate and undergraduate students and developing new areas of research.

    Visit the website to find out more at www.unlv.edu/NIPM and www.unlv.edu/lifesciences

    RESPONSIBILITIES

    • The main responsibility will be to apply machine learning and statistical methods to link multiple modes of omics data and classify the metastatic cancer samples into correct tissue types.
    • The postdoctoral researcher will be able to explore other projects independently in addition to the main project.

    REQUIREMENTS

    Postdoc Requirements:
    • PhD degree in Bioinformatics, Computer Science, Biological Sciences, Mathematics, Biostatistics or related fields
    • Proven skills in programming (Python, R, C/C++) and experience with Linux/Unix environments
    • Practical experience of high-throughput data analysis, data management, data mining/ integration
    • Practical experience of next-generation sequencing data analysis and skills in bioinformatic tools and databases
    • Self-motivation with excellent communication skills and an ability to work well in a team environment
    Postdoc Preferences:
    • Experience in machine learning and heterogeneous data integration
    • Experience with molecular biology of next generation sequencing
    Ph D Requirements:
    • Experience with programming (Python, R, C/C++) and Linux/Unix environments
    • Self-motivation with excellent communication skills and an ability to work well in a team environment

    TERMS

    Appointment is for two years with a possibility of extension of one more year.

    LOCALE

    The UNLV campus offers a stimulating and rewarding environment. Here, you will find a friendly community dedicated to learning and research. Las Vegas has its safe communities, affordable home prices, high quality of life, little traffic.

    COMPENSATION

    Postdoc stipend level is commensurate with the NIH level.

    PhD stipend level will be $30,000 or more depending on your experience.

    HOW TO APPLY

    Please send a CV/resume and a brief statement of research interests to Dr. Mira Han (mira.han[at]unlv.edu).

    BACKGROUND

    The Knowledge Systems Group at Dana-Farber Cancer Institute (DFCI) is currently seeking an Informatics Scientist, specifically devoted to the development and application of clinical data standards for large-scale data sharing projects. Your work will critically enable the sharing of harmonized data sets across multiple Cancer Moonshot data sharing projects sponsored by the National Cancer Institute (NCI).

    Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

    RESPONSIBILITIES

    • Assess, adopt, and extend existing data standards for representing and exchanging clinical data elements for cancer studies and cancer clinical trials.
    • Integrate and extend clinical data standards into multiple Cancer Moonshot data sharing projects sponsored by the National Cancer Institute (NCI), including the Cancer Immunologic Data Commons (CIDC), and the Human Tumor Atlas Network (HTAN).
    • Lead an interdisciplinary working group to develop and extend clinical data standards across multiple NCI Moonshot data sharing projects.
    • Develop new tools and methods for mapping existing and legacy clinical data to new clinical data standards, and oversee the entire clinical data mapping process for the Cancer Immunologic Data Commons (CIDC), and the Human Tumor Atlas Network (HTAN).

    REQUIREMENTS

    • Bachelor or Masters degree in related health field, e.g. public health, epidemiology, informatics or bioinformatics – Masters degree preferred.
    • 3+ years working in the clinical data standards space, and the clinical trials research space
    • Strong knowledge of data housed in electronic medical records, cancer registries, and other healthcare systems, as well as medical terminologies, controlled vocabularies, ontologies, HIPAA regulations, and industry standards is required. Knowledge of Oncology data and related areas strongly preferred.
    • Prior experience or expertise in any existing clinical data standards, including ICD-03, SNOMED, LOINC, RxNorm, Genome Data Commons (GDC), or Clinical Data Interchange Standards Consortium (CDISC)
    • Prior experience in mapping existing and legacy clinical data to existing clinical data standards
    • Prior experience working with clinical data mapping software and/or computational researchers involving clinical data
    • Strong organizational, communication and interpersonal skills
    • Able to work independently to resolve time-sensitive issues and balance multiple projects
    • Able to communicate with collaborators at all levels
    • Strong interest in contributing to translational cancer research

    HOW TO APPLY

    Apply Here: www.Click2apply.net/3j83k3qkzdhqgbk6

    POLICY

    Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other groups as protected by law.

    PI105198973

    Submitter

    BACKGROUND

    Postdoctoral positions are available immediately in the Oncinfo Lab at The University of Texas Health Science Center in San Antonio (UT Health San Antonio). Also, interested predoctoral and MS applicants should apply to the appropriate graduate program (i.e, IBMS for PhD students, CSA MS for MS students) using the links provided under application procedures.

    Dr. Habil Zare is the PI of the Oncinfo Lab (see oncinfo.org for more details). He has joint appointments at: 1) The Department of Cell Systems and Anatomy, consistently ranks high for NIH funding, and 2) The Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases. The UT Health San Antonio is a Tier One research institution, and has ranked 1st in NIH funding for studies in aging, which provides a good foundation for research in neuroscience and cancer. San Antonio is a dynamic and multicultural city with an outstanding educational environment.

    RESPONSIBILITIES

    Successful candidates will contribute to development and application of cutting-edge computational methods and machine learning techniques to analyze next-generation sequencing data from large cohorts. They will contribute to highly collaborative studies in the areas of cancer research and neuroscience. Various data are generated in these studies including RNA-Seq, WGS, WES, CHIP-Seq, etc. The primary focus of research in the Oncinfo Lab is on quick analyses of data, and efficiently incorporating them with publicly available datasets including TCGA, GEO, GTEx, etc, to infer useful biological information. While methodological advancements is secondary to this goal, we have developed novel tools and algorithms to improve data analysis using Bayesian networks and integrative correlation networks. The results are expected to be published in highly ranked journals.

    REQUIREMENTS

    Applicants should have a strong background in molecular biology and computer programming. However, exceptionally strong candidates with either background who are highly motivated for learning new concepts in biology and improving their programming skills will be considered. Ability for critical thinking and independent learning, and excellent written and oral communication skills are essential.

    PREFERENCES

    Above average knowledge in machine learning, mathematics, computational biology, bioinformatics, statistics, R, prior experience in a related field, or experience in multidisciplinary research that has led to high-impact publications can increase chance for acceptance.

    LOCALE

    San Antonio, TX, USA

    COMPENSATION

    Salary is competitive, and in the range of $50K-$60K for the postdoctoral positions. Cost of living is relatively low in San Antonio and there is no state income tax.

    HOW TO APPLY

    All interested candidates are encouraged to email a current CV and a cover letter to Dr. Habil Zare at zare[at]uthscsa.edu. Potential graduate students should also apply to the corresponding programs at: gsbs.uthscsa.edu/pros[...]ation.

    DEADLINE

    The postdoctoral positions are open until filled.

    PhD: See The Integrated Multidisciplinary Graduate Program (IMGP) gsbs.uthscsa.edu/graduate_programs; apply before 15 January 2019.

    MS: See Master of Science in Biotechnology uthscsa.edu/csa/grad-ms.asp; apply before 15 February 2019.

    POLICY

    All postdoctoral appointments are designated as security sensitive positions. UT Health San Antonio is an Equal Employment Opportunity/Affirmative Act on Employer including protected veterans and persons with disabilities.

    BACKGROUND

    The Center for Infection and Immunity (cii.columbia.edu) in the Mailman School of Public Health at Columbia University – one of the world's most advanced academic centers for research in infectious disease surveillance, diagnosis and discovery in acute and chronic illnesses – has an opening for an experienced Sr. Programmer Analyst on the bioinformatics team to develop pipelines to analyze large-scale protein microarrays for immune response studies and investigate next generation sequencing (NGS) datasets for pathogen discovery. The successful applicant will join a dynamic, state of the art research laboratory at Columbia University and a global network of researchers who work on projects related to infectious disease surveillance and discovery in humans and wildlife, host response to infections, microbiome research and large-scale studies on chronic fatigue syndrome/myalgic encephalomyelitis and neurodevelopment disorders.

    RESPONSIBILITIES

    Essential Functions:
    • Bioinformatics support for protein array analysis – 50%
    • Bioinformatics support for projects related to microbial detection and discovery – 25%
    • Database management – 10%
    • Server hardware management – 5%
    • Contribute to publications and research grants – 5%
    • Perform other related duties as assigned – 5%

    REQUIREMENTS

    The candidate is expected to demonstrate the following skills and experience:
    • Experience in bioinformatics, statistics, microarray and/or NGS data analysis
    • Proficiency with writing high-quality code for pipelines to analyze very large datasets
    • Advanced working knowledge of NGS experimental design, data quality control, mapping and alignment software, normalization and clustering methods
    • Basic knowledge of genetics and molecular biology with practical knowledge of genomic databases from major bioinformatics resources such as NCBI and EMBL
    • Proficiency in Unix environments with high performance clusters
    • Familiarity with multi-threading tools, resource management and optimization for parallel processing of very large datasets
    • Advanced working knowledge of scripting languages Python, R, Shell and/or Perl (proficiency is desirable) in an academic or industrial environment
    Minimum Qualifications:
    Requires a Bachelor's degree in bioinformatics or computer science and at least four years of experience in bioinformatics.

    Preferred Qualifications:
    Master's degree with at least two years of related experience. Three years of experience in bioinformatics, statistics, microarray and/or NGS data analysis. Two plus years of experience with scripting languages Python, R, Shell and/or Perl. An applied mathematics/statistics/biostatistics background. Knowledge of statistical and machine learning techniques is a plus.

    HOW TO APPLY

    Apply online at the Columbia University Jobs Website: jobs.columbia.edu/appl[...]71540

    POLICY

    Columbia University is an Equal Opportunity/Affirmative Action employer.

    DESCRIPTION

    A postdoctoral position is available in the laboratory of Khuloud Jaqaman, Ph.D., in the Department of Biophysics and the Lyda Hill Department of Bioinformatics at UT Southwestern Medical Center to develop machine learning and related approaches to investigate how the actin cortex regulates cell surface receptor dynamics and clustering, and consequently signaling.

    Our lab has several exciting projects related to the spatiotemporal organization of signaling proteins in the plasma membrane. Please visit our lab website for more details at www.utsouthwestern.edu/labs/jaqaman/.

    Information on the UT Southwestern postdoctoral training program and benefits can be also found at www.utsouthwestern.edu/postdocs.

    REQUIREMENTS

    Candidates must hold a Ph.D. in statistics, bioinformatics, computer/computational science, biomedical engineering or a related field, with experience in computational data analysis and machine learning. Publications in peer-reviewed journals are recommended.

    LOCALE

    Dallas, TX, USA

    HOW TO APPLY

    Interested individuals should send a CV, a research statement describing past accomplishments and current interests, and a list of three references to khuloud.jaqaman[at]utsouthwestern.edu.

    POLICY

    UT Southwestern Medical Center is an Affirmative Action/Equal Opportunity Employer. Women, minorities, veterans and individuals with disabilities are encouraged to apply.

    BACKGROUND

    The Department of Biological Sciences and the Center for Computation and Technology at Louisiana State University jointly invite applications for a tenure-track Assistant Professor in Interdisciplinary Data Science and Biology. The ideal candidate is a biologist conducting hypothesis-driven research with data science approaches. Although the position is open to all areas of biology, preference will be given to those candidates who actively develop cutting-edge data science techniques including, but not limited to, informatics, data mining, machine learning, artificial intelligence, statistics, and large-scale data visualization. This hire is part of a larger initiative to establish a university-wide program in Interdisciplinary Data Science.

    RESPONSIBILITIES

    50% Develop and maintain an independent and extramurally funded research program at the intersection of data science and biology.
    50% Teach undergraduate and/or graduate level courses in a biological sciences discipline, and direct/supervise graduate students. Participate in service activities pertaining to the mission of the Department and the Center, and the advancement of the profession.

    REQUIREMENTS

    PhD in biology, data science, computational biology, bioinformatics, computer science, or related field; and a successful track record of independent research

    PREFERENCES

    Postdoctoral Experience or its equivalent preferred.

    LOCALE

    Department of Biological Sciences
    Louisiana State University
    Baton Rouge, LA

    COMPENSATION

    Benefits – LSU offers outstanding benefits to eligible employees and their dependents including health, life, dental, and vision insurance; flexible spending accounts; retirement options; annual and sick leave; 14 paid holidays; wellness benefits; tuition exemption; training and development opportunities; employee discounts and more!

    HOW TO APPLY

    Quick link at ad URL: lsu.wd1.myworkdayjobs.com/LSU/[...]29285

    HCM Contact Information:
    Questions or concerns can be directed to the LSU Human Resources Management Office at 225-578-8200 or emailed HR[at]lsu.edu.

    POLICY

    LSU is committed to diversity and is an equal opportunity/equal access employer.

    An offer of employment is contingent on a satisfactory pre-employment background check.

    BACKGROUND

    A staff position as scientific programming and software engineering is available in the Statistical Genomics and Systems Genetics group at our laboratory in the Genome Biology Unit at EMBL Heidelberg in Germany.

    Our research group is relocating from Cambridge to Heidelberg, where we bridge the excellence in molecular biology and biotechnology at EMBL Heidelberg with disease models and access to large biomedical datasets at the German Cancer Research Center Heidelberg.

    RESPONSIBILITIES

    The programmer will lead the development of Kipoi (kipoi.org), a software repository and API that seeks to unify recent advances in machine learning and deep neural networks for regulatory genomics. Kipoi builds on 3-way collaboration with international partners (Gagneur lab, LMU Munich, Kundaje lab, Stanford), and is increasingly used and extended by the research community. The position is funded via the recently awarded BMBF project MechML, which we are coordinating. The core aims of the post is to maintain and extend the Kipoi framework and its API, to implement new models within Kipoi and to support users of the system. We are also seeking to expand Kipoi to new fields and domains, including imaging and single-cell genomics. The latter aims are closely connected to the Human Cell Atlas, to which our group contributes as a node in the analysis working group. You will be located in the Stegle group and collaborate with partners in the MechML projects, collaborators at EMBL, DKFZ and elsewhere. We seek to build on previous developments and expertise in the group, including in deep learning methods (see below). The position will be jointly located at EMBL Heidelberg and DKFZ.

    Recent relevant publications:
    • Argelaguet, R., et al. (2018). Multi‐Omics Factor Analysis – a framework for unsupervised integration of multi‐omics data sets. Molecular Systems biology, 14, e8124.
    • Buettner, F., et al. (2017). f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq. Genome biology 18.1 (217): 212.
    • Angermueller, Christof, et al. (2017). DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning. Genome biology 1 (2017): 67.
    • Angermueller, Christof ,et al. (2016). Deep learning for computational biology. Molecular Systems Biology, 12, 878.
    • Buettner, F., et al. (2015). Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nature biotechnology, 33(2), 155.

    REQUIREMENTS

    • The successful applicant will hold a doctoral degree or equivalent qualification in computer science, statistics, mathematics, physics, and/or engineering with demonstrated experience in scientific programming, ideally combined with computational and statistical methods development.
    • Previous experience the management of substantial software projects is expected. Expertise in deep learning, the development of methods for genomics and genetics is beneficial, as is communicating results in scientific conferences and papers.
    • We especially seek candidates with prior experience in the development of software systems that utilize machine learning methods, including methods based on deep learning.
    • Proficiency with a high-level programming language (e.g., C++, Java) and/or appropriate scripting languages, and statistical data analysis tools such as R, MATLAB or Python is required.
    • The ideal applicant should have demonstrated the ability to work independently and creatively. (S)he should have excellent communications skills and be able to articulate clearly the scientific and technical needs, set clear goals and work within an interdisciplinary setting, communicating with other partners within the MechML project and within the Human Cell Atlas project.
    • A good foundation in, and previous usage of methods in any of the following fields is advantageous: statistics, machine learning, genetics, optimization and mathematical modelling. A background in molecular biology, or previous experience tackling biological questions is not necessary.

    COMPENSATION

    EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, as well as financial support for relocation and installation, including your family and the availability of an excellent child care facility on campus. EMBL has a large thriving community of bioinformaticians, working in close collaboration with experimental scientists and with strong links to other local scientists and institutions.

    ABOUT US

    We are Europe's flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1600 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.

    Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research.

    HOW TO APPLY

    Please apply online: www.embl.de/jobs[...]01377

    DEADLINE

    4 November 2018

    POLICY

    Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.
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