USA: Center for Solutions for ME/CFS - news and updates from Columbia University's NIH funded center

Solstice said:
Provided they get the funding they needed.
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Just like nuclear fusion. 50 years ago it was 30-50 years away. Then budgets dropped and kept dropping until almost nothing and we are still 30-50 years away. A reasonable budget would be to spend annually what is spent on the whole ITER project, we are not even close to adequate fusion research funding and, surprise, have not made much progress.

Not trying generally leads to not succeeding. There are exceptions but for hard problems it almost always holds up. Here over the years not trying explains at least 90% of the failure by now, and growing over time. Ironically this is exactly what we are blamed for, that we are not magically cured by CBT because we are not trying. Because one thing you can always count on with this damned disease is that no matter the level of injury, there will always be a much larger heap of insult on top of it.
 
Ron said:
Apparently the video has been pulled. I hope all were able to watch it.
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Shoot. I should have grabbed the full transcript when I was at it, but the weekend was really rough so I took a shortcut. This is all I have
The budget for these centers is roughly,
49:09
what would you say Beth?
49:10
Fifteen percent?
49:11
Twenty percent of what we're promised?
49:15
So we have, we don't have the samples
49:18
to do the appropriate controls.
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I guess the above might have been slightly controversial!

Did anyone else manage to capture the full transcript?
 
Wilhelmina Jenkins said:
I didn’t get a chance to watch, but I was very curious about the comments about a promised amount of funding. That seemed odd to me. Does anyone know what promise he’s referring to?
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I remember that he was lobbying hard for funding before the centers were announced. I remember Ron saying a minimum of $5M a year for 5 years was really needed to support a team to do the work - and this number would approximately tie in with the 20% or so number Lipkin quoted..

Also before the centers, Lipkin used to talk about all the samples he had stored but no funding to process all of them. So I was interested yesterday to read this from @Simon M


Reading between the lines (and it's a pure guess, might be wrong) it looks like he doesn't have funding to process his own samples so is now making them available to others. Link to @Simon M post
https://www.s4me.info/threads/news-from-nih-me-cfs-webinar-october-17-2019.11766/#post-224981

I'm worried the same thing will happen to other researchers who have large bio-repositories with disease comparison but no funding as yet. As these samples age, who knows what effect that will have.
 
What We Do
The CfS for ME/CFS is designed to rapidly adapt to the insights and opportunities that are continuously emerging in the field of ME/CFS research. Accordingly, we are a center without walls—we recruit new investigators nationally and internationally based on their commitment and expertise rather than their institutional affiliation.

Our funding during the first two years of the Collaborative Center Program will be used to mine the rich data and sample sets established with the support of the NIH, the Hutchins Family Foundation, and the Microbe Discovery Project. This work is inspired by discoveries in our laboratory and others pointing to the importance of the microbiome, the virome, and the fungome as determinants of health. We will look for immune responses that may persist long after an infectious agent has either been cleared from the body or become dormant, and for autoantibodies. We will also profile metabolites in plasma and gene expression in white blood cells.

Clinical research studies will connect with the laboratory studies. We will examine the impact of physical activity on the microbiome, the metabolome, and the transcriptome for clues to understanding the basis of persistent fatigue, cognitive dysfunction, and other symptoms after exercise. We will design a mobile app and mine existing datasets for insights into clinical features, comorbidities, and sub-types that could refine laboratory analyses and enhance care.

We are hoping to find additional resources for epigenetic studies that could explain how genes are turned on or off in response to exercise. Clinical trials are not part of our current mandate. However, we are aware of the urgency and need for progress in clinical care. Each of our projects has been prioritized for its potential to lead to solutions for ME/CFS through the development of animal models of ME/CFS or clinical trials of antibiotics, pre- and probiotics, antifungals, antivirals, or immunomodulatory treatments.

Learn more information about each of the three main projects supported by the NIH award below.
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https://www.publichealth.columbia.e...y/research/center-solutions-me-cfs/what-we-do
 
wigglethemouse said:
Oliver Fiehn states that there is a central website for storing metabolomic data from studies (blood, tissue, all species). At present there are 994 studies posted.
https://www.metabolomicsworkbench.org/

You can search for Human=> Blood => Chronic Fatigue Syndrome here
https://www.metabolomicsworkbench.org/data/metsearch_MS_form2.php

This brings up studies from Robert Naviaux (2 datasets) and Oliver Fiehn/Ian Lipkin (4 datasets) for those interested in raw data number crunching.

ETA: If you leave the sample source blank and search Human => <Blank> => Chronic Fatigue Syndrome there are also three datasets for CSF fluid from Fiehn/Lipkin. Does anyone know if this study of CSF has been published?




ETA2: FYI - Raw data for CSF fluid is 6G + 4.5G + 0.5G.
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Strangely, this was never published as far as I'm aware. It's a shame because I don't know a study of it's type has been performed before.
 
job ad
Staff Associate III

Columbia University
Published 19 August 2023
Workplace New York City, New York, USA
Category
Computer Science
Health
Position
Regular Employment / Collaborator
The Center for Infection and Immunity at Columbia University Irving Medical Center (CUIMC) and the Mailman School of Public Health is hiring for the position of Staff Associate (Bioinformatics) to join one of the world’s largest and most advanced center for basic and translational science, with a global network of researchers, focused on chronic and infectious diseases, microbial surveillance, discovery and diagnosis in humans and wildlife. The successful candidate will be part of a talented team of bioinformaticians and statisticians that work on the development and maintenance of clinical pipelines for FDA and New York State Clinical Laboratory Evaluation Program (CLEP) approval of microbial diagnostic assays.

The candidate will participate in the data analysis and integration of single-cell/bulk RNA-Seq and other multi-omics datasets for large-scale studies on Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (ME/CFS) with the goal of unraveling the underlying host-response mechanisms that will lead to methods for diagnosing, treating, and preventing ME/CFS.

The candidate will write programs for data analysis of Next Generation Sequencing (NGS) data generated from a variety of sequencing-based applications and perform data processing using on-site high-performance clusters (HPC) and Amazon Cloud. Ability to write code in Python, R and Shell scripting using containerization and workflow management tools would be considered a plus. The candidate will be responsible for maintaining the existing pipelines and genomic databases. The various high-impact projects will provide opportunities to participate in manuscript and grant writing. Responsibilities include: Provide bioinformatics support for multi-omics analysis in a large and dynamic laboratory - 50% Provide support for projects related to microbial detection and discovery - 30% Manage databases and data - 10% Contribute to publications and research grants - 5% Perform other related duties as assigned - 5% Candidate must possess the following for consideration: Bachelor’s degree in computer science, bioinformatics, or related field Minimum of 4-6 year’s related experience Knowledge of commonly used bioinformatics tools and algorithms, writing pipelines for analysis of NGS datasets generated using Illumina sequencing platform, along with strong programming and analytical skills. Experience in NGS experimental design, data quality control, mapping software such as Bowtie, BWA and STAR, genome annotations from major bioinformatics resources (ENSEMBL, EMBL, NCBI). RNA-Seq data analysis using featureCounts, DESeq2, cellranger and Seurat package would be desirable. Knowledge and experience working with basic statistical analysis, supervised and unsupervised techniques in R. High proficiency in scripting languages, such as Python, Bash and R in an academic or industrial environment. Ability to work in Linux environments consisting of high-performance clusters or Amazon Cloud. Familiarity with SGE or Slurm schedulers, resource management, multi-threading tools. Familiarity with Gene Set Enrichment Analysis or Ingenuity Pathway analysis

Thank you for your interest in the Columbia University Center for Infection and Immunity (CII). If interested and qualified for this position, please submit a CV and Cover Letter to the link provided. Salary Range - Staff Associate III: $90,000 - $120,000 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. Columbia University is an Equal Opportunity Employer / Disability / Veteran Pay Transparency Disclosure 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.
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https://www.myscience.org/jobs/id2689960-staff_associate_iii-columbia_university-new_york_city
 
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