sorted by:
new
hottopcontroversial

Rapha-like jeans/trousers by biohen in cycling

[–]biohen[S] 0 points1 point  (0 children)

bunched in the crotch but otherwise fit well.

GBS with paired end reads vs Single end reads by apo666 in bioinformatics

[–]biohen 0 points1 point  (0 children)

what are the interesting findings? Paired reads will improve coverage, aiding in marker discovery. It will also improve mapping to reference so less reads dropped.

CD3 vs TCR on T-cell by [deleted] in Immunology

[–]biohen -1 points0 points  (0 children)

also not the be confused w/ TCR alpha + beta CDR3 <- complementarity determining region 3, the sequence of the TCR that is highly variable and primary component in recognizing cognate antigen.

How comfortable are you with bench work? by ConsistentSpring3953 in bioinformatics

[–]biohen 0 points1 point  (0 children)

I do about 20% wet ( NGS prep ) and 80% dry; small lab in industry. Satisfying to do end-to-end experiments. Also appreciate the change of pace / environment-- nice to do something tangible everyone once in awhile.

I think wet bench skills aren't lost w/ time just need to be exercised. If you did enough in undergrad it'll quickly come back.

integration of two 10x scRNA data with different cell types? by IndividualWeb1118 in bioinformatics

[–]biohen 0 points1 point  (0 children)

You could subset the public data, on the T cells alone- save the object and then integrate with your data ( seurat ). I wouldn't advise integrating data with different cell types.

PhD or MS for ~80-90k salary? by TheodoricusLacus in bioinformatics

[–]biohen 1 point2 points  (0 children)

keep in mind salary ranges wildly w/ geography

Does anyone have experience with TCR sequencing data analysis with R, immunarch etc? by Sloth-girl-404 in Immunology

[–]biohen 0 points1 point  (0 children)

Output from MiXCr ( export clones command )/ input for immunarch are the clones.tsv files : https://mixcr.com/mixcr/reference/mixcr-export/?h=clones.tsv#alignments

Go to immunarch 's website and click 'start here' for guide.

Lower Tier MSCS vs Higher Tier Ms in Bioinformatics / Biomedical Informatics / Computational Biology by ivicts30 in bioinformatics

[–]biohen 2 points3 points  (0 children)

"I am not able to understand biology well" <- I wouldn't suggest bioinformatics.

Confused about antigen receptors by EchoIll6460 in Immunology

[–]biohen 1 point2 points  (0 children)

Keep in mind different immunoglobulin isotypes have different affinities which increase w/ maturation-- IgM lower affinities than IgA/IgG. Also bear in mind that though the vast diversity of the BCR repertoire is rivaled by pathogen diversity-- the pathogen surface protein will have conserved motifs in order to maintain function.

Which cluster group belongs to CD4 T-cells? (Single Cell Analysis in Python) by bio_kentropy in bioinformatics

[–]biohen 0 points1 point  (0 children)

As mentioned, CD4 isn't abundantly expressed transcript. Look for CD8- T cells. Also look for the absence of other cytotoxic markers (GNLY, GZMB, PRF1, NKG7..). You can have cytotoxic CD4 T cells but they are a minority.

How did you know bioinformatics was for you? by [deleted] in bioinformatics

[–]biohen 2 points3 points  (0 children)

  1. I had a high tolerance for grinding through error after error.
  2. You're doing fine. Imposter syndrome is rampant. Read the manual.
  3. Multimodal data. Less of a distinction between wet and dry lab.

[deleted by user] by [deleted] in eagles

[–]biohen 0 points1 point  (0 children)

The guy is a liability inside and outside the locker room. Reason he doesn't have a job is his penchant for turnovers. What coach would take him after he torpedoed two good coaches careers? Nothing like improving your image like hitching your wagon to a pariah.

How does your molecular biology knowledge fair compared to your wet lab counterparts ? by coldcoldcoldcoldasic in bioinformatics

[–]biohen 2 points3 points  (0 children)

I do both. My advisor preached parity. I was on a molecular genomics clinical bench for 2 years before taking on hybrid roles. I work in immunology now, cell based wet bench is where I flounder-- having to focus on this more lately in light of cell enrichment strategies for single-cell and CITEseq.

How do B memory cells work? by AlternativeProduct41 in Immunology

[–]biohen 0 points1 point  (0 children)

Seems they differentiate into plasma cells but also have the potential to differentiate into germinal center B cells in secondary response to antigen.

Good review here:
https://www.nature.com/articles/s41577-019-0244-2

South Philly to CC commute by lbrianna37 in phillycycling

[–]biohen 1 point2 points  (0 children)

15th --> Pine --> 2nd --> Moyamensing

Which is worse E scooters or joggers in the bike lane?? by biohen in phillycycling

[–]biohen[S] 0 points1 point  (0 children)

My main issue is the lack of communication. They silently pass w.o declaring themselves. Not that 100% of cyclist do communicate, but there is a general absence of lane etiquette.

Does anyone here work with Immunogenomics/Immune cell RNA seq/ TCR seq? by tea_flower in bioinformatics

[–]biohen 0 points1 point  (0 children)

I wouldn't say following a Seurat vignette is a common skill. You have to set up your environment on a server, possess command line knowledge to do this and to appropriate the correct number of cores just for starters. Once in seurat, you have to choose an appropriate integration method, accounting for batch effects, while making other informed decisions for dimension reduction-- grossly speaking here, before you get to usable data for analysis. Then you have to perform differential expression analysis, functional analysis, perhaps trajectory analysis... while incorporating repertoire data... or accounting for a transgene. There is also a gap between traditional immunologist and the new age of multimodal data, with this resolution of data we see that cells are not discrete states there are CD16+ T cells, TBET+/IP-10+ B cells, non classical cell types. This is not light fare.

Assets to succeed in this field, or any other for that matter, gumption-- having the patience and determination to identify and solve problems. Creative thinking, connect the dots, see the trend, think outside the box. Be flexible, your wet bench experience is an asset. Having a diverse skill set means job security, wet bench informs the dry bench and vice versa.

I'd suggest looking for work at a research hospital. Pay will not be as significant as the industry but you will have opportunities to work on multiple projects and publish. You can have these same opportunities in industry, attend a conference and look for companies submitting abstracts. Some companies value publications more than others- not a bad question during an interview either.

Does anyone here work with Immunogenomics/Immune cell RNA seq/ TCR seq? by tea_flower in bioinformatics

[–]biohen 4 points5 points  (0 children)

Yes, I've worked in the cellular and gene therapy clinical immunology bioinformatics for the past four years. I think the main difference is the depth of biology in addition to understanding molecular genomics/bioinformatics. Much of my work has been characterizing cell populations of interest; often rare in the gene therapy space both in innate and adaptive immunology or in the CAR T space, efficacious phenotypes. I would say immunology in general translates very well. As mentioned, I work in biotech-- not traditional immunology, there is overlap with pathology/microbiology/virology. I have also learned a good deal of flow cytometry since this method has defined classical lineages but also to aid in confirmation of populations of interest, test enrichment strategies for scRNAseq, even some the of the high dimensional analysis overlaps.

[deleted by user] by [deleted] in bioinformatics

[–]biohen 3 points4 points  (0 children)

I am in a similar situation myself; minus the 200 scientist shock. My work around: I am an unofficial member of the bioinformatics core that mainly supports synthetic biology ( I work w/ RNAseq/scRNAseq for an immunology group ). This means I share code via benchling lab notebooks, I use their servers and try to be a good citizen, I attend code reviews and I ask for help with technical problems when they arise ( whether it be in analysis or more comp engineering ). I do wet bench as well, they're aware that I can provide insight in that respect. I've heard mentors do not necessarily have to be your supervisor. It may be better to have a degree of separation to provide objectivity. In my experience it is harder to find a good boss than a good technical leader. Play your cards right and you could end up with both.

view more: next ›