User: Ashwini Patil

gravatar for Ashwini Patil
Reputation:
20
Status:
New User
Location:
Japan/Tokyo/Combinatics Inc.
Website:
https://www.combinatic...
Last seen:
2 months, 1 week ago
Joined:
5 months, 1 week ago
Email:
a******@combinatics.com

I am a scientist and entrepreneur working in bioinformatics for over 20 years. I recently transitioned out of academia from my faculty position at the University of Tokyo to start a bioinformatics company, Combinatics. I am currently developing a cell type marker database, CellKb. I also maintain the open source protein-protein interaction database, HitPredict, since 2004.

Posts by Ashwini Patil

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Annotation of Single Cell Clusters
... Take a look at the [CellKb][1] database. You can enter a ranked gene list and get matching cell types previously published in literature through the web interface. Matching of the query gene list to other cell types is performed using a variation of the rank bias overlap algorithm. CellKb contains ...
written 3 months ago by Ashwini Patil20
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Tool: CellKb 2.0: A database of cell type marker gene sets
... **[CellKb][1]** **- a database of cell type markers** ---------------------------------------- CellKb is a knowledgebase of cell type marker gene sets **manually collected** from scientific literature and annotated with cell, tissue and disease ontologies. **Contents** ------------------- - 22, ...
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Comment: C: Cell Type Marker Databases?
... Thanks for the examples. That helps! ...
written 3 months ago by Ashwini Patil20
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Comment: C: Cell Type Marker Databases?
... Those are all very pertinent points and excellent suggestions. As an ex-academic myself, I actually agree with you. Ideally, I would like CellKb to be freely accessible to as many academics as possible and I am trying to figure out a model that will make it sustainable over the long term. ...
written 3 months ago by Ashwini Patil20
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Comment: C: Cell Type Marker Databases?
... CellKb is a collection of marker gene sets published in literature and uses a rank-based overlap method to identify gene sets that match a query gene list in your search. You can download the list of marker gene sets that match with your query list from CellKb along with the source publication. This ...
written 3 months ago by Ashwini Patil20
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Answer: A: Cell Type Marker Databases?
... Try CellKb https://cellkb.combinatics.com. It contains about 19,000 cell type signatures manually collected from literature and extensively curated. We are making mouse cell type signatures available for free for one month. Please get in touch with me for extended access. ...
written 5 months ago by Ashwini Patil20

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