Principal computational scientist, Johnson&Johnson innovative Medicine
Bay area
Joined January 2016
- Tweets202
- Following75
- Followers174
- Likes1.6K
Our latest study out in eLife: This work integrates scRNAseq with genetic perturbation to map developmental trajectories and causal mechanisms in the brain. elifesciences.org/articles/1…
I am deeply grateful to @Garret and the Stuber lab for the opportunity to be part of the work.
Koichi Hashikawa retweeted
Excited to share Nicheformer! Led by @Alejandro__TL & @AnnaCSchaar, Nicheformer is a foundation model for single-cell & spatial omics. Its innovation is going beyond disassociated analysis to capture & predict local tissue context at single-cell level. biorxiv.org/content/10.1101/…
Koichi Hashikawa retweeted
Very excited to announce our new preprint together with Nikolai Hecker! Dive into our findings on the conserved regulatory codes shaping cell identity across species. 🧬 [1/n]
biorxiv.org/content/10.1101/…
Koichi Hashikawa retweeted
As my lab develops Seurat, I wanted to share some thoughts on the important Seurat and scanpy package selection preprint from @Josephmrich/@lpachter 🧵
Koichi Hashikawa retweeted
Excited to share that my graduate dissertation work is now finally live on bioarxiv! Take a look if you're interested in learning more about the lateral septum's role in opioid withdrawal: biorxiv.org/content/10.1101/…
Koichi Hashikawa retweeted
I’m so exited to share that Pixel-seq has been published! We describe a stamping method to scale production of polony gels with <1 um resolution for #spatialbiology and a clustering algorithm to segment cells based on their UMIs and transcript similarity. authors.elsevier.com/c/1g3VX…
Koichi Hashikawa retweeted
Here comes "spatial-ATAC-seq"!!! A wonderful collaboration between my lab at @YaleSEAS and @GoCasteloBranco at @karolinskainst
#epigenetics #spatialomics #spatialbiology
Spatial profiling of chromatin accessibility in mouse and human tissues | Nature nature.com/articles/s41586-0…
Koichi Hashikawa retweeted
Our scCUT&Tag-pro and scChromHMM manuscript is out @NatureBiotech! Led by @Bingjie_Zhang_ and @k3yavi, we use surface proteins to integrate data from six histone modifications, RNA and ATAC - and explore chromatin state heterogeneity in single cells: nature.com/articles/s41587-0…
Koichi Hashikawa retweeted
Our new preprint, led by @YUHANHAO2, introduces bridge integration: cross-modality alignment via a multiomic 'bridge' dataset.
We map single-cell ATAC-seq, methylation, CUT&Tag and CyTOF profiles onto scRNA-seq references- scaling to millions of cells.
biorxiv.org/content/10.1101/…
Koichi Hashikawa retweeted
We are excited to introduce CaRPool-seq, a new technology that utilizes Cas13 to perform combinatorial single-cell perturbation screens! Check it out, esp. if you're interested in simultaneously perturbing multiple genes and exploring genetic interactions: biorxiv.org/content/10.1101/…
Koichi Hashikawa retweeted
Interested in single cell genomics but need help getting started? Check out my lab's Single Cell Genomics Day on March 4. Talks will feature recent exciting computational and experimental advances and will be livestreamed at satijalab.org/scgd. Please RT/spread the word!
Koichi Hashikawa retweeted
Our next @cegs_ica virtual seminar is Nov 16 at 12PM EST. @Bingjie_Zhang_ and @k3yavi will introduce scCUT&Tag-pro and scChromHMM - tools to measure, integrate, and analyze histone modification profiles in single cells.
Free registration at: nygenome.zoom.us/meeting/reg…
Koichi Hashikawa retweeted
Very excited to have this out! Though this is "only" a perspective piece, I personally feel that this is my most important work yet. 1/15 authors.elsevier.com/c/1dy89…
Koichi Hashikawa retweeted
👇👇 @WhoIsMarkRossi is awesome!
Latest and final paper from @WhoIsMarkRossi‘s time in the lab. Mark is now at @RutgersU and is recruiting. Get in touch w/him if this work interests you.
authors.elsevier.com/a/1dtD6…
Koichi Hashikawa retweeted
Happy to share the last of my postdoc work. A huge thank you to the team of @gstuber @MarcusBasiri @koichihashikawa Yoshiko Hashikawa and Jill Liu (not on twitter) and collaborators at Stanford who made it possible 🧵1/6 authors.elsevier.com/c/1dtD6…
Koichi Hashikawa retweeted
Latest and final paper from @WhoIsMarkRossi‘s time in the lab. Mark is now at @RutgersU and is recruiting. Get in touch w/him if this work interests you.
authors.elsevier.com/a/1dtD6…
Koichi Hashikawa retweeted
Computational challenges and opportunities in spatially resolved transcriptomic data analysis
nature.com/articles/s41467-0…
Koichi Hashikawa retweeted
Are you or someone you know interested in studying hypothalamic regulation of feeding? Do you want to do cutting edge science in an inclusive and supportive environment? Apply to work with us today!
JOB ALERT! We are hiring a postdoc to study hypothalamic feeding circuits using 2p imaging and ephys.
APPLY HERE: jobs.rutgers.edu/postings/14…
more info: markrossilab.org
Koichi Hashikawa retweeted
Here is link to the paper: rdcu.be/cxgbj 🐵🧠
Distribution of brain oxytocin & vasopressin V1a receptors in chimpanzees pubmed.ncbi.nlm.nih.gov/3448…
"One notable difference is the lack of OXTR in reward regions such as the ventral pallidum and nucleus accumbens in chimpanzees, whereas OXTR is found in these regions in humans"
ALT Comparison of OXTR and AVPR1a binding across primates studied to date
Koichi Hashikawa retweeted
Want to genetically target neurons that integrate monosynaptic inputs from two upstream areas? A simple combination of AAV1 and INTRSECT makes it possible! Happy to share our new preprint. biorxiv.org/cgi/content/shor…