New powerful computational framework will help understand aggressive behaviors of cancer cells

By | Feature, Research

Cancer is an illness caused by an uncontrolled division of transformed cells, which can originate in almost  any organ of the body.  Cancer is not a single disease, even when it arises in the same site of the body. Tremendous variability exists in progression of disease and response to therapy among different persons with the same general type of cancer, such as breast cancer. Even at the level of a single person, cancer cells show tremendous heterogeneity within a single tumor and among a primary tumor and metastases. This heterogeneity causes drug resistance and fatal disease. The prevailing dogma is that heterogeneity among cancer cells arises randomly, generating greedy individual cancer cells that compete for growth factors and optimal environments. The rare “winners” in this competition survive and metastasize. However, tumors consistently maintain heterogeneous subpopulations of cancer cells, some of which appear less able to grow and spread. This observation prompted Gary and Kathy Luker, cancer cell biologists at the University of Michigan, to hypothesize that cancer cells may actually collaborate under some circumstances to cause disease and not just compete. The idea that single, heterogeneous cancer cells work collectively within a constrained range of variability to drive population-level outputs in tumor progression is a ground-breaking concept that may revolutionize how we approach cancer biology and therapy.

The team is using innovative approaches to extract and merge data streams from models that generate heterogeneous cell behaviors

...cancer cell biologists have teamed up with computational scientists and experts in artificial intelligence to focus the power of these fields on understanding and overcoming heterogeneity in cancer.

To understand causes of single-cell heterogeneity in cancer and conditions that motivate cancer cells to collaborate, an interdisciplinary team of scientists at UM formulated an entirely new conceptual approach to this challenging problem. The cancer cell biologists have teamed up with computational scientists and experts in artificial intelligence to focus the power of these fields on understanding and overcoming heterogeneity in cancer. Building on large, single-cell data sets unique to the team, they will combine inverse reinforcement learning, an artificial intelligence method typically applied to discover motivations for human behaviors, with computational models inferred on the basis of the physics and chemistry of cell signaling and migration. They have proposed an entirely new conceptual approach combining single cell data, physics-based modeling and artificial intelligence to single-cell heterogeneity and intercellular interactions. By discovering  testable molecular processes underlying “decision-making” by single cells and their “motivations” for acting competitively or collaboratively, this research blazes a new path to understand and treat cancer. Their high-risk, high-reward approach to understand how each cell in a population processes information and translates that to action driving cancer progression, has attracted an award of $1 million dollars by the Keck Foundation. 

The team includes Gary Luker (Radiology, Microbiology and Immunology; Biomedical Engineering), and Kathryn Luker (Radiology), who are leading the experimental studies of cell signaling and migration; Jennifer Linderman (Chemical Engineering; Biomedical Engineering); and Krishna Garikipati (Mechanical Engineering; Mathematics), who are leading the machine learning and modeling side of the project. Nikola Banovic (Electrical Engineering and Computer Science) and Xun Huan (Mechanical Engineering) are using artificial intelligence approaches to discover decision-making policies and rewards for cancer cells, working with the rest of the investigators to incorporate experimental data and physics/chemistry-based models into their approaches.

The Keck Foundation research program seeks to benefit humanity by supporting projects in medical research, science and engineering. This project combines all of these research areas to tackle cancer in a new way. The idea for this project originated in the 2020 MICDE faculty workshop in AI for Physically based Bio-medicine Workshop. The workshop brought together an interdisciplinary group of faculty members to discuss ways to advance artificial intelligence and machine learning methods for biomedical problems. After seeding the idea, a subset of these researchers were awarded an MICDE catalyst grant and a MIDAS PODS grant. These funds were used to establish the proof of concept and to generate preliminary results. 

Computational science is becoming increasingly indispensable in many areas of biomedical science. While the current proposal focuses on cancer, this innovative computational framework represents a transformative leap with widespread applications in multiple other biomedical, physical, and social sciences. MICDE supports innovative and interdisciplinary projects aiming to advance the current paradigms.

Portraits of Kathryn Luker, Gary Luker, Krishna Garikipati, Jennifer Linderman, Nikola Banovic and Xun Huan

Project’s principal investigators (left to right): Kathryn Luker (Radiology), Gary Luker (Radiology, Microbiology and Immonology, and Biomedical Engineering), Krishna Garikipati (Mechanical Engineering, and Mathematics), Jennifer Linderman (Chemical Engineering, and Mathematics), Nikola Banovic (Electrical Engineering and Computer Science) and Xun Huan (Mechanical Engineering).

Helmholtz Information and Data Science Academy Visiting Researcher Grant

By | Educational, SC2 jobs

Are you a doctoral researcher or Postdoc and your research has a strong link to the (applied) data and information sciences? The Helmholtz Visiting Researcher Grant offers doctoral students and Postdocs the opportunity to do a fully-funded short-term research stay (1 – 3 months) at one of the 18 Helmholtz centers. With more than 43,000 employees and an annual budget of 5 billion euros, Helmholtz is Germany’s largest scientific organization. Its research fields include: Energy; Earth and Environment; Health; Aeronautics, Space and Transport; Matter, and Information.

The Helmholtz Visiting Researcher Grant is promoted by HiDA, the Helmholtz Information and Data Science Academy. Its aim is to enable new research collaborations, to foster knowledge exchange, and to explore new or emerging research topics in the field of information and data sciences. The program addresses researchers in both academia and in industry. It offers researchers the opportunity to get to know the Helmholtz Association of German Research Centers.

Next Application Deadline: 15 March, 2022

For more information: https://www.helmholtz-hida.de/en/new-horizons/helmholtz-visiting-researcher-grant/

Info Session on the Program (via Zoom) on Tuesday, 18 January, 2022, 14.00 – 15.00pm  CET

Sign up here: https://tms.aloom.de/info-session-hida-research-grants-/

Postdoctoral position in neuroscience in the Renart Lab, Champalimaud Foundation, Portugal

By | Educational, SC2 jobs

The Renart Lab, in the Champalimaud Centre for the Unknown (Lisbon, Portugal), is looking for candidates for a postdoc position in within a project whose goal is to understand the neural basis of simple sensory judgements using modern methods in system’s neuroscience together with theory.

Successful applicants are expected to have experience studying controlled behavior in rodents using recordings and perturbations. The project has a strong quantitative component, so experience on computational neuroscience and statistics/machine-learning methods for behavioral and neural data analysis will be highly valued.
Some recent publications and methodologies relevant for the project are:
The Champalimaud Neuroscience Programme is a vibrant research community focussed on understanding the links between neural activity and behavior. The Renart lab promotes a horizontal and collaborative environment. The position offers a competitive salary and is available immediately for a duration of 3 years (with flexibility).

Interested applicants should send their CV, a brief motivation statement and the names of at least 2 references by email to:
careers@research.fchampalimaud.org and alfonso.renart@neuro.fchampalimaud.org

Flagship Pioneering Summer Fellowship Opportunity Information Session

By | Educational, SC2 jobs

Flagship Pioneering is a life science venture creation firm based out of Cambridge, MA. Flagship’s unique venture creation process is behind companies such as Moderna, Rubius Therapeutics, Indigo Agriculture, and several dozen others.

The Flagship Pioneering Summer Fellowship Program is a one-of-a-kind opportunity to work alongside scientist-entrepreneurs at the earliest stage of ideation and develop the next breakthrough life science companies. Over the course of an immersive 12-week paid program, you will be exposed to our proprietary innovation process, connect with scientific and business leaders within our vast ecosystem, and assess employment opportunities.

Ideal candidates are creative Ph.D., M.D., M.S., or science-oriented M.B.A. students that are within 1 year of graduating upon starting the fellowship or have recently graduated. Applications are rolling, but interested candidates are strongly encouraged to apply before January 31, 2022. 

During the 1-hour information session, you will learn about Flagship Pioneering from Associates Ayse Muñiz, PhD (University of Michigan Class of 2021), and Rahi Punjabi who will discuss a new AI Fellows track launching this summer. Those with a strong background in computer science, statistics, applied mathematics, physics, and computational biology are encouraged to attend to learn more about this new track.
 
DateThursday, January 13, 2022
Time: 11AM-12PM

Zoom info: https://flagshippioneering.zoom.us/j/96455167438?pwd=eWYxOURrZXkveUY3VHlMTnl6ZW9Gdz09&from=addon

Password: 756102

Applications to the 2022 Annual Argonne Training Program on Extreme-Scale Computing are due March 1

By | Educational, HPC

Argonne Training Program on Extreme-Scale ComputingThe annual Argonne Training Program on Extreme-Scale Computing (ATPESC), for doctoral students, postdocs, and computational scientists, is set to take place July 31-August 12, 2022. This year’s program will mark the 10th anniversary of ATPESC.

Submit your application for an opportunity to learn the tools and techniques needed to carry out computational science on the world’s most powerful supercomputers. ATPESC participants will have access to DOE’s leadership-class systems at the ALCF, OLCF, and NERSC.

Learn more and apply here

PROGRAM CURRICULUM
Renowned scientists and leading HPC experts will serve as lecturers and guide the hands-on sessions. The core curriculum will cover:

  • Hardware architectures
  • Programming models and languages
  • Approaches for performance portability
  • Numerical algorithms and mathematical software
  • Performance measurement and debugging tools
  • Data analysis, visualization, and methodologies for big data applications
  • Approaches to building community codes for HPC systems
  • Machine learning and data science

ELIGIBILITY AND APPLICATION
Doctoral students, postdocs, and computational scientists interested in attending ATPESC can review eligibility and application details on the website.

There are no fees to participate in ATPESC. Domestic airfare, meals, and lodging are also provided.
Application deadline: March 1, 2022.

ATPESC is funded by the Exascale Computing Project, a collaborative effort of the DOE Office of Science’s Advanced Scientific Computing Research Program and the National Nuclear Security Administration.

Idaho National Laboratory (INL) Graduate Fellowship Program

By | Educational, SC2 jobs

Idaho National Laboratory is now accepting applications for the INL Graduate Fellowship program. This program is designed to identify exceptional graduate students in research areas aligned with INL’s strategic agenda to enable the current and future mission of the lab. A collaboration between INL and universities, the INL Graduate Fellowship program provides mentoring and financial support for outstanding students who are enrolled, or plan to enroll, in graduate degree programs. Selected students will receive a salary of $60,000/year, plus tuition coverage from INL.

Flyer: INL_Graduate_Fellowship

How to apply

Applicants are invited to apply online through inl.gov/careers job posting numbers 16803 (for applicants in the fields of nuclear energy and clean energy development) and 16806 (for applicants in National & Homeland Security). Letters of recommendation should be submitted via email to graduatefellowships@inl.gov.

Important dates

  • February 13, 2022 – posting closes
  • May 2022 – selections will be announced