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Apr 7

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Apr 7

Alin Moga, Mario Medvedovic2

Feb 10

Just wanted to let you know that you sent this to a wrong email address. ilincs team. On Sun, Feb 8,

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Just wanted to let you know that you sent this to a wrong email address. ilincs team. On Sun, Feb 8,

Feb 10

Bharath, Ananya, mario.me...@gmail.com3

12/9/25

iLINCS Signature Analysis - Server Error

Hi Ananya, The problem that you encountered is fixed now. Thanks again for alerting us to it and let

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iLINCS Signature Analysis - Server Error

Hi Ananya, The problem that you encountered is fixed now. Thanks again for alerting us to it and let

12/9/25

Elmezayen, Ammar - (elmezayen), mario.me...@gmail.com2

12/8/25

Request for Bulk Access to Signature Data for All Perturbagens in L1000 Dataset

Hi Ammar, Sorry for the slow follow up. iLINCS at this point does not provide bulk download of all

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Request for Bulk Access to Signature Data for All Perturbagens in L1000 Dataset

Hi Ammar, Sorry for the slow follow up. iLINCS at this point does not provide bulk download of all

12/8/25

Elmezayen, Ammar - (elmezayen)

6/19/25

Request for Guidance on Downloading L1000 Signature Data for Multiple FDA-Approved Drugs

Dear iLINCS Team, I hope this email finds you well. My name is Dr. Ammar Elmezayen, and I'm a

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Request for Guidance on Downloading L1000 Signature Data for Multiple FDA-Approved Drugs

Dear iLINCS Team, I hope this email finds you well. My name is Dr. Ammar Elmezayen, and I'm a

6/19/25

Noval, Cam, Michal Kouril2

4/22/25

Question About iLINCS API Access to Signature Data

Hi Cameron, I'm curious where did you see the documentation for the endpoints you mentioned (eg /

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Question About iLINCS API Access to Signature Data

Hi Cameron, I'm curious where did you see the documentation for the endpoints you mentioned (eg /

4/22/25

Ines, Michal Kouril2

3/20/25

Hi Inês, Thanks for getting in touch -- we currently don't have a commercial license. Please

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Hi Inês, Thanks for getting in touch -- we currently don't have a commercial license. Please

3/20/25

James Hardwick, Michal Kouril2

3/20/25

SSL certificate GREIN

Please let us know if you are still experiencing issues. Thanks, Michal On Monday, May 1, 2023 at 1:

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SSL certificate GREIN

Please let us know if you are still experiencing issues. Thanks, Michal On Monday, May 1, 2023 at 1:

3/20/25

Amy McCarthy, Michal Kouril2

2/27/25

Hi Amy, Thanks for getting in touch. We recently switched from http:// to https:// -- could you

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Hi Amy, Thanks for getting in touch. We recently switched from http:// to https:// -- could you

2/27/25

María Ponce Rodríguez

5/10/24

Gene list maximum size 500

Hello! We have being trying to submit a gene list for a signature enrichment (http://www.ilincs.org/

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Gene list maximum size 500

Hello! We have being trying to submit a gene list for a signature enrichment (http://www.ilincs.org/

5/10/24

7/5/23

method of knockdown and overexpression

Hello, I am emailing in regards to a question about iLINCS datasets. What methods are used to achieve

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method of knockdown and overexpression

Hello, I am emailing in regards to a question about iLINCS datasets. What methods are used to achieve

7/5/23

6/9/23

Error when launching SPIA Analysis on differential expression Signature

I created a signature based on ER status from the TCGA_BRCA_RNASeqV2 dataset. http://www.ilincs.org/

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Error when launching SPIA Analysis on differential expression Signature

I created a signature based on ER status from the TCGA_BRCA_RNASeqV2 dataset. http://www.ilincs.org/

6/9/23

Peter Arnesen, mario.me...@gmail.com2

4/16/23

Connected compound perturbations in R/API different than submitted to web

Hi Peter, Not sure what went wrong with your analysis. iLINCS API and UIs should generally give

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Connected compound perturbations in R/API different than submitted to web

Hi Peter, Not sure what went wrong with your analysis. iLINCS API and UIs should generally give

4/16/23

Guia Guffanti, mario.me...@gmail.com2

3/24/23

problem with file jnlp

Hello, I am really sorry the slow followup. We have had troubles with maintaining the Java TreeView

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problem with file jnlp

Hello, I am really sorry the slow followup. We have had troubles with maintaining the Java TreeView

3/24/23

Eamon Fitzgerald, mario.me...@gmail.com2

1/14/23

Hi Eamon, The enrichment results (z-scores) are based on two-tailed p-values of expression changes of

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Hi Eamon, The enrichment results (z-scores) are based on two-tailed p-values of expression changes of

1/14/23

Bark, Steven Joel, mario.me...@gmail.com2

1/10/23

Problems With TreeMap View .jnlp Files

Hello, I am really sorry about this. We have had troubles with maintaining the Java TreeView

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Problems With TreeMap View .jnlp Files

Hello, I am really sorry about this. We have had troubles with maintaining the Java TreeView

1/10/23

Kinnaird, Brian T, mario.me...@gmail.com2

9/29/22

iLINCS relation to CMap at clue.io

Hello, iLINCS contains original LINCS project L1000 signatures released through GEO and does not

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iLINCS relation to CMap at clue.io

Hello, iLINCS contains original LINCS project L1000 signatures released through GEO and does not

9/29/22

Andrea Matlock, mario.me...@gmail.com2

9/13/22

Re: Update: NeuroLINCS PWG manuscript and need DCIC LINCS data portal confirmation

Hi Andrea, The data should still be downloaded from LINCS LDP (https://lincsportal.ccs.miami.edu/dcic

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Re: Update: NeuroLINCS PWG manuscript and need DCIC LINCS data portal confirmation

Hi Andrea, The data should still be downloaded from LINCS LDP (https://lincsportal.ccs.miami.edu/dcic

9/13/22

devi priya, mario.me...@gmail.com2

8/26/22

Regarding NEUROLINCS platform

For specific questions regarding NeuroLINCS project and data please refer to their web page: http://

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Regarding NEUROLINCS platform

For specific questions regarding NeuroLINCS project and data please refer to their web page: http://

8/26/22

Davide Vitiello, mario.me...@gmail.com2

5/31/22

Number of Genes in iLINCS group analysis

I am sorry for the slow reply - had some technical issues with my gmail. Could you be a little more

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Number of Genes in iLINCS group analysis

I am sorry for the slow reply - had some technical issues with my gmail. Could you be a little more

5/31/22

Lape, Mike (lapema), mbfazel2

5/30/22

Error with connected perturbations analysis

Hi Mike, I'm not sure if you have figured this out yet, but here is the answer: yes, there should

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Error with connected perturbations analysis

Hi Mike, I'm not sure if you have figured this out yet, but here is the answer: yes, there should

5/30/22

CHEN Shiau Haln, mario.me...@gmail.com2

3/29/22

iLINCS Error when uploading signatures

Hello Haln, I checked all upload functionalities and they seem to be working fine. Would you mine

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iLINCS Error when uploading signatures

Hello Haln, I checked all upload functionalities and they seem to be working fine. Would you mine

3/29/22

Hamoud, Abdul-Rizaq Ali, mario.me...@gmail.com2

2/25/22

ILINCS dataset upload

Hello Abdul, Please correct me if I am wrong, but looks like you are trying to use a system (

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ILINCS dataset upload

Hello Abdul, Please correct me if I am wrong, but looks like you are trying to use a system (

2/25/22

Mahdavian, Elahe, Medvedovic, Mario (medvedm)2

10/22/21

iLINCS- two group Proteo-transcriptomic analysis

Dear Elahe, Unfortunately the CCLE dataset, to the best of my knowledge, does not contain “normal

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iLINCS- two group Proteo-transcriptomic analysis

Dear Elahe, Unfortunately the CCLE dataset, to the best of my knowledge, does not contain “normal

10/22/21

Su, Shang, mbfazel2

8/19/21

Error in loading signatures to iLINCS

This answer might help you (look for "Signature Upload Error" in google group) Signature

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Error in loading signatures to iLINCS

This answer might help you (look for "Signature Upload Error" in google group) Signature

8/19/21

Charlotte Jendresen (DK), mario.me...@gmail.com2

6/28/21

Conversion of data to X2K

Dear Charlotte, I apologize for belated reply. For some reason I missed your message. iLINCS

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Conversion of data to X2K

Dear Charlotte, I apologize for belated reply. For some reason I missed your message. iLINCS

6/28/21

Breidenbach, Joshua David, mario.me...@gmail.com2

6/28/21

Signature Upload Error

Hi Josh, We went through all steps that you outlined, including submission of the file you shared and

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Signature Upload Error

Hi Josh, We went through all steps that you outlined, including submission of the file you shared and

6/28/21

3/19/21

Hello ilincs.org Team, Hope you are doing great. I feel so curious to know your thought and help you

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Hello ilincs.org Team, Hope you are doing great. I feel so curious to know your thought and help you

3/19/21

Yojana Gadiya, Mario Medvedovic2

2/21/21

Dear Yoyana, At this moment iLINCS does not facilitate download of the whole collection of signatures

unread,

Dear Yoyana, At this moment iLINCS does not facilitate download of the whole collection of signatures

2/21/21

Hendrik Weisser, Mario Medvedovic2

2/21/21

Disease related signatures and treatment/baseline conditions

Dear Hendrik, You are correct about the ordering of the "Treatment" and "control"

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Disease related signatures and treatment/baseline conditions

Dear Hendrik, You are correct about the ordering of the "Treatment" and "control"

2/21/21

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