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DESCRIPTION
Interested in bioinformatics, eDNA metabarcoding, and want to work in Hawaii?
Join the Cooperative Institute for Marine and Atmospheric Research (CIMAR) at NOAA's Pacific Islands Fisheries Science Center (PIFSC) and the National Marine Fisheries Service (NMFS) 'Omics Network as a Bioinformatics Assistant Researcher. Contribute to improving the analytical workflows needed to operationalize environmental DNA (eDNA) metabarcoding surveys to enhance biodiversity exploration and monitoring across marine ecosystems from coral reefs to the deep-sea. Together with other new hires at NOAA Science Centers across the nation, be a part of the newly established NMFS 'Omics Network designed to collaboratively develop powerful, reproducible, and streamlined end-to-end operational workflows that automate the analysis of eDNA metabarcoding data.
About Us: PIFSC provides science to support the conservation and management of fisheries and living marine resources across the Pacific Ocean. Our group in the Ecosystem Sciences Division has already generated two big 6-assay ecosystem-scale eDNA datasets from both pelagic and coral reef ecosystems in the Hawaiian Islands, each of which offer exciting opportunities to explore new ecological patterns and generate novel biodiversity products.
The Opportunity: We are seeking a Bioinformatics Assistant Researcher (Postdoc/early Career Researcher) to co-lead the improvement of analytical workflows for eDNA metabarcoding in our marine ecosystem surveys. This is a 3-year, full-time position supported by the Inflation Reduction Act, located at NOAA's Inouye Regional Center in Honolulu, Hawaii. Annual Salary range $67,200-$75,600, commensurate with experience. You'll work closely with a collaborative team of researchers to improve data analysis techniques, refine existing resources and/or develop novel tools to build reproducible, flexible, and automated workflows for multi-marker, multi-trophic level eDNA metabarcoding data streams using rich existing datasets.
Opportunities include: Working with two robust datasets, which couple eDNA with classical field survey techniques to deepen our understanding of ecosystem structure and generate novel products in both Pacific coral reef and pelagic ecosystems. Leading and contributing to impactful scientific papers advancing the integration of eDNA with existing surveys. Collaborating with a diverse and inclusive team of researchers at PIFSC, and the broader NMFS 'Omics Network.
Qualifications: We are looking for a highly motivated candidate with a strong background in Bioinformatics and a PhD in Bioinformatics, Molecular Ecology, Data Science, Biology or related field. You should ideally be knowledgeable of current metabarcoding pipelines, have strong programming skills in one or more languages, and be proficient in R. Ideally you will have a background in genomics, community ecology, biodiversity analyses, and data visualization. Knowledge of marine ecology is preferred, but not required. Skillsets and expertise in other systems could be easily applied.
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BACKGROUND
To strengthen our team in the division "Molecular and Applied Entomology" in Berlin-Steglitz, starting 01.05.2024, we are looking for a
PhD student (m/f/d) in the field of biology, bioinformatics, biochemistry or comparable
Salary group 13 TVöD
Temporary contract for 36 months
The working time is 65%
The Bundesanstalt für Materialforschung und -prüfung (BAM) is a materials research organization in Germany. Our mission is to ensure safety in technology and chemistry. We perform research and testing in materials science, materials engineering and chemistry to improve the safety of products and processes. At BAM we do research that matters. Our work covers a broad array of topics in the focus areas of energy, infrastructure, environment, materials, and analytical sciences.
We are looking for talented people to join us.
RESPONSIBILITIES
Your responsibilities include:
Working on the DFG-funded project "The evolution of symbiont, pathogen and immune system interactions in Blattodea", which has the overarching goal of exploring how symbiont transitions have shaped pathogen defenses and immune systems in Blattodea. The project will involve:
- Identification and testing of immune genes involved in the regulation of symbionts and exploration of how they have evolved
- Tissue-specific transcriptomics in conjunction with microbiota and symbiont manipulation experiments
- Insect field sampling
- Use of available high-quality genomes to characterize immune genes and to better understand evolutionary changes between hosts and their symbionts
- Collaboration with project partners to quantitatively analyze genome, microbiota and pathogen data
- Active contribution to the DFG research group "Insect Infect (FOR 5026)"
- Writing scientific articles for publication in peer-reviewed journals
- Writing a doctoral thesis
- Presentation of project results at international scientific conferences
REQUIREMENTS
Your qualifications:
- Successfully completed scientific university degree (master's degree or equivalent) in the field of biology, bioinformatics, biochemistry or comparable
- Practical experience with insects and microbes
- Very good knowledge and experience in molecular biology
- In-depth knowledge of evolutionary biology and genetics
- Experience in the quantitative and statistical analysis of data with Python, R, or similar
- Knowledge of computer-based analysis of large data sets, especially nucleotide sequences
- Willingness to collaborate across disciplines
- Excellent written and spoken English skills
- Good communication and information processing, goal-oriented and structured way of working, ability to work in a team and willingness to cooperate
COMPENSATION
We offer:
- Interdisciplinary research at the interface of politics, economics and society
- Work in national and international networks with universities, research institutes and industrial companies
- Outstanding facilities and infrastructure
- Flexible working hours and mobile working
HOW TO APPLY
Your application:
We welcome applications via the online application form (https://recruitingapp-5507.de.umantis.com/Vacancies/1837/Application/New/2) by 20.03.2024. Alternatively, you can also send your application by post, quoting the reference number 39/24-4.6 to:
Bundesanstalt für Materialforschung und -prüfung
Referat Z.3 - Personal
Unter den Eichen 87
12205 Berlin
GERMANY
http://www.bam.de
Dr. McMahon will be glad to answer any specific questions you may have. Please get in touch via the telephone number +49 30 8104‑3837 and/or by email to dino-peter.mcmahon[at]bam.de.
POLICY
BAM promotes professional equality between women and men. We therefore particularly welcome applications from women. At the same time, we strive to reflect social diversity. Every application is therefore welcome, regardless of gender, cultural or social background, religion, ideology or sexual identity.
In addition, BAM has set itself the goal of promoting the professional participation of people with severe disabilities. The fulfillment of the job requirements is considered on an individual basis. Severely disabled persons or persons of equal status will be given preferential consideration if they are equally qualified.
The advertised position requires a high level of physical aptitude.
BAM actively supports the compatibility of work and family and has been certified as a family- and life-phase-conscious employer by the "audit berufundfamilie" since 2015.
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BACKGROUND
The Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) is seeking outstanding faculties in clinical data science research.
The Bioinformatics Institute (BII) is a computational biology research and postgraduate training institute as well as a national resource centre in bioinformatics within the Biomedical Research Council (BMRC) of A*STAR. Our scientists aim to understand the biomolecular mechanisms that underlie biomedical phenomena by developing sophisticated computational methods to support discovery from a secure and sustainable data hub to cross-disciplinary AI/ML analysis and data integration. We analyse a wide spectrum of biological and clinical data, including omics data (biomolecular sequences, expression profiles, epigenetics data), 3D structures of macromolecules, and biological tissue and macroscopic images from local and international academic, hospital and industry collaborators, public resources and also from in-house efforts. The institute has a vibrant and diverse research portfolio that includes infectious diseases, computational toxicology, precision medicine, oncology and drug discovery.
Watch the videos of BII Scientific Conference 2022 to know more about the research by different groups in BII:
https://www.youtube.com/playlist?list=PLcenRySmzqv76JVbdzg3z5kndDHN3FzBk
RESPONSIBILITIES
1. Heading a laboratory specializing in either one of the following:
a. Quantum Computing for biomedical applications
b. Clinical data hub and clinical data analysis
c. AI and generative models in healthcare applications (e.g. synthetic data)
d. AI in drug discovery
2. Collaborate closely with clinicians and with faculties within the Bioinformatics Institute and within the local ecosystem.
3. Collaborate with industrial partners to translate technologies into the clinics.
4. Lead or participate in research grant proposals (~SGD5million to SGD15million quantum).
REQUIREMENTS
- Outstanding research outcomes with strong publication records
- Excellent communication (oral and written) and public speaking skills
- Strong records of strategic thinking ability
COMPENSATION
The salary will commensurate with the experience and expertise.
HOW TO APPLY
Interested applicants please send your application package to Faculty Search committee:
- Maple Ye Maple_Ye[at]bii.a-star.edu.sg
- Sebastian Maurer-Stroh sebastianms[at]bii.a-star.edu.sg
- Lee Hwee Kuan leehk[at]bii.a-star.edu.sg
- Neerja Karnani Neerja_Karnani[at]bii.a-star.edu.sg
- Chandra Verma chandra[at]bii.a-star.edu.sg
Or apply here: https://careers.a-star.edu.sg/jobdetails.aspx?ID=Gtn0gsck%2fAUXA1g380NlGw%3d%3d
Application packages should consist of:
1. Curriculum Vitae which should include a list of publications
2. Research proposal
3. Names and emails of referees
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BACKGROUND
Dr. Zizhang Sheng's lab at Columbia University Irving Medical Center, Department of Medicine, Division of Infectious Diseases, the Aaron Diamond AIDS Research Center (ADARC), applies bioinformatics and biochemical approaches to elucidate the mechanisms of humoral immune response to infection (HIV, SARS-CoV-2, influenza, malaria, etc.) and to understand the role and origin of autoreactive B cells in autoimmunity (systemic lupus erythematosus, IgA nephropathy, etc.).
Sheng Lab details can be found here: https://www.infectiousdiseases.cuimc.columbia.edu/profile/zizhang-sheng-phd
The Sheng Lab pursues scientific research in cutting-edge fields and has published over 80 papers in Cell, Nature, Nature Communications, Cell Reports, etc.
Position Summary: We are seeking a highly motivated and talented individual to join our team as a Bioinformatics Associate Research Scientist. This position offers an exciting opportunity to contribute to cutting-edge research in the field. The position will involve analyzing next-generation sequencing data of single cell transcriptome and antibody repertoire to study affinity maturation mechanisms of pathogen or auto-antigen specific antibodies and disease pathogenesis. In addition to NGS analysis skills, the incumbent with experience on structural bioinformatics, deep-learning, or biochemical assays including protein expression and production, ELISA, SPR are preferred. The incumbent will work closely with a multidisciplinary team of both computational and experimental researchers and gain valuable experience in advanced data analysis techniques, algorithm development, and the interpretation of NGS data.
RESPONSIBILITIES
- Conduct bioinformatics analyses to interpret high-throughput sequencing data, including transcriptomics and antibody repertoire.
- Using structural bioinformatics approaches to study the mechanisms of antibody-antigen interaction, antibody design, and viral escape.
- Collaborate with experimental biologists to design and execute bioinformatics experiments that address key research questions.
- Participate in scientific discussions, present research findings at meetings and/or conferences, and contribute to scientific publications.
- Mentor and assist junior researchers in bioinformatics techniques and data analysis.
REQUIREMENTS
Minimum qualifications:
- Ph.D. in Bioinformatics, Computational Biology, Genomics, or a related field.
- Strong programming skills in languages such as Python, R, or Perl.
- Experience with next-generation sequencing data analysis (e.g., RNA-Seq, antibody repertoire).
- Proficiency in using bioinformatics software and tools (e.g., CellRanger, Seurat, SAMtools, PyMOL, alchemical free energy perturbation, molecular dynamics simulation, deep-learning etc.).
- Knowledge of statistical analysis methods.
- Excellent problem-solving skills and the ability to work both independently and collaboratively.
- Effective communication skills, including the ability to present research findings to diverse audiences.
- A strong publication record and a demonstrated passion for bioinformatics research.
COMPENSATION
$77,000 - $80,000 per year
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POSITION SUMMARY
SFARI Cohorts and Data Collections:
Since its beginning, SFARI (Simons Foundation Autism Research Initiative) has partnered with families and clinical centers across the country to build large and diverse cohorts of well-characterized individuals with autism or with specific genetic alterations associated with neurodevelopmental risk. These include the Simons Simplex Collection (SSC), Simons Searchlight, Autism Inpatient Collection, and SPARK. The principles of community-based participatory research have been key to all cohort activities. The Simons Foundation Informatics group manages the collection and distribution of large-scale aggregate and deidentified clinical and genomic data from these cohorts, which are made available to autism researchers through SFARI Base, a clearinghouse for autism and autism-related research data and biospecimens supported by SFARI.
Bioinformatics Data Manager
The Bioinformatics group at the Simons Foundation is seeking a dedicated full-time bioinformatics data manager. The ideal candidate has outstanding attention to detail, with experience in data science or bioinformatics, and will be at the forefront of the Foundation's open data initiatives.
This critical position is responsible for overseeing an extensive and ever-expanding collection of genomics (over 170K whole-exomes and genomes) and biomedical data across Simons Foundation autism cohorts and neuroscience collaborations. The data manager will be instrumental in enhancing data accessibility and utility for both internal staff and external investigators, aligning with the principles of open data and science. The data manager will be part of the bioinformatics team and will collaborate with informatics' engineering team, the SFARI science team, and external investigators.
Key responsibilities include meticulous handling and processing of incoming data, such as genomic sequencing or biosensor data, as well as performing detailed quality control checks and downstream bioinformatics analyses. Additionally, the candidate will be responsible for preparing regular data releases and facilitating coordination among different teams, contributing to the Foundation's dynamic and collaborative environment.
ESSENTIAL FUNCTIONS/RESPONSIBILITIES
Data releases:
- Maintain the Bioinformatics quality control pipeline, used to verify consistency with phenotypic data and ensure the integrity of released genomic data
- Execute existing variant calling pipelines, which will be included in data releases
- Package whole-exome and whole-genome data for regular curated and rapid releases
- Manage ad hoc genetic data releases for various SFARI cohorts and datasets
Data organization:
- Coordinate data receipt from external investigators, vendors, and research groups
- Perform incoming data cleaning, including deidentifying sample identifiers, organizing data files, and ensuring consistent metadata
- Manage the organization of raw, cleaned, and released data on our local cluster environment
- Harmonize our large collection of heterogeneous datasets hosted on SFARI Base
Data sharing and support:
- Support data sharing for SFARI investigators and collaborations, such as the Autism Rat Consortium (ARC), and Simons Sex Differences Collaboration (SSDC)
- Respond promptly to dataset questions from external investigators
- Support data access for cloud platforms
MINIMUM QUALIFICATIONS
Education:
- B.S. or M.S. in data science, bioinformatics, or a related discipline.
Required experience:
- At least 4+ years' relevant work experience
- Extensive experience with Linux/bash
- Experience working in an HPC environment
- Experience with Python
- Experience with version control using git / GitHub
- Basic skills in data analysis and statistics
- Strong organizational skills and outstanding attention to detail
- Effective oral and written communicator
- Ability to thrive in collaborative environments
Desired Experience:
- Enthusiasm for open science and collaboration
- Experience with genomics data processing and analysis
- Experience writing technical documentation
- Experience with cloud storage solutions (AWS, Google Cloud, Terra)
- Working knowledge of SQL
- Familiarity with data privacy and security regulations in the healthcare or research domain
COMPENSATION AND BENEFITS
The full-time annual compensation range for this position is $130,000 – $145,000, depending on experience.
In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package.
HOW TO APPLY
To apply, visit: https://apptrkr.com/5055069
Required application materials:
- Resume
- Cover letter stating your interest in the position.
- Links to code repositories or GitHub, if available
POLICY
The Simons Foundation's diversity commitment:
Many of the greatest ideas and discoveries come from a diverse mix of minds, backgrounds and experiences, and we are committed to cultivating an inclusive work environment. The Simons Foundation actively seeks a diverse applicant pool and encourages candidates of all backgrounds to apply. We provide equal opportunities to all employees and applicants for employment without regard to race, religion, color, age, sex, national origin, sexual orientation, gender identity, genetic disposition, neurodiversity, disability, veteran status, or any other protected category under federal, state and local law.
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DESCRIPTION
A three-year postdoctoral position in immunology and bioinformatics is available at the Neuroimmunology Research Group in the Laboratory of Immunobiology. The position is funded by the Norwegian Research Council and hosted by the Department for Molecular Medicine, University of Oslo (UiO). This represents a unique opportunity to contribute to cutting-edge research in a field of scientific and health-related significance.
More about the position:
We seek a motivated individual to join us as a Postdoctoral Research Fellow, embarking on an ambitious project aimed at enhancing our understanding of human immunoglobulin genes.The postdocs' primary focus will be on developing computational pipelines to assemble and annotate these genes , tasks that present unique and challenging opportunities due to the large structural variations within these loci. Despite their critical importance, the extensive variability of immunoglobulin genes has not been fully recognized within the immunological community, yet it has profound implications for antibody structure and function, with direct relevance for autoimmunity, infectious diseases, and vaccine development.
Additionally, the postdoc will engage in other projects, including the analysis workflows of high-dimensional single-cell sequencing and multi-omics data. We foster an environment that values creative freedom, encouraging our postdocs to pursue innovative ideas and approaches.
The ideal candidate possesses a solid foundation in bioinformatics, including proficiency in programming languages such as Python and R, and comfort working within a Linux environment. A background in genetics and experience with Oxford Nanopore sequencing technologies will be considered an advantage. We also welcome applicants with a strong biology background and foundational programming skills who are eager to enhance their computational skills.
The main purpose of the fellowship is to qualify researchers for work in higher academic positions within their disciplines.
Qualification requirements and personal skills:
- Candidates must hold a PhD equivalent to a Norwegian doctoral degree at the time of employment.
- Background in bioinformatics or immunology
- Preferably experience with genetics
- Demonstrated strong motivation
- Exceptional problem-solving abilities
- Proficient in both written and oral English
- Effective interpersonal and teamwork skills
We offer:
- Salary NOK 575 400 – 635 400 per annum depending on qualifications in position as Postdoctoral Research Fellow (position code 1352)
- A professionally stimulating working environment
- Attractive welfare benefits and a generous pension agreement, in addition to Oslo's family-friendly environment with its rich opportunities for culture and outdoor activities
HOW TO APPLY
The application must include:
- Application letter describing how she/he fits the description of the person we seek, including a summary of the applicant's scientific work and interests
- CV summarizing education, positions held, details of academic work, pedagogical and administrative experience and other qualifying activities
- List of publications, published abstracts, presentations that the applicant wishes to be considered by the evaluation committee
- Copies of educational certificates and transcripts of records
- Names and contact details of 2-3 referees stating relation to candidate, e-mail and telephone number
The application with attachments must be delivered in our electronic recruiting system. Foreign applicants are advised to attach an explanation of their University's grading system. Please note that all documents should be in English (or a Scandinavian language).
In the evaluation of applications, significant weight will be placed on the applicants' academic and personal abilities for completing the project. Qualified candidates may be invited for an interview.
POLICY
Formal regulations:
Please see the guidelines and regulations for appointments to Postdoctoral fellowships at the University of Oslo.
No one can be appointed for more than one Postdoctoral Fellow period at the University of Oslo.
According to the Norwegian Freedom of Information Act (Offentleglova) information about the applicant may be included in the public applicant list, also in cases where the applicant has requested non-disclosure.
Inclusion and diversity are a strength. The University of Oslo has a personnel policy objective of achieving a balanced gender composition. Furthermore, we want employees with diverse professional expertise, life experience and perspectives.
If there are qualified applicants with disabilities, employment gaps or immigrant background, we will invite at least one applicant from each of these categories to an interview.
Contact information:
Associate Professor Andreas Lossius email: andreas.lossius[at]medisin.uio.no
ABOUT US
About the University of Oslo:
The University of Oslo is Norway's oldest and highest ranked educational and research institution, with 28 000 students and 7000 employees. With its broad range of academic disciplines and internationally recognised research communities, UiO is an important contributor to society.
The Institute of Basic Medical Sciences overall objective is to promote basic medical knowledge in order to understand normal processes, provide insight into mechanisms that cause illness, and promote good health. The Institute is responsible for teaching in basic medical sciences for the programmes of professional study in medicine and the Master's programme in clinical nutrition. The Institute has more than 300 employees and is located in Domus Medica.
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DESCRIPTION
A full-time position at the Lee Kong Chian School of Medicine is open for an Assistant Professor of Digital Health. Reporting to the Dean and Vice Dean, Research, the appointee is expected to undertake high quality research in the area of Digital Health Sciences, in line with the research strategy of the School. The appointee is also expected to contribute to education commitments, on top of the overarching research strategy and any other duties assigned by the Vice Dean, Research and Dean of LKCMedicine.
Person Specification:
- MBBS/MD and/or PhD
- Relevant management experience
- Significant experience and outstanding, record of translational research and teaching with a high level of scientific achievement, productivity and impact in the field of Digital Health Sciences
- Ability to supervise and mentor junior faculty members, research staff
- Good communication skills, collaborative and able to build and sustain effective working relationships both internally and externally
- Recognises the importance of translating research findings into clinical practice and policy
- Fully conversant with patient-centred approach to modern medicine and the use of new technologies in both education and patient care
- Willing to participate in postgraduate and undergraduate education and training
- Experience and desire to participate in postgraduate and undergraduate education and training
- Track record of having supervised graduate students to successful completion of PhDs, as main supervisor
POLICY
To achieve our vision of redefining medicine and transforming healthcare, LKCMedicine is committed to building a diverse and inclusive community where every individual is highly valued.
Singapore is a thriving metropolis with excellent infrastructure, a vibrant business environment, a convenient island-wide transport network, and rich ethnic diversity. It offers an attractive lifestyle in terms of cultural and gastronomical attractions. We are the UNESCO home of hawker culture, with affordable 'famous dishes' like chicken rice. Also dubbed the Garden City, its lush greenery and clean environment create pleasant living spaces for all. There are plenty of amazing places for children to go on the weekends.
Video Guide of Singapore by Expedia: https://youtu.be/P_q3BdrFsLI
Nanyang Technological University, Singapore (Corporate Video): https://youtu.be/jw4qS7kvfXE
Lee Kong Chian School of Medicine (Corporate Video): https://youtube.com/watch?v=W6gtwMPeIqo
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DESCRIPTION
The Center for Systems Biology Dresden (CSBD) is seeking applications for
ELBE Postdoctoral Fellows
The ELBE Postdoctoral Fellows Program welcomes independent researchers on the postdoctoral level, who come with their own research proposal and freely choose which groups to affiliate with. The program provides an ideal springboard to an independent research career in systems biology, theoretical biophysics, computational biology, mathematics in the life sciences, computer science, and machine learning with application to biological systems and related areas.
What we provide:
The CSBD provides fully funded, 2-3-year positions in an international and cross-disciplinary research environment. ELBE postdoctoral fellows benefit from close collaborations with scientists at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), the Max Planck Institute for the Physics of Complex Systems (MPI-PKS), and the Technische Universität Dresden (TUD), and a stimulating and inspiring atmosphere. Further information can be accessed by visiting our webpage at http://www.csbdresden.de.
Fellows have full access to state-of-the-art research facilities and infrastructure on the campus. Dresden is a vivid and international scientific city, with a large number of research institutions that collaborate under the DRESDEN-concept umbrella. Its position as an outstanding location for research and science is recognized worldwide. Since 2012, the TU Dresden is one of eleven excellence universities in Germany.
What we seek:
The ELBE program seeks outstanding external candidates who are passionate about bringing new ideas, concepts, or systems to the Center. ELBE postdoctoral fellows pursue an interdisciplinary research project in collaboration with members of the CSBD. They are encouraged to develop and use theoretical or computational approaches to study biological systems in close collaboration with experimental groups at the MPI-CBG and the TUD. Ideal candidates should have backgrounds in physics, computer science, mathematics, or a related discipline, with a strong interest in working in a cross-disciplinary life science environment. In some exceptional cases, ELBE fellows can be analytically-minded experimentalists in the field of cell or developmental biology, who work between a lab and a CSBD research group.
HOW TO APPLY
For details about the application procedure, please visit our website http://www.csbdresden.de/join-us/as-a-postdoc/.
Selection of ELBE fellows is based on scientific merit with two application cycles per year. Short-listed candidates should be prepared to join a selection symposium held in Dresden on May 7, 2024. Travel costs will be covered by the CSBD.
DEADLINE
The deadline for applications is February 29, 2024.
POLICY
The Max Planck Society is an equal opportunity employer. Disabled individuals are strongly encouraged to apply. The Center for Systems Biology, the MPI-CBG, and the MPI-PKS aim to increase the number of women in scientific positions, therefore female applicants are particularly welcome. For more information on our efforts to balance family and career, please see http://www.csbdresden.de/about-us/equal-opportunities.
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BACKGROUND
The Max Planck Institute for Multidisciplinary Sciences is a leading international research institute of exceptional scientific breadth. With more than 40 research groups and some 1,000 employees from over 50 nations, it is the largest institute of the Max Planck Society.
The department of Tissue Dynamics and Regeneration (Prof. Dr. Jochen Rink) invites applications for a position as
Bioinformatics Staff Scientist/genome database manager (f/m/x)
About us:
We are a young, international department and our working language is English. We study the fascinating ability of planarians to regenerate complete animals from tissue pieces and conduct worldwide expeditions to study the evolution of regenerative abilities within the taxon. Our scientific approach includes genome sequencing, comparative genomics and various next generation sequencing techniques. Further, we established and maintain PlanMine, the Planarian research community's online resource (https://planmine.mpinat.mpg.de/planmine/begin.do).
About the position:
We are looking for an experienced model organism genome researcher to spearhead and curate the further evolution of the PlanMine web resource. You will be an integral part of the department's bioinformatics subgroup and involved in our ongoing genomics research. You will also interface with the local IT service provider (GWDG) and the university informatics department re technical aspects of PlanMine hosting and development. You will also bridge to the world-wide user community, e.g. by organizing curation efforts, parsing and implementing user suggestions or presenting new database features at international meetings. Thus, you will have the opportunity to remain at the cutting edge of big data management, expand your world-wide contact network or to additionally pursue your own research interests in genome evolution.
RESPONSIBILITIES
- Overseeing the maintenance and further development of the PlanMine web resource.
- Coordinating and publishing new database releases/features.
- Implementing and overseeing web-based curation efforts.
- Developing and implementing web applications for the exploration of large datasets.
- Databasing and analysis of large biological datasets, primarily, but not exclusively produced from NGS experiments.
REQUIREMENTS
Your profile:
- You hold a PhD in a Life Sciences or Bioinformatics subject.
- You have extensive hands-on experience with the use, upkeep and management of model organism genome browsers.
- You are familiar with Linux-based server environments and have demonstrated experience in one or more of the following: Java/Javascript, HTML/CSS, MySQL, PostgreSQL and server administration.
- As a person, you are a team player, you have excellent communication skills, you are fluent in English and a biologist at heart.
- You are self-motivated and able to multitask/prioritize different projects.
Additional experience in one or more of the following will be considered a plus:
- Community-based workshops/hackathlons.
- Biological dataset visualization on the web (e.g. intermine, bluegenes, wormbase, biomart, R Shiny).
- RNA-Seq data analysis of bulk or single cell data (e. g. clustering, differential gene expression, gene set enrichment, trajectory analysis).
- Genome/transcriptome assembly; novel gene or protein annotation, orthology assignment.
- Advanced statistics & machine learning techniques.
- Supervision of students or other team members.
WE OFFER
- Inspiring, world-class research environment.
- Opportunities to participate in the department's world-wide field expeditions.
- Moving assistance for the ones joining us from abroad and help with getting settled in Göttingen.
- Professional training, networking and career-development opportunities; free language courses.
- On-site health management: free fitness and yoga room, sports groups, beach volleyball league, and courses for a "moving lunch break".
- A wide range of opportunities to balance work and family life, including an on-campus kindergarten and vacation care.
- Initiatives for sustainability and a green environment with an on-site biotope.
- Close proximity to the historic town center of Göttingen with rich cultural opportunities and a vibrant student scene.
- Green and peaceful surroundings that are great for running, hiking, cycling and other outdoor activities.
COMPENSATION/RECRUITMENT
The position should be filled as soon as possible; the exact start date is flexible. The payment and benefits are based on the TVöD (wage agreement for public service personnel) guidelines. Positions are initially limited to two years with a possibility of extension.
HOW TO APPLY
Please submit your application including a cover letter, CV, transcripts and publication record (if applicable), and the contact addresses of three referees as a single document, preferably as a PDF file. Please make sure that the cover letter clearly states your motivation for why you want to join the department and your relevant experience that qualifies you for this position. Review of applications will begin immediately. Please submit your application to
ausschreibung58-23[at]mpinat.mpg.de
Max Planck Institute for Multidisciplinary Sciences
Department "Tissue Dynamics and Regeneration"
Herrn Prof. Dr. Jochen Rink
Am Fassberg 11
37077 Göttingen
Germany
POLICY
The Max Planck Society is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals.
The Max Planck Society strives for gender and diversity equality. We welcome applications from all backgrounds.
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DESCRIPTION
A Postdoc in computational biology is available in the Diaz lab at UCSF (https://diazlab.ucsf.edu), funded by grants from the NIH and private foundations. As a member of the UCSF Brain Tumor Center (https://braintumorcenter.ucsf.edu) our mission is the development of therapeutics for brain cancer. Our core competencies include single-cell and spatial genomics, bioinformatics, and brain-tumor biology.
We have ongoing research efforts studying immune brain tumors via functional genomics approaches. We have been profiling clinical specimens using single-cell and spatial technologies and have generated several million single-cell mRNA, ATAC, scCUT&Tag, ST, and other libraries from hundreds of human adult and pediatric brain tumors. Additionally, we are pioneering digital spatial profiling and single-cell epigenetic assays, as well as machine-learning and bioinformatics approaches to analyze these data.
The duties of bioinformatics postdocs include bioinformatics analyses of single-cell, spatial, and bulk 'omics data. The minimum requirements for the position are: 1) a PhD in the biomedical sciences or a related discipline; 2) experience with 'omics data analysis and strong programming skills in a relevant language (e.g. R, Python); 3) a first-author paper in a respectable journal; 4) fluency in English, and the interpersonal skills to negotiate professional interactions in a diverse environment; and 5) the willingness to work hard in the pursuit of shared goals.
HOW TO APPLY
Interested candidates should send an email to aaron.diaz[at]ucsf.edu, with the following:
- CV
- Cover letter, please indicate your preferred start date.
- Names and contacts of three references.
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BACKGROUND
A Postdoctoral Research Associate position is currently open within the Division of Epidemiology, Department of Medicine at Vanderbilt University Medical Center (VUMC). Our research focus spans cancer etiology, prevention, precision medicine, and drug repurposing, employing advanced bioinformatics, statistical, machine learning, and deep learning methodologies. We also integrate multi-omics and Electronic Health Records (EHR) in our investigations. The lab has received funding from multiple NIH grants, including R37/R01 (i.e., NCI-funded transcriptome-wide association study and proteome-wide association studies in colorectal cancer). The Principal Investigator (PI) has authored >110 peer-reviewed publications, including recent high impact publications as lead author in Cancer Discovery, Gastroenterology, Journal of the National Cancer Institute, Nature communications, and American Journal of Human Genetics.
Our ongoing research is centered on population-based molecular, genetic, and genomic epidemiologic studies aimed at identifying susceptibility genes, biomarkers and therapeutic drug targets for various cancers and diseases. We utilize and develop bioinformatics/statistical tools and pipelines to analyze extensive multi-omics data, including whole genome sequencing (WGS), whole exome sequencing (WES), RNA-seq, array-based genotyping, epigenetics, proteomics data, metabolomics, and single-cell omics data. We also conduct integrative analyses of omics data and develop natural language processing algorithms using resources from approximately 5.5 million patients' EHRs at VUMC. These efforts aim to provide potential avenues for the prevention and therapeutic intervention of human cancers and other diseases. The selected candidate will lead independent research projects focusing on statistical genetics, epigenetics, and bioinformatics in genetic epidemiology related studies.
Please find more information about us @ http://www.guoxlab.org
RESPONSIBILITIES
Under guidance from Dr Xingyi Guo, the candidate is expected to work on a wide range of Bioinformatics, Genetic Epidemiology, and Multi-omics projects. He/she should have:
- A PhD in bioinformatics, genetic epidemiology, biostatistics, genomics/epigenetics, machine/deep learning or related fields.
- Strong experience with script languages such as Python, Perl or R. Experience with the Linux/Unix environment is required.
- Good knowledge in statistical computing or machine/deep learning.
- Good interpersonal skills.
- An excellent grasp of English, both in writing and speech.
COMPENSATION
Salary is commensurate with the NIH pay scale. The postdoc positions will be provided with benefits following the VUMC standards.
HOW TO APPLY
To apply, please send a cover letter, CV, summary of past work, and the names and email addresses of three references to Dr. Xingyi Guo at xingyi.guo[at]vumc.org.
ABOUT US
The Vanderbilt Epidemiology Center is committed to conducting research to enhance and expand our understanding of the distribution and determinants of disease, to promoting collaboration aimed at the translation of research into cost-effective strategies of disease prevention and health care delivery, and to training independent investigators in epidemiology research and disease prevention. The center has considerable strengths in international epidemiologic research and training and has close ties with multiple domestic and international institutions, furthering our mission to improve the health of human beings.
POLICY
VUMC wishes to reflect the diversity of society and welcomes applications from all qualified candidates, regardless of backgrounds and individual characteristics.
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The New York Stem Cell Foundation (NYSCF) Research Institute is a growing and successful nonprofit whose mission is to accelerate cures for the diseases of our time through stem cell research.
As a (Senior) Staff Scientist, Computational Biology / Bioinformatics, you will be responsible for building custom tools and developing novel algorithms for analyzing genomic and (single-cell) transcriptomic data created at the NYSCF Research Institute. Your expertise should encompass a strong foundation in statistics, deep/machine learning and data science, coupled with in-depth knowledge of molecular biology and genetics. You will also have experience building pipelines for high-throughput molecular sequencing technologies and a proven track record of data analysis method development. We encourage applications from individuals with knowledge of stem cell / developmental biology or any diseases studied at NYSCF. In this role, you will report to the VP, Computational Biology.
What you'll do:
- Develop deep/machine learning models for the integration and interrogation of multimodal data sets comprising molecular sequencing, health records, microscopic imaging, and other modalities
- Create tools for the optimization of cell fate engineering protocols and screening experiments
- Maintain and improve tools for ancestry inference from genotyping arraysImprove the detection of genomic abnormalities from sequencing and genotyping data to support QC of cell line production
- Prototype, develop, deploy, and document pipelines for quality control, analysis and annotation of high-throughput sequencing data
- Keep track of recent developments in computational biology, benchmark newly published methods and incorporate them into gold standard pipelines
- Develop and implement novel data visualization strategies to summarize results and QC features
- Migrate data storage and analysis pipelines to cloud-computing infrastructure (AWS)
- Connect molecular profiling data with cell line metadata database
- Support experimental groups with data organization and analysis and advise on experiment design for sequencing and other high-throughput assays
- Report new methods and scientific results in presentations and publications
What we're looking for:
- PhD in Biology, Bioinformatics, Genomics, Computational Biology or a similar field, or MS degree and 5+ years of relevant work experience
- A firm grasp of statistics, deep/machine learning and bioinformatics
- Programming experience in Python and/or R and knowledge of software design principles
- Experience with Linux command line tools and shell scripts
- Basic database skills (SQL) and experience with database integration
- Grasp of molecular biology and genetics
- Knowledge of sequencing technologies such as (single-cell) RNA-seq, WGS/WES, ATAC-seq, etc.
- Familiarity with standard tools for QC, alignment, quantification and downstream analysis of sequencing data
- Ability to work in a multi-disciplinary environment of computational biologists, wetlab biologists and translational scientists
- Familiarity with cloud computing infrastructures (ideally AWS)
- Experience with visualization tools such as matplotlib or ggplot2 is a plus
- Knowledge of or a keen interest in stem cell and disease biology is a plus
- Level will be commensurate with experience
The base starting salary range for the Staff Scientist position is $85,000 - $110,000 USD. The base starting salary range for the Senior Staff Scientist position is $110,000 - $150,000 USD. NYSCF has a 35-hour workweek. The (Senior) Staff Scientist level is classified as exempt. Multiple factors, including your experience, determine final offer amounts and levels and may vary from the amounts listed above.
At NYSCF, we believe diversity in all forms makes us a better team, and we celebrate it. Yet studies have shown that women, people of color, and other minoritized individuals in STEM may be less likely to apply to jobs where they do not meet all of the criteria. Therefore, if you are excited about this role but your past experience does not align perfectly with every qualification in the job description, we encourage you to apply anyways. You may be just the right candidate for this or other roles.
We offer all full-time employees a comprehensive benefits package that goes into effect on the first of the month following your start date. It includes a choice of medical, dental, and vision insurance (with 100% of the premiums paid for employees and subsidies for any dependents), 403b retirement plan with 5% employer match (immediate vesting schedule which starts after your first 90 days), short and long term insurance, life insurance, inclusive paid parental leave program, pretax transit and parking, legal aid benefits and wellness benefits. Our paid time off includes vacation, sick, personal days, flexible holidays, summer flex program, and all company holidays. If a visa is required, NYSCF will cover all of those costs. Relocation will sometimes be necessary; therefore, we will provide you with an allowance.
In compliance with federal law, all persons hired will be required to verify identity and eligibility to work in the United States and complete the required employment eligibility verification upon hire.
NYSCF is an equal opportunity employer, and we value diversity in our organization. We provide equal opportunities to all applicants for employment without discrimination or harassment based on race, color, religion, sex (including pregnancy, childbirth, or related medical conditions), sexual orientation, gender identity or expression, age, disability, national origin, marital or domestic/civil partnership status, genetic information, citizenship status, veteran status, or any other characteristic protected by law.
The position is based at our location in Manhattan.
Recruitment Phishing Scams:
Fake job advertisements and offers are increasingly appearing on the internet. If you have encountered a job posting or have been approached with a job offer that you suspect may be fraudulent, we strongly recommend you do not respond and report it to the Federal Trade Commission (https://reportfraud.ftc.gov/#/) and the FBI at https://www.ic3.gov/Home/ComplaintChoice. You can also contact our team jobs[at]nyscf.org to report details of your experience.
Please be mindful of the following:
- NYSCF will only reach out to you through an @nyscf.org email address.
- Other than your email address or telephone number, which you may provide via a job application portal, NYSCF will never ask you to provide personally identifiable information about yourself (such as a Social Security Number or Driver's License Number) via a messaging application (like that used on the LinkedIn platform or Microsoft Teams or Zoom).
- NYSCF will conduct interviews face-to-face over Zoom or in person.
- All job postings will be listed on NYSCF's official career page (https://nyscf.org/careers). If someone contacts you about a job or position that is not listed on the official career page, please contact the NYSCF recruitment team at the contact information below.
- If you have any questions regarding the validity of a recruitment inquiry or an interview, please contact the NYSCF's recruitment team at jobs[at]nyscf.org to confirm before proceeding.
Apply Here: https://www.click2apply.net/zWp7ezUdr12XPtG46sb5yG
PI234797468
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DESCRIPTION
The University of North Carolina Charlotte (UNC Charlotte) announces the search for the Chair of the Department of Bioinformatics and Genomics (BIG) in the College of Computing and Informatics (CCI). This is a unique opportunity to lead and grow innovative programs with a mission to turn biological data into knowledge for the benefit of humanity. This is a 12-month, tenured position at the rank of professor.
With enrollment exceeding 30,000 students, UNC Charlotte is North Carolina's urban research university nestled in one of America's fastest growing and most diverse cities. The University has a strong focus going forward on student success and access, and research results that strive to advance the institution's quality and growth through diversity, equity, and inclusivity.
The Bioinformatics and Genomics (BIG) department is one of the three departments in the College of Computing and Informatics (CCI) and employs 21 faculty members dedicated full-time to the Department and its programs as well as research staff, full-time office and laboratory staff, and part-time instructors.
HOW TO APPLY
A complete position description and more information about the University can be https://apptrkr.com/4810341.
Academic Search is pleased to be assisting with the recruitment of this position. Two senior consultants welcome confidential conversations: Cynthia M. Patterson at Cynthia.Patterson[at]academicsearch.org or Maria Thompson at Maria.Thompson[at]academicsearch.org. For full consideration, applicant materials should be submitted by January 29, 2024 to Please send materials by email as PDF document attachments to BIOGCHAIR[at]academicsearch.org.
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BACKGROUND
Dr. Zizhang Sheng's lab at Columbia University applies bioinformatics and biochemical approaches to elucidate the mechanisms of humoral immune response to infection (HIV, SARS-CoV-2, influenza, malaria, etc.) and to understand the role and origin of autoreactive B cells in autoimmunity (systemic lupus erythematosis, IgA nephropathy, etc.). More descriptions of the Sheng lab can be found here: https://www.infectiousdiseases.cuimc.columbia.edu/profile/zizhang-sheng-phd. The Sheng lab purses scientific research in cutting edge fields and have published over 80 papers in Cell, Nature, Nature Communications, Cell Reports, etc. (https://scholar.google.com/citations?user=40ZwAOgAAAAJ&hl=en).
We are seeking a highly motivated and talented individual to join our team as a Bioinformatics Postdoctoral Research Fellow. This position offers an exciting opportunity to contribute to cutting-edge research in the field. The position will involve analyzing next-generation sequencing data of single cell transcriptome and antibody repertoire to study affinity maturation mechanisms of pathogen or auto-antigen specific antibodies and disease pathogenesis. The position will also involve developing machine learning and/or deep learning methods to predict potency of HIV broadly neutralizing antibodies. The successful candidate will work closely with a multidisciplinary team of both computational and experimental researchers and gain valuable experience in advanced data analysis techniques, algorithm development, and the interpretation of NGS data.
RESPONSIBILITIES
- Conduct bioinformatics analyses to interpret high-throughput sequencing data, including transcriptomics and antibody repertoire.
- Develop and implement machine learning and/or deep learning methods to predict potency of HIV broadly neutralizing antibodies.
- Collaborate with experimental biologists to design and execute bioinformatics experiments that address key research questions.
- Participate in scientific discussions, present research findings at conferences, and contribute to scientific publications.
- Mentor and assist junior researchers in bioinformatics techniques and data analysis.
REQUIREMENTS
- Ph.D. in Bioinformatics, Computational Biology, Genomics, or a related field.
- Strong programming skills in languages such as Python, R, or Perl.
- Proficiency in using bioinformatics software and tools (e.g., CellRanger, Seurat, SAMtools, etc.).
- Experience with next-generation sequencing data analysis (e.g., RNA-Seq, antibody repertoire).
- Knowledge of statistical analysis methods and machine learning techniques.
- Excellent problem-solving skills and the ability to work both independently and collaboratively.
- Effective communication skills, including the ability to present research findings to diverse audiences.
- A strong publication record and a demonstrated passion for bioinformatics research.
PREFERENCES
Applicants with earlier starting date, strong programing background. Wetlab experience (e.g., PCR, protein expression, ELISA, PCR) will be preferred but not required.
LOCATION
Aaron Diamond AIDS Research Center, Columbia University, New York
COMPENSATION
- Competitive postdoctoral salary ($70K+) and benefits package.
- Access to state-of-the-art computational resources and research facilities.
- Opportunities for collaboration with leading researchers in the field (see our publications).
- Career development and mentorship opportunities.
- A stimulating and inclusive research environment.
The salary of the finalist selected for this role will be set based on a variety of factors, including but not limited to departmental budgets, qualifications, experience, education, licenses, specialty, and training. The above hiring range represents the University's good faith and reasonable estimate of the range of possible compensation at the time of posting.
HOW TO APPLY
Interested candidates are invited to submit the following documents to the Columbia ASR system (https://apply.interfolio.com/135947) or email to zs2248[at]cumc.columbia.edu.
- Cover Letter detailing their research interests and qualifications.
- Curriculum Vitae (CV) with a list of publications.
- Contact information for at least three professional references.
- A brief research statement (up to 2 pages) outlining their past research, current interests, and future goals in bioinformatics.
POLICY
We are an equal opportunity employer and welcome applications from individuals of all backgrounds and experiences. We encourage candidates from underrepresented groups to apply.
Columbia University is committed to fostering a diverse and inclusive research community. We look forward to welcoming new talent to our team and advancing the field of bioinformatics together.
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BACKGROUND
Senior Research Scientists are available in Dr. Zhongming Zhao's Bioinformatics and Systems Medicine Laboratory (BSML,www.uth.edu/bioinfo/), Center for Precision Health, McWilliams School of Biomedical Informatics (MSBMI), University of Texas Health Science Center at Houston (UTHealth). The successful candidate is expected to join an established bioinformatics team. The ongoing projects in BSML focus on precision medicine, functional roles of genetic variants in complex disease, next-generation sequencing and single cell omics, and deep learning. Funding (multiple NIH grants (U01, 4 R01s, R03), CPRIT grants, Vice President Office for Cancer Genomic Medicine, lab/center/professorship startup) is available to support this position for 3+ years and promotion to faculty positions is possible. The candidate will have the opportunity to access many high throughput datasets and interact with investigators across UTHealth and Texas Medical Center. The lab is highly productive (>400 papers since 2009) and has an excellent post-doctoral training track record (e.g. 25 former postdocs are currently faculty members, two received Young Investigator Awards from national foundations, two received CPRIT Scholar faculty recruitment, one NIH K99 awardee, one received NIH MIRA grant, and three were finalists for the Vanderbilt University Postdoc of the Year Award). Recent publications appeared or accepted in journals such as Nature, Nature Medicine, Nature Neurosciences, Nature Communications, Nature Machine Intelligence, Cancer Discovery, Genome Research, Genome Biology, Genome Medicine, NAR, Advances Science, GigaScience, etc.
The BSML lab is part of the new Center for Precision Health (CPH), a joint enterprise by the School of Biomedical Informatics and School of Public Health, The University of Texas Health Science Center at Houston. The center is established in UTHealth in response to the emerging need of precision health and artificial intelligence. The center focuses on precision cancer medicine, pharmacogenomics, deep learning, and translational bioinformatics. UTHealth is part of the world-renowned Texas Medical Center located in cosmopolitan Houston, Texas, the fourth largest city in the United States. SBMI is the first School of its kind and one of the largest biomedical informatics programs in the country.
RESPONSIBILITIES
Key responsibilities:
- Independently design and conduct interdisciplinary genomics and bioinformatics research.
- Assist grant proposal development and manuscript writing.
- Present results in a written paper for publication, in a presentation at a meeting, or through personal contact with faculty members and other researchers.
- Train, support and supervise junior lab members.
- Manage research protocols and research data.
- Provide support and training of genome technologies and bioinformatics analysis to other researchers.
- Other duties as assigned.
REQUIREMENTS
The qualified candidates should be highly motivated in research and have a Ph.D. in bioinformatics, quantitative science, computational biology, genetics, molecular biology, pharmacology, or related field upon the job start date. The successful candidate should have some experience in analyzing high-throughput genomic data and proven skills in at least one programming language (e.g., Perl, Python, R, or C/C++). Good understanding of genetics or molecular biology is a plus, but not required. For more information about our research, please visit the web site http://www.uth.edu/bioinfo/.
LOCATION
Houston, Texas, USA
COMPENSATION
Salary and Benefits: Salary are commensurate with the experience. Promotion to other positions is available too. All postdocs are provided with the benefits according to the university standard (medical and dental insurance, retirement, etc.).
DEADLINE
Open until it is filled.
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