Benjamin James

Ph.D student studying computational biology with @manoliskellis at @MIT_CSAIL @BroadInstitute | BS ‘19 @utulsa
Views are my own.

[Benjamin James @__ben_james__]

@epigenci Congrats on the great paper, very interesting! Can you post the edgeR/DESeq2 supplementary figure code to the GitHub as well? I’m wondering how the offsets differ from the default library size * norm factors or size factors. Thanks!

[Benjamin James @__ben_james__]

@ben_lengerich @UWMadisonSTATS @manoliskellis @ericxing Congrats and well earned!!

[Benjamin James @__ben_james__]

@jsxlei Congrats Lei!!

[Zunpeng Liu @ZunpengLiu]

Really fortunate to work with the amazing and lovely team! 😊 ❤️ Thank you so much Kellis lab family! 🙏 🫶

[Manolis Kellis @manoliskellis]

Don't miss @ZunpengLiu 's #ASHG talk on #SingleCell #MultiRegion #Epigenomic dissection of #Alzheimers next in Room 207A/Level 2 (11:30am) #ASHG23
Integrate: 576 samples, 2.3M cells (1.5M #scRNA x 900k #scATAC), 6 brain regions, 30 cell types and subtypes
Results: 419k regulatory elements, active/repressed compartments, Epigenome Erosion, Transposon Reactivation, Entorhinal Cortex & Hippocampus selective epigenomic vulnerability,
Team: @ZunpengLiu, @__Ben_James__, @Xushen18, @Carles_Boix, #KikiGalani, #LiLunHo in @DrLiHueiTsai and @ManolisKellis labs.
Very proud of the whole team at @MIT, @BroadInstitute, @MIT_CSAIL, @MIT_Picower, @MITEECS, @MIT_SCC
More info: https://t.co/VobNG66sQI
Big thanks to: @NIH, @NIHAging, @CureAlzheimers

[Cell @CellCellPress]

In the latest issue! Epigenomic dissection of Alzheimer’s disease pinpoints causal variants and reveals epigenome erosion https://t.co/173QfdchSu

[Lei Hou侯磊 @HouGroup_sysGxG]

Exciting to see our work is out: Epigenomic regulation could reveal function of genetic variants with context information.
Very grateful to be in such a great team! @Xushen18 @manoliskellis @broadinstitute
Pls check openings in my new lab (https://t.co/hJEdleU0Km) @BUMedicine

[Manolis Kellis @manoliskellis]

Proud to share our #eGTEx multi-tissue dissection of #enhancer H3K27ac across 387 brain, muscle, heart, and lung samples from #GTEx in @NatureGenet
#eQTLs #haQTLs #SexDiffs #Epigenomics #GWAS #linking
Paper: https://t.co/5clMtduwWf (H3K27ac, today)
News: https://t.co/XImwpihTKT
m6A paper: https://t.co/CJPvNh4GOE (2021)
@MIT @MIT_CSAIL @BroadInstitute @MITEECS @MIT_SCC @harvard @harvardmed @GTExPortal

[Massachusetts Institute of Technology (MIT) @MIT]

Decoding the complexity of Alzheimer’s disease: By analyzing epigenomic and gene expression changes that occur in Alzheimer’s disease, researchers identify cellular pathways that could become new drug targets. https://t.co/Ao1QPgjoCt

[Vishnu Dileep @vishnudileep200]

Excited to share our work, out today @CellCellPress.
We show that DNA double-strand break accumulation leads to mosaic gene fusions and 3D genome disruption in human samples and mouse models with Alzheimer's disease pathology.
https://t.co/5rPlP6rlsj

[Eric Topol @EricTopol]

A remarkable tour de force on multi-omic spatial biology of #Alzheimers disease with 4(!) @CellCellPress articles and the cover

[MIT Picower Institute @MIT_Picower]

Four (!) papers in Cell today co-led by the lab of @DrLiHueiTsai offer the most detailed picture yet of the genetic and molecular underpinnings of Alzheimer’s. https://t.co/etjAnULESl @ScienceMIT @mitbrainandcog #alzheimers #neuroscience

[Manolis Kellis @manoliskellis]

Paper 2 by @Xushen18 @__ben_james__ #CarlesBoix et al reports the largest #SingleCell #Epigenomic atlas of #Alhzeimers across 850k #scATAC cells and 92 post-mortem samples, enabling:
1. #RegulatoryGenomics of TF-Enhancer-TargetGene single-cell links by multi-omics integration and module analysis
2. #GWAS dissection of #AD #genetics loci in microglia and upstream TFs SPI1, ELF2, RUNX1
3. #scQTL analysis of ATAC-QTLs for AD variant circuitry and prioritization
4. #EpigenomeErosion in late-stage AD with global accessibility upheavals and cell identity loss
https://t.co/ztNJBEjrAO

[Manolis Kellis @manoliskellis]

Immensely proud to share our four papers on #SingleCell dissection of #Alzheimers Disease coming out in @CellCellPress today, reporting 2.3M #scRNA profiles and 850k #scATAC profiles across 427 post-mortem human brain samples from AD and non-AD donors in a wonderful #interdisciplinary collaboration with @DrLiHueiTsai between @MIT @MIT_Picower @MIT_CSAIL @BroadInstitute @RushUniversity
Paper 1: scRNA + vulnerability + resilience https://t.co/I7cmizyj9C
Paper 2: scATAC + GWAS + Epigenome Erosion https://t.co/bdtlu9bWDr
Paper 3: Microglia States + reprogramming https://t.co/NzEJF1wY3t
Paper 4: DNA damage + gene fusions https://t.co/hIY1tMMhLo
MIT News: https://t.co/oLDuBBb45S
Issue: https://t.co/Mup3orjhcl
News & Views: https://t.co/xQk5mepDqz

[Matheus Victor @MatBVictor]

This issue of Cell comes with 3 other papers from collaborations across the labs of @DrLiHueiTsai @manoliskellis 🔥🔥🔥

Check out the cover art designed by our very own Carles Boix!

[Cell @CellCellPress]

The new issue is out! Just in time for #WorldAlzheimersMonth, Cell features four articles that together demonstrate the genomic, epigenomic, and transcriptomic dysregulations underpinning Alzheimer's disease at single-cell resolution across cell types.

To read more click here👉https://t.co/DWf0VlDvUt

[Matheus Victor @MatBVictor]

What do you do when you have 2.3 million single-cell transcriptomes from 427 human brains with varying degrees of AD pathology?

You spend 3 years exploring the microglia cluster obviously!!💁🏻‍♂️

Excited to share our work out today @CellCellPress !

https://t.co/Emu0mTPUKf

[Jiekun (Jackie) @yangjiekun]

Please RT that the Yang Lab will be open on 1/1/24 @RutgersU and is seeking talented individuals for various positions!! @RutgersResearch @RutgersSAS

Postdoc | Ph.D. Student | Research Scientist | Lab Manager | Research Assistant More details: https://t.co/4Y5VIjrfHN

[Benjamin James @__ben_james__]

@ChoudharyLabCPR @NatureGenet @TakeoNarita80 Amazing paper with great implications for the field!

[Benjamin James @__ben_james__]

@ZunpengL @Faulkner_Lab @CellCellPress Important distinction that the LP WT hMPCs used for RNA-seq + WGBS analysis are pre-senescent which can be easily missed!