PCOMPBIOL-D-25-00805

Sparse deconvolution of cell type medleys in spatial transcriptomics

PLOS Computational Biology

Dear Dr. Sogunmez Erdogan,

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We look forward to receiving your revised manuscript.

Kind regards,

Ilya Ioshikhes

Section Editor

PLOS Computational Biology

Ilya Ioshikhes

Section Editor

PLOS Computational Biology

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: Thank the authors for addressing my comments!

Reviewer #2: Dear authors,

Many thanks for the updated draft. I am particularly appreciative of the time and effort that you took to make these changes, and the associated responses to the review comments. I am satisfied that these modifications mitigate the concerns raised previously. I have a few further minor suggestions regarding the text, but none of these issues compromise the scientific content of the paper.

l16: Maybe split this into two sentences here '..datasets. Neglecting ... results in increased noise'

l47: 'accurately infer deconvolutions...' - deconvolutions as a noun sounds a little weird, maybe '...accurately perform deconvolution, accurately estimating underlying cell-type composition, from observations'?

l77: 'a high throughput sequencing' - remove 'a'

l75: 'targeting' sounds strange - perhaps 'intending' or 'aiming'?

l190: Maybe break the sentence into two '..boundaries. This is expecially problematic in...'

l591: It's not super clear what 'visualization' here refers to - maybe 'characterization' instead?

l603: Maybe 'The heart ventricle anatomy is depicted in yellow.'? (And similar for l613)

l812: According to HGNC, C4orf48 is now apparently called NICOL1. I'm not sure what would be more consistent in this case (maybe leaving it as what it was called in the original paper is better), but it would be good to make a note somewhere.

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Reviewer #1: None

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: No

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Dear Assist. Prof. Sogunmez Erdogan,

We are pleased to inform you that your manuscript 'Sparse deconvolution of cell type medleys in spatial transcriptomics' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

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Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Ilya Ioshikhes

Section Editor

PLOS Computational Biology

Ilya Ioshikhes

Section Editor

PLOS Computational Biology

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