Carl de Boer

191 Followers
108 Following
15 Posts
Assistant Professor at UBC. Likes fun experiments, tech dev, big data, genomics, gene regulation, genetics.
Websitedeboer.bme.ubc.ca/
Twittertwitter.com/CarldeBoerPhD

Do you make/clone plasmid DNA libraries? We make a ton, so finding the best way to culture the E coli to ensure uniform amplification was an important question. We quantified amplification bias for each culture method (plates, liquid, semisolid). The best may surprise you...

Main thread (xorial?) on the (let x=)bird site https://x.com/nmateyko/status/1795575770414542932?t=zWsel5bie2FNXCJrvizqCg&s=19

Nick Mateyko (@nmateyko) on X

Do you really need to spread plasmid libraries on mountains of plates to get uniform growth, or can you just dump them in a flask and call it a day? We make huge plasmid libraries in the de Boer Lab, so we tested whether culture method really matters. 1/ https://t.co/3HbkGnBw6G

X (formerly Twitter)
Excited to be organizing SynBio6.0 on May 16-17, 2024 @ UBC, and grateful to have such a great lineup of speakers: Pulin Li [MIT], Leo Parts [Wellcome Sanger], Ron Weiss [MIT], Rebecca Shapiro [U Guelph]! Join us! More info/register here: https://de-boer-lab.github.io/synbio6-0.github.io/ #syntheticbiology
SynBio6.0

**6th Annual Synthetic Biology Symposium** May 16-17, 2024, Vancouver, BC, Canada

SynBio6.0

We are looking for postdocs/research associates for an exciting collaborative project that aims to decode the cell circuits underpinning stem cell differentiation to lung cells using cutting-edge omics approaches to enable cell-based therapies. Come chat with me about it @ #KSSingleCell24

Apply below!
http://tinyurl.com/bdp972dt
http://tinyurl.com/39x5ay3u

Research Associate, United Therapeutics

Academic Job Category Faculty Non Bargaining Job Title Research Associate, United Therapeutics Department Yachie Laboratory | School of Biomedical Engineering | Faculty of Medicine (Nozomu Yachie) Posting End Date February 9, 2024 Note: Applications will be accepted until 11:59 PM on the day prior to the Posting End Date above. Job End Date Feb 28, 2025 The expected pay for this position is $5,600/month. At UBC, we believe that attracting and sustaining a diverse workforce is key to the successful pursuit of excellence in research, innovation, and learning for all faculty, staff and students. Our commitment to employment equity helps achieve inclusion and fairness, brings rich diversity to UBC as a workplace, and creates the necessary conditions for a rewarding career. Position Summary The School of Biomedical Engineering (SBME) at the University of British Columbia (UBC) in Vancouver, BC, Canada invites applications for a Research Associate position to work on a team-based project spanning pluripotent stem cells, lung differentiation, and genomics in the de Boer (https://deboer.bme.ubc.ca/), Shakiba (https://shakiba.bme.ubc.ca/), Yachie (https://yachie-lab.org/), Zandstra (https://www.stemcellbioengineering.ca/), and Lynn (https://www.lynnlab.com/) labs. The project is in collaboration with United Therapeutics and seeks to enable the robust, large-scale production of lung cells from patient-specific induced pluripotent stem cells (iPSCs). The project involves the use of single-cell RNA-seq, DNA barcoding, reprogramming, and lung cell differentiation. The Faculties of Medicine and Applied Science have partnered to create the SBME, a new flagship entity at UBC, and a top strategic priority for the University and both Faculties. The SBME is a nucleus for education and training, research, and innovation in biomedical engineering, creating new knowledge, new academic and training programs, and fostering translation and innovation. UBC SBME distinguishes itself by deep training in biology, and engineering science and design, enabling SBME researchers to address the most pressing biomedical challenges of the day. Our SBME faculty conduct research that advances our fundamental understanding of human biology, and yields technologies and therapies that advance our health and wellbeing. Organizational Status Individual will report to one or more of Drs. Nika Shakiba, Dr. Carl de Boer, Dr. Nozomu Yachie, Dr. Francis Lynn, or Dr. Peter Zandstra, depending on the position, but will work collaboratively with teams across these labs regardless. Responsibilities Successful candidate will have the unique opportunity to collaborate with the members of the laboratories involved in this project, integrating cutting-edge stem cell, bioinformatics and synthetic biology techniques. The responsibilities of this position, to be determined by the Supervisor, are flexible and depend on the skills and research interests of the successful applicant. Specific tasks may include: Human pluripotent stem cell culture including maintenance, expansion, and characterization Derivation of induced pluripotent stem cells through reprogramming of PBMCs Lung cell differentiation and culture Genetic engineering of mammalian cells Next generation sequencing and bioinformatics analysis Machine learning/AI Single-cell RNA-seq, perturb-seq, and/or other transcriptomic analysis Analyzing data and presenting the data in reports, publications, and presentations at local and international conferences Helping to enhance our collaborative and interdisciplinary research environment. Contributing to cutting-edge knowledge in the scientific community Preparing grants and assisting with grant applications, publications and with fulfilling regulatory requirements (animal ethics, biosafety etc.) Designing and performing experiments, analyzing results, and presenting findings Training and mentoring lab personnel Coordinating the maintenance of lab equipment Qualifications Candidates with experience in project management will be prioritized Candidates must hold a PhD or MD Candidates should have a strong research background, as demonstrated by past publications, accomplishments, and references Candidates with strong background in either computational or experimental biology (or both) will be considered The successful candidate will be a passionate, self-driven, independent thinker with excellent organizational, oral and written communication, and interpersonal skills, and a strong work ethic Preference will be given to experimental candidates who have skills in any of the following areas: stem cell culture, lentiviral delivery, lung cell differentiation and culture, iPSC derivation, transcriptomics, bioinformatics, single-cell RNA-seq Preference will be given to computational candidates who have skills in any of the following topics: bioinformatics, statistics, machine learning, deep learning, single cell omics, transcriptomics, and programming in R, Python, and Bash Supervision received The incumbent will receive supervision directly from one or more of Drs. Shakiba, de Boer, Yachie, Lynn, and Zandstra, depending on their exact role, but will have the opportunity to work closely with all laboratories involved in this project. Supervision given The incumbent may be required to supervise trainees involved in the research program. Start date and stipend The start date is as soon as possible but flexible; funding has already been received. The position is full-time for one year with the possibility of extension subject to work performance. Salary will be commensurate with qualifications and experience. How to Apply Candidates should provide a CV, names and contact information of 3 references, and a cover letter describing past achievements and future research interests. Note that there are several similar positions available and candidates should apply to any that interest them. Please submit your applications directly via Workday from this link. For any inquiries regarding this position, please contact Dr. Nika Shakiba ([email protected]), Dr. Nozomu Yachie ([email protected]), and Dr. Carl de Boer ([email protected]). Equity and diversity are essential to academic excellence. An open and diverse community fosters the inclusion of voices that have been underrepresented or discouraged. We encourage applications from members of groups that have been marginalized on any grounds enumerated under the B.C. Human Rights Code, including sex, sexual orientation, gender identity or expression, racialization, disability, political belief, religion, marital or family status, age, and/or status as a First Nation, Metis, Inuit, or Indigenous person. All qualified candidates are encouraged to apply; however, Canadians and permanent residents of Canada will be given priority. UBC - One of the World's Leading Universities As one of the world's leading universities, the University of British Columbia creates an exceptional learning environment that fosters global citizenship, advances a civil and sustainable society, and supports outstanding research to serve the people of British Columbia, Canada and the world. UBC hires on the basis of merit and is committed to employment equity. All qualified persons are encouraged to apply. Equity and diversity are essential to academic excellence. An open and diverse community fosters the inclusion of voices that have been underrepresented or discouraged. We encourage applications from members of groups that have been marginalized on any grounds enumerated under the B.C. Human Rights Code, including sex, sexual orientation, gender identity or expression, racialization, disability, political belief, religion, marital or family status, age, and/or status as a First Nation, Metis, Inuit, and/or Indigenous person. All qualified candidates are encouraged to apply; however Canadians and permanent residents will be given priority. If you have any accommodation or accessibility needs during the job application process, please contact the Centre for Workplace Accessibility at [email protected].

Happy to present this update to our (Jussi Taipale+me) plan to solve the cis-regulatory code using high-throughput assays of non-genomic DNA and ML, online today in Nature.
Despite the plan, the problem is so huge that we are looking to start a global effort in this space. Please email us if you want to join forces!
Thanks to all those who helped shape our thoughts!

https://rdcu.be/dtwyc

Why do reimbursement processes (in particular when invited to the USA) have to be such a pain?

We are looking for computational/experimental folks experienced in single cell genomics, iPSCs, lung development, and/or genetic screens (e.g. perturb-seq).

Many positions available(!), including postdoc, research associate, and technician: https://jobrxiv.org/job/the-university-of-british-columbia-27778-staff-faculty-positions-at-sbme-ubc-in-pluripotent-stem-cell-lung-differe/

This is an exciting collaboration with United Therapeutics, with UBC's Yachie, Shakiba, Lynn, Zandstra, and my own group.

Re-toots greatly appreciated! 🙏

Staff/faculty positions at SBME, UBC in Pluripotent Stem Cell, Lung Differe

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

jobRxiv

For all the folks starting their #PhD (or their master thesis) today - a reminder why your PhD advisor can solve a problem so "easily" ...

#astrodon #academia #AcademicChatter #research #VicisArt

I support the early career scientists in Canada who are walking out today to ask for their first pay raise in 20 years.

The federal government's track record in science has been on of neglect, and it's time to change that.

https://www.supportourscience.ca

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Support Our Science

NEW PAPER led by Grace Vezeau! We rationally engineered synthetic riboswitches to carry out sense & respond for human biomarker proteins [mCRP and IL32-gamma] that indicate disease or infection. 16-fold activation without trial-and-error!

https://www.nature.com/articles/s41467-023-38098-0

Automated design of protein-binding riboswitches for sensing human biomarkers in a cell-free expression system - Nature Communications

Cell-free genetically encoded biosensors have been developed to detect small molecules and nucleic acids, but they have yet to be reliably engineered to detect proteins. Here the authors develop an automated platform to convert protein-binding RNA aptamers into riboswitch sensors that operate within low-cost cell-free assays.

Nature

Happy to share a new preprint wherein Jussi Taipale and I argue that the functional genomics/machine learning research community should work towards the long-term goal of training our cis-regulatory computer models solely on non-genomic sequences.
https://doi.org/10.1101/2023.04.20.537701

Here is a link to the tweetorial:
https://twitter.com/CarldeBoerPhD/status/1649773500734017540