Moderator: Qdjm

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Qdjm1.9k
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Toronto
Website:
http://morrislab.med.u...
Last seen:
1 year, 9 months ago
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7 years ago
Email:
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I'm an associate professor in computational biology at the University of Toronto. I'm particularly proud of our GeneMANIA webserver for interaction networks, gene queries and gene function prediction.

Posts by Qdjm

<prev • 103 results • page 1 of 11 • next >
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Answer: A: Isoform Reconstruction
... As a computational biologist who understands a bit about how these programs work but who has never worked with this data, I'm not comfortable with any isoform reconstructions yet unless the splicing graph has only has one or a small number of possible isoforms. In most RNA-seq technologies, the rea ...
written 5.1 years ago by Qdjm1.9k
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Comment: C: How Does A High Gc Content Cause Waviness?
... Hi seidel, thanks for your comments and I agree completely. The example I was thinking of is junction arrays for detecting alternative splice junctions in which there is limited scope for Tm optimization. Tiling arrays, by virtue of the fact that the probes need to target particular regions, are als ...
written 5.2 years ago by Qdjm1.9k
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Comment: C: How Does A High Gc Content Cause Waviness?
... I don't follow your arguments and there's a good chance I don't understand the chemistry but the observation that higher Tm leads to higher probe intensity given the same concentration of the target is certainly true for mRNA expression arrays. ...
written 5.2 years ago by Qdjm1.9k
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Answer: A: How Does A High Gc Content Cause Waviness?
... Summarizing what's already in the comments and adding a few of my own educated guesses, I think that the answer to your question is: The human genome contains large regional variation in GC-content -- presumably in "waves". Probes with high GC content bind better to their target sequence (because ...
written 5.2 years ago by Qdjm1.9k
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Comment: C: Hidden Markov Model On Copy Number Data
... See the last sentence: " I would recommend, if possible, to avoid the hard imputation and work with the conditional distribution of states given emissions as provided by the model. For instance through simulations." The recommendation of NRH is the same as mine. You do want to be careful if the tr ...
written 5.2 years ago by Qdjm1.9k
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Comment: C: Hidden Markov Model On Copy Number Data
... Yes. Smoothing is just a different way of deciding on a hidden state sequence. ...
written 5.2 years ago by Qdjm1.9k
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Comment: C: Hidden Markov Model On Copy Number Data
... If your observed data is already clearly defining the predicted state, then there's no hidden states to learn -- so an HMM-based smoothing of your data is going to be roughly equivalent to a simple rule like : "don't change state unless you see two observations of the new state in a row", depending ...
written 5.2 years ago by Qdjm1.9k
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Answer: A: Hidden Markov Model On Copy Number Data
... If your input is already Gain, Loss and Normal then it's not clear how much more useful an HMM would be over a simple heuristic. Consider using maximum marginal probability (MMP) to infer Gain, Loss or Normal at each position rather than Viterbi. Viterbi gives you the most likely path through the ...
written 5.2 years ago by Qdjm1.9k
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Comment: C: Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
... If you log transform the target value, then you are assuming that a unit increase in your feature values gives a multiplicative increase in the target value. If you don't log transform them, then a unit increase in the feature value is additive. Which is the better assumption? Also, if you don't ...
written 5.3 years ago by Qdjm1.9k
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Comment: C: Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
... What are the inputs and targets in the regression? ...
written 5.3 years ago by Qdjm1.9k

Latest awards to Qdjm

Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Topics In Higher-Level Mathematics Used Frequently In Your Research.
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: E-Value In Blast
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Bioinformatics Approach To Summarize Functional Diversity Of A Gene
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: What Is The Best Resource For Protein/Genetic Interactions?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Which Bayesian Classifiers (Binary Data, Large-Scale) Are People Using?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Gene Network Construction... Web Based Tool
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Communicating With Non-Computational Biologists
Appreciated 3.5 years ago, created a post with more than 5 votes. For Creating Sequence Logos From The Command Line
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: How Important Is Bioinformatics And How To Make A Case For It?
Appreciated 3.5 years ago, created a post with more than 5 votes. For An Interactive Heatmap For Viewing Expression Data Matrices
Appreciated 3.5 years ago, created a post with more than 5 votes. For Best Resources To Learn Molecular Biology For A Computer Scientist.
Great Question 3.5 years ago, created a question with more than 5,000 views. For Best Resources To Learn Molecular Biology For A Computer Scientist.
Librarian 3.5 years ago, created a post with more than 10 bookmarks. For Best Resources To Learn Molecular Biology For A Computer Scientist.
Good Question 3.5 years ago, asked a question that was upvoted at least 5 times. For Creating Sequence Logos From The Command Line
Good Question 3.5 years ago, asked a question that was upvoted at least 5 times. For An Interactive Heatmap For Viewing Expression Data Matrices
Good Question 3.5 years ago, asked a question that was upvoted at least 5 times. For Best Resources To Learn Molecular Biology For A Computer Scientist.
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Topics In Higher-Level Mathematics Used Frequently In Your Research.
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: E-Value In Blast
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: What Is The Best Resource For Protein/Genetic Interactions?
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Which Bayesian Classifiers (Binary Data, Large-Scale) Are People Using?
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Gene Network Construction... Web Based Tool
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Communicating With Non-Computational Biologists
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: How Important Is Bioinformatics And How To Make A Case For It?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Creating Sequence Logos From The Command Line
Popular Question 3.5 years ago, created a question with more than 1,000 views. For An Interactive Heatmap For Viewing Expression Data Matrices

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