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

dreampop · Oct 22, 2019

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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To my knowledge, this is the first study on metabolites in the csf. I believe it's yet unpublished work. It's not clear how differentiated mannose was from controls, but it would be great to finally have something really out of whack. I have no idea what low mannose could mean.

Andy · Oct 22, 2019

Today we are hosting the second annual ME/CFS Consortium Meeting in #NYC. Looking forward to hearing from our Collaborating Research Centers presenting new findings in #MECFS research.

We are grateful to be joined by members from the following organizations for this event: National Institutes of Health (NIH)The #MEAction Network USA Solve MECFS Initiative and The Microbe Discovery Project. Stay tuned for updates #CenterforSolutions
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Code:
https://www.facebook.com/CfSforMECFS/posts/671748796683881

Andy · Oct 23, 2019

https://twitter.com/user/status/1187010212236054528

Andy · Oct 25, 2019

ME/CFS Q&A- How many true subsets are there with ME/CFS patients?

Copy and paste
Code:
https://youtu.be/iVZ5z4HyKxY
https://www.youtube.com/watch?v=iVZ5z4HyKxY

Sunshine3 · Oct 26, 2019

Was it worth their while posting that. Give us 5 minutes at least!

Susan K · Oct 29, 2019

Sunshine3 said: ↑

Was it worth their while posting that. Give us 5 minutes at least!
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The media folks also thought it would be helpful to put a old unplugged microscope plus 3 volumetric flasks on the desk in front of the speakers to give credibility. Same setup/desk used for the Dr Komaroff talk.
Someone’s trying anyway.

Forbin · Oct 29, 2019

Susan K said: ↑

Someone’s trying anyway.
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They'll get the hang of it. Columbia's film school was ranked 5th in the country by the Hollywood Reporter. Maybe the Center for Solutions should try to enlist the help of some of their film students, if they haven't already.

Guest 2176 · Nov 19, 2019

strategist said: ↑

Using the medicine subreddit to observe attitudes towards ME/CFS, I think there has been a shift. The JAMA article by Komaroff in particular seemed to make a particularly big impact. This video is good too: easy to understand without going into technical details or controversy, with a positive message. We need this kind of PR to undo some of the negative attitudes towards ME/CFS.

There should alsways be room to discuss controversies and technicalities but the average person really just needs to hear that views towards ME/CFS are changing, that it's real and that we're beginning to discover its associated biology and that it's a problem that should be taken seriously.
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I can't stomach looking at that subreddit. They have pretty awful attitudes toward pwME

Andy · Dec 12, 2019

We have a holiday treat for our friends in the #MECFS community: To start off 2020 on a high note, we are excited to announce that Dr. Lipkin will be recording his #AskOurResearchers video. Comment on this post with questions that you would like to have Dr. Lipkin address and stay tuned for a special opportunity to be announced before the holidays.

View Dr. Lipkin's holiday message here:
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Code:
https://www.facebook.com/CfSforMECFS/videos/427861854759469/
https://twitter.com/user/status/1204471187478208513

Andy · Mar 19, 2020

A new website has been launched, which includes their videos and a blog, https://cfsformecfs.org/

wigglethemouse · Mar 19, 2020

Dr. Oliver Fiehn of @WCMC_UCDavis discusses metabolic abnormalities in #MECFS cases in this week’s episode of #AskOurResearchers. Watch it here:

https://www.youtube.com/watch?v=fQvztZCUjLw

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https://twitter.com/user/status/1240685132090138628

Short version : No answers yet but trying to map metabolites to symptoms.

wigglethemouse · Apr 29, 2020

A short update - one paper submitted another in process
https://twitter.com/user/status/1255567714724253696

Trish · Jul 16, 2021

Sly Saint said: ↑

ME/CFS Research: State of the Art, State of the Science
Written by Dr. Anthony Komaroff
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Thread on this here:
https://www.s4me.info/threads/trend...covid-19-syndrome-komaroff-lipkin-2021.20883/

Sly Saint · Jul 25, 2023

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

Dolphin · Jul 25, 2023

Not sure how new this list is?

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dreampop · Jul 31, 2023

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.
Click to expand...

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.

Sly Saint · Aug 20, 2023

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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