{ "id": 346686, "title": "Computational Challenges using Single-Cell by Kagglers A. Chervov and A. Zinovyev", "url": "/competitions/open-problems-multimodal/discussion/346686", "author_name": "", "post_date": "2022-08-20T22:03:26.296580700Z", "votes": 14, "comment_count": 7, "views": 0, "content": "

Computational challenges of cell cycle analysis using single cell transcriptomics

\n

Authors: Alexander Chervov, Andrei Zinovyev - https://doi.org/10.48550/arXiv.2208.05229
\nSubmitted on 10 Aug 2022

\n

\"The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle transcriptome dynamics in an unprecedented range of conditions (cell types and perturbations), with thousands of publicly available datasets.\"

\n

\"There the authors reviewed the main computational tasks in such analysis: 1) identification of cell cycle phases, 2) pseudotime inference, 3) identification and profiling of cell cycle-related genes, 4) removing cell cycle effect, 5) identification and analysis of the G0 (quiescent) cells. They reviewed seventeen software packages that are available today for the cell cycle analysis using scRNA-seq data. Despite huge progress achieved, none of the packages can produced complete and reliable results with respect to all aforementioned tasks.\"

\n

\"One of the major difficulties for existing packages is distinguishing between two patterns of cell cycle transcriptomic dynamics: normal and characteristic for embryonic stem cells (ESC), with the latter one shared by many cancer cell lines. Moreover, some cell lines are characterized by a mixture of two subpopulations, one following the standard and one ESC-like cell cycle, which makes the analysis even more challenging. In conclusion, the authors discussed the difficulties of the analysis of cell cycle-related single cell transcriptome and provided certain guidelines for the use of the existing methods.\"

\n

https://arxiv.org/abs/2208.05229

\n

Congratulations Alexander Chervov and Andrei Zinovyev for your brilliant paper.

\n

You're an inspiration for Bioinformatics and Kagglers.

", "messages": [ { "id": "1907550", "postDate": "08/20/2022 22:03:26", "content": "

Computational challenges of cell cycle analysis using single cell transcriptomics

\n

Authors: Alexander Chervov, Andrei Zinovyev - https://doi.org/10.48550/arXiv.2208.05229
\nSubmitted on 10 Aug 2022

\n

\"The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle transcriptome dynamics in an unprecedented range of conditions (cell types and perturbations), with thousands of publicly available datasets.\"

\n

\"There the authors reviewed the main computational tasks in such analysis: 1) identification of cell cycle phases, 2) pseudotime inference, 3) identification and profiling of cell cycle-related genes, 4) removing cell cycle effect, 5) identification and analysis of the G0 (quiescent) cells. They reviewed seventeen software packages that are available today for the cell cycle analysis using scRNA-seq data. Despite huge progress achieved, none of the packages can produced complete and reliable results with respect to all aforementioned tasks.\"

\n

\"One of the major difficulties for existing packages is distinguishing between two patterns of cell cycle transcriptomic dynamics: normal and characteristic for embryonic stem cells (ESC), with the latter one shared by many cancer cell lines. Moreover, some cell lines are characterized by a mixture of two subpopulations, one following the standard and one ESC-like cell cycle, which makes the analysis even more challenging. In conclusion, the authors discussed the difficulties of the analysis of cell cycle-related single cell transcriptome and provided certain guidelines for the use of the existing methods.\"

\n

https://arxiv.org/abs/2208.05229

\n

Congratulations Alexander Chervov and Andrei Zinovyev for your brilliant paper.

\n

You're an inspiration for Bioinformatics and Kagglers.

", "rawMarkdown": "#Computational challenges of cell cycle analysis using single cell transcriptomics\n\nAuthors: Alexander Chervov, Andrei Zinovyev - https://doi.org/10.48550/arXiv.2208.05229\nSubmitted on 10 Aug 2022\n\n\"The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle transcriptome dynamics in an unprecedented range of conditions (cell types and perturbations), with thousands of publicly available datasets.\"\n\n\"There the authors reviewed the main computational tasks in such analysis: 1) identification of cell cycle phases, 2) pseudotime inference, 3) identification and profiling of cell cycle-related genes, 4) removing cell cycle effect, 5) identification and analysis of the G0 (quiescent) cells. They reviewed seventeen software packages that are available today for the cell cycle analysis using scRNA-seq data. Despite huge progress achieved, none of the packages can produced complete and reliable results with respect to all aforementioned tasks.\"\n\n\"One of the major difficulties for existing packages is distinguishing between two patterns of cell cycle transcriptomic dynamics: normal and characteristic for embryonic stem cells (ESC), with the latter one shared by many cancer cell lines. Moreover, some cell lines are characterized by a mixture of two subpopulations, one following the standard and one ESC-like cell cycle, which makes the analysis even more challenging. In conclusion, the authors discussed the difficulties of the analysis of cell cycle-related single cell transcriptome and provided certain guidelines for the use of the existing methods.\"\n\nhttps://arxiv.org/abs/2208.05229\n\nCongratulations Alexander Chervov and Andrei Zinovyev for your brilliant paper. \n\nYou're an inspiration for Bioinformatics and Kagglers.", "votes": null }, { "id": "1909126", "postDate": "08/22/2022 10:56:23", "content": "

Can you share the kaggle profile of these authors?

", "rawMarkdown": "Can you share the kaggle profile of these authors?", "votes": null }, { "id": "1909204", "postDate": "08/22/2022 12:25:41", "content": "

Better take a look of Alexander's code:

\n

On this competition:
\nhttps://www.kaggle.com/code/alexandervc/mmscel-eda-bioinfo

\n

https://www.kaggle.com/code/alexandervc/use-h5py-for-huge-h5-file-backing-it-on-disk

\n

That Notebook below was made by both Researchers however I was Not able to find Andrei Zinovyev on Kaggle
\nhttps://www.kaggle.com/code/alexandervc/cell-cycle-1-broad-institute-collection

\n

I hope it helps. Alexander has more than 300 Notebooks, take a look and learn with his amazing Bioinformatics work.

", "rawMarkdown": "Better take a look of Alexander's code:\n\nOn this competition:\nhttps://www.kaggle.com/code/alexandervc/mmscel-eda-bioinfo\n\nhttps://www.kaggle.com/code/alexandervc/use-h5py-for-huge-h5-file-backing-it-on-disk\n\nThat Notebook below was made by both Researchers however I was Not able to find Andrei Zinovyev on Kaggle\nhttps://www.kaggle.com/code/alexandervc/cell-cycle-1-broad-institute-collection\n\nI hope it helps. Alexander has more than 300 Notebooks, take a look and learn with his amazing Bioinformatics work.", "votes": null }, { "id": "1909206", "postDate": "08/22/2022 12:28:49", "content": "

cheers thank you for the information

", "rawMarkdown": "cheers thank you for the information", "votes": null }, { "id": "1909241", "postDate": "08/22/2022 13:06:41", "content": "

Andrei Zinovyev, Researcher at Institut Curie, Paris, Île-de-France, France:

\n

https://www.kaggle.com/andreizinovyev

", "rawMarkdown": "Andrei Zinovyev, Researcher at Institut Curie, Paris, Île-de-France, France:\n\nhttps://www.kaggle.com/andreizinovyev", "votes": null }, { "id": "1909243", "postDate": "08/22/2022 13:08:44", "content": "

Hey, @alexandervc if I want to be on your team for any future research. Is there any possibility?

", "rawMarkdown": "Hey, @alexandervc if I want to be on your team for any future research. Is there any possibility?", "votes": null }, { "id": "1917016", "postDate": "08/28/2022 10:59:38", "content": "

Hi, Abdul,
\nThank you for your kind words.
\nPlease take a look:

\n

https://www.kaggle.com/competitions/open-problems-multimodal/discussion/348293

\n

https://www.kaggle.com/competitions/open-problems-multimodal/discussion/348294

\n

https://www.kaggle.com/competitions/open-problems-multimodal/discussion/348295

", "rawMarkdown": "Hi, Abdul,\nThank you for your kind words.\nPlease take a look:\n\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348293\n\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348294\n\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348295", "votes": null }, { "id": "2979739", "postDate": "09/05/2024 05:59:04", "content": "

Is any open problem competition in 2024 year?

", "rawMarkdown": "Is any open problem competition in 2024 year?", "votes": null } ], "comments": [ { "id": 1909126, "author_name": "abdulbasitniazi", "author_url": "", "post_date": "08/22/2022 10:56:23", "content": "

Can you share the kaggle profile of these authors?

", "votes": null, "replies": [ { "id": 1909204, "author_name": "mpwolke", "author_url": "", "post_date": "08/22/2022 12:25:41", "content": "

Better take a look of Alexander's code:

\n

On this competition:
\nhttps://www.kaggle.com/code/alexandervc/mmscel-eda-bioinfo

\n

https://www.kaggle.com/code/alexandervc/use-h5py-for-huge-h5-file-backing-it-on-disk

\n

That Notebook below was made by both Researchers however I was Not able to find Andrei Zinovyev on Kaggle
\nhttps://www.kaggle.com/code/alexandervc/cell-cycle-1-broad-institute-collection

\n

I hope it helps. Alexander has more than 300 Notebooks, take a look and learn with his amazing Bioinformatics work.

", "votes": null, "replies": [] }, { "id": 1909206, "author_name": "abdulbasitniazi", "author_url": "", "post_date": "08/22/2022 12:28:49", "content": "

cheers thank you for the information

", "votes": null, "replies": [] }, { "id": 1909241, "author_name": "alexandervc", "author_url": "", "post_date": "08/22/2022 13:06:41", "content": "

Andrei Zinovyev, Researcher at Institut Curie, Paris, Île-de-France, France:

\n

https://www.kaggle.com/andreizinovyev

", "votes": null, "replies": [] }, { "id": 1909243, "author_name": "abdulbasitniazi", "author_url": "", "post_date": "08/22/2022 13:08:44", "content": "

Hey, @alexandervc if I want to be on your team for any future research. Is there any possibility?

", "votes": null, "replies": [] }, { "id": 1917016, "author_name": "alexandervc", "author_url": "", "post_date": "08/28/2022 10:59:38", "content": "

Hi, Abdul,
\nThank you for your kind words.
\nPlease take a look:

\n

https://www.kaggle.com/competitions/open-problems-multimodal/discussion/348293

\n

https://www.kaggle.com/competitions/open-problems-multimodal/discussion/348294

\n

https://www.kaggle.com/competitions/open-problems-multimodal/discussion/348295

", "votes": null, "replies": [] }, { "id": 2979739, "author_name": "", "author_url": "", "post_date": "09/05/2024 05:59:04", "content": "

Is any open problem competition in 2024 year?

", "votes": null, "replies": [] } ] } ], "raw_markdown_by_id": { "1907550": "#Computational challenges of cell cycle analysis using single cell transcriptomics\n\nAuthors: Alexander Chervov, Andrei Zinovyev - https://doi.org/10.48550/arXiv.2208.05229\nSubmitted on 10 Aug 2022\n\n\"The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle transcriptome dynamics in an unprecedented range of conditions (cell types and perturbations), with thousands of publicly available datasets.\"\n\n\"There the authors reviewed the main computational tasks in such analysis: 1) identification of cell cycle phases, 2) pseudotime inference, 3) identification and profiling of cell cycle-related genes, 4) removing cell cycle effect, 5) identification and analysis of the G0 (quiescent) cells. They reviewed seventeen software packages that are available today for the cell cycle analysis using scRNA-seq data. Despite huge progress achieved, none of the packages can produced complete and reliable results with respect to all aforementioned tasks.\"\n\n\"One of the major difficulties for existing packages is distinguishing between two patterns of cell cycle transcriptomic dynamics: normal and characteristic for embryonic stem cells (ESC), with the latter one shared by many cancer cell lines. Moreover, some cell lines are characterized by a mixture of two subpopulations, one following the standard and one ESC-like cell cycle, which makes the analysis even more challenging. In conclusion, the authors discussed the difficulties of the analysis of cell cycle-related single cell transcriptome and provided certain guidelines for the use of the existing methods.\"\n\nhttps://arxiv.org/abs/2208.05229\n\nCongratulations Alexander Chervov and Andrei Zinovyev for your brilliant paper. \n\nYou're an inspiration for Bioinformatics and Kagglers.", "1909126": "Can you share the kaggle profile of these authors?", "1909204": "Better take a look of Alexander's code:\n\nOn this competition:\nhttps://www.kaggle.com/code/alexandervc/mmscel-eda-bioinfo\n\nhttps://www.kaggle.com/code/alexandervc/use-h5py-for-huge-h5-file-backing-it-on-disk\n\nThat Notebook below was made by both Researchers however I was Not able to find Andrei Zinovyev on Kaggle\nhttps://www.kaggle.com/code/alexandervc/cell-cycle-1-broad-institute-collection\n\nI hope it helps. Alexander has more than 300 Notebooks, take a look and learn with his amazing Bioinformatics work.", "1909206": "cheers thank you for the information", "1909241": "Andrei Zinovyev, Researcher at Institut Curie, Paris, Île-de-France, France:\n\nhttps://www.kaggle.com/andreizinovyev", "1909243": "Hey, @alexandervc if I want to be on your team for any future research. Is there any possibility?", "1917016": "Hi, Abdul,\nThank you for your kind words.\nPlease take a look:\n\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348293\n\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348294\n\nhttps://www.kaggle.com/competitions/open-problems-multimodal/discussion/348295", "2979739": "Is any open problem competition in 2024 year?" }, "source": "meta" }