ASE analysis within your article (A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals)

I am writing to your regarding the code to analyse ASE in RNA-seq data present within this Article, specifically the beta diversity evaluation and application test. I was wondering if the code is available, I would like to apply it compare samples.

The code for calling allele-specific sites is available at

The specific scripts for the beta-binomial test are

Question regarding RNA-seq data uploaded to “Synapse”

I was referred to you by Micheal Gandal for a question I have regarding you RNA-seq data from the fascinating shared article "Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder"

I know you’ve uploaded the TPM data to to PsychEncode website – could you tell me if the data this file is normalized DER-02_PEC_Gene_expression_matrix_TPM

We didn’t run any quantile normalization on this file.

Request about Pubnet

I am looking for an easy-to-handle application to analyse collaborative networks in science, and I am very interested by Pubnet, that you published quite a while ago. Unfortunately, event if it looks very simple to use the web interface, after submitting a query with a author name, I always have a page indicating the pubmed xml was generated, but it is never analysed. It always blocks as this: (see image)

We’ve managed to revive pubnet. Please check it out.

Running FunSeq

I recently read your paper on Funseq, and I am pretty interested in using it in solving some of my interested questions regarding cortex plasticiy. However, I’m not very familiar with Linux/UNIX running environment for this software, and what I have is just a mac laptop….Could you give me some information about how I could use this software on a mac computer, or where I could find some useful information instructing me how I could use this software on a mac computer?

You should be able to download this software on a mac and use it.
You can download it from

Since you are not familiar with downloading software, have you tried to use the online version at .
You can upload your file and see what you get.

Asking or data used in finding processed psedogenes in the human genome

Recently, I was reading one of your papers about finding processed pseudogenes published in 2003: "Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome". Because I want to find processed pseudogenes among several recently released mammalian genomes. Your paper is very interesting and helpful for my work. And to ensure the method i grasped is correct, I want to use your original data to redo your analysis process.

But I come across a problem when I download nonredundant human proteome set from the EBI Web site. Because the data was published in June 2002, and I can’t successfully download them from EBI website. Here I write to you with the hope of getting nonredundant human proteome set you used released in June 2002. Although I know many years have passed since the paper was published and you may also lost the original data, I still want to have a try!

The data associated with the paper is here: You can also find the latest human pseudogene annotation here:

HingeAtlas (2007)

I am reading your Hinge Atlas (2007) paper.
I searched for your dataset to study the pdb structures you used and their
hinge residues, but I could not download it from the page:
Could you please send a file if it is possible by email, or please check and
fix if there is a bug on the web page.

Please try the Hinge Atlas Gold while we investigate the webpage. This may take time.