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Articles and updates on the lab are published here periodically. Please follow our lab's Twitter feed @MaggieLamLab for additional updates.

  • June 1, 2020, 8:17 p.m.June

    What does oxidative stress do to the heart? Examining proteomic changes

    The heart is an organ that is very sensitive to oxidative stress. In many heart diseases including cardiomyopathy and heart failure, research has found telltale signs of oxidative damage. Reactive oxygen species can create free radicals that react with and modify the molecular components that make up the heart. Because of this many efforts have been given to explore whether antioxidants can be used to delay or reverse the progression of heart disease, but so far the outcome has not been very satisfactory. This is partially because we still do not completely understand how the heart responds to oxidative stress and what are the specific components inside the heart that are changed.To address this question, we used quantitative mass spectrometry …

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  • April 11, 2020, 1:50 a.m.April

    Alternative splice isoform companion data on website

    We recently published our study on finding protein alternative isoforms in the human proteome (https://www.ncbi.nlm.nih.gov/pubmed/31825849). The paper describes a method that uses RNA sequencing data to compile a list of alternative splice sites in a human tissue, then translating the data into protein sequences to re-analyze mass spectrometry data. We reprocessed over 80 million mass spectra on ProteomeXchange and found over 1,000 non-canonical protein isoforms, including a couple hundred peptides that were not previously documented in popular protein sequence databases. Alternative Splicing Transcripts Translated as ProteinsThe results show that not only are more alternative splicing isoforms translated into proteins than previously analyzed, many are tissue-specific and can influence protein functions through excising known protein-protein interaction and post-translational modification sites. We …

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  • Sept. 25, 2018, 1:16 a.m.September

    Popular protein manuscript released on bioRxiv

    Our manuscript on popular proteins across the human diseasome is now on preprint. In this manuscript we worked with collaborators at Cedars-Sinai and Stanford to identify proteins that are preferentially associated with each of over 10,000 disease terms recorded in three standardized vocabularies (Disease Ontology, Pathway Ongology, and Human Phenotype Ontology). One of the interesting things we looked at is whether we can use this massive collection of popular protein lists across disease terms to analyze gene and protein list data such as from a list of differentially regulated proteins in a proteomics experiment comparing normal and diseased tissues. We attempted to achieve this by allowing "protein-to-topic" queries. For instance, since we know that the disease terms “acute myocardial infarction”, …

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  • June 1, 2018, 1:14 p.m.June

    Lab receives 5-year R01 funding

    We are excited to receive a generous 5-year 1.4M direct-cost funding from the National Institutes of Health (NIH)/National Heart, Lung, and Blood Institute (NHLBI). The funding will support our project to investigate "Alternative Protein Isoforms in Ventricular Modeling". The human genome contains a large number of alternative splice isoforms which collectively allow our ~20,000 coding genes to produce >100,000 transcripts. Although alternative splicing is broadly implicated in gene regulation in human physiology and disease, the molecular functions of most alternative transcripts are poorly understood and indeed for most scientists do not know which ones are actually translated as proteins or degraded as aberrant transcriptional project. In the proposed project, our laboratory and our collaborators at UPenn will combine bioinformatics and …

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  • Oct. 20, 2017, 3:55 p.m.October

    BioArXiV article on Gene Annotation Bias

    We previously published a data science method PubPular to calculate the co-occurrence of genes and queried topics on PubMed articles, and suggested that normalized co-publication distance (NCD) may be used as a metric to discover the connection its between a gene/protein and a disease or physiological process. A manuscript posted on the bioRxiv preprint server earlier this year examined how bibliometrics methods such as PubPular may be used to determine the state of gene annotation in biomedical research. The articles authored by Haynes, Tomczak and Khatri at Stanford University borrowed the Gini coefficient from economics to measure the inequality in annotation counts between different genes. Gini coefficient was developed by the sociologist Corrado Gini in 1912 as a statistic on …

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  • Sept. 7, 2017, 3:04 a.m.September

    Quantifying the value of basic science

    In this era of constrained research funding, the value of basic research to the public is sometimes debated. Arguments are often advanced anecdotally: on the one hand well known example on the unpredictable later applicability of basic research abound, from CRISPR to modern innovations on smart phones, which built upon research in the 60s on transtistors which built upon quantum mechanisms from 100 years ago. On the other hand, the value of basic research is doubted by a spectrum of individuals from the public to well meaning medical professionals who lament that not more research is oriented towards direct translation into health care. Despite strong arguments on both sides, actual data on the value of basic research have been scarce. …

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  • Sept. 6, 2017, 3:14 a.m.September

    PubPularDB and FaBian Updates

    Our lab recently received funding from the NIH Common Funds Cloud Credit Model Pilot Program for our bioinformatics project and web app Pubpular. The NIH Cloud Credits Model is a new component within the NIH Big Data to Knowledge (BD2K) program that gives out pre-paid credits for accessing cloud technologies in NIH-supported research. More information can be found on the NIH Common Funds website. With the help of the cloud credits we will be able to move Pubpular to a new web host shortly and also implement a planed functionality of the web app called Fabian (Functional Annotation via Bibliometrics Analysis). Currently the Pubpular web app allows users to calculate the normalized co-publication distance of genes and proteins of interest …

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  • Aug. 20, 2017, 6:18 p.m.August

    Mass Spectrometer Delivered!

    We acquired a Thermo Q-Exactive HF mass spectrometry, which has just been delivered. This instrument has a high-field Orbitrap that combines a resolution of up to 240,000 with high scan speed, and will be used for our major proteomics and method development projects. We can't wait to have it set up!

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  • July 11, 2017, 3:02 a.m.July

    AHA BCVS Meeting 2017

    For this year's BCVS in Portland, I co-chaired a Big Data Workshop session. We had four wonderful speakers (Peipei Ping from UCLA; Karen Ross from Georgetown University; Vidya Venkatraman from Cedars Sinai and Mike MacCoss from University of Washington) who talked about the impact of data science on multiple ‘omics fields. AHA was generous to produce a highlight video for the session in which I interviewed Dr. Karen Ross, an expert in data science and text mining, about her experience with big data and how it has impacted her research programs. Dr. Ross also talks about the major challenges that researchers face today in data science and some developments on the horizon that might help advance the field. Play the …

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  • May 30, 2017, 6:15 p.m.May

    Lab opens in Colorado!

    Hello! I have recently moved to from the University of California Los Angeles to University of Colorado Anschuts Medical Campus to set up a new laboratory on computational and experimental proteomics. The new focus of the laboratory in beautiful Colorado will be to develop mass spectrometry methods to examine dynamic proteomics parameters in human diseases. You can see all the empty spaces in the lab. We are working hard to fill up the lab space. I would like to welcome our first lab member Cody Thomas. Cody came to us from the University of Colorado Boulders where he received his bachelor in Chemical Engineering and worked as a Research Assistant in the Anseth lab. He will be working with me …

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