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

  • Oct. 6, 2022, 9:45 p.m.October

    Lab awarded 1.96 millions to study stress response and senesence

    Highlighted in Dean's weekly message of CU School of Medicine: We are very excited to receive a four-year NIH NIGMS R01 for our proposed project "Post-transcriptional regulations of proteomes in stress and senescence". Post-transcriptional mechanisms play a fundamental role in regulating gene expression at the protein level, and are frequently implicated in stress response, aging, and diseases. The goal of this project is to develop and apply multi-omics methods to examine the post-transcriptional mechanisms that regulate protein composition of multiple tissues and their ability to respond to proteostatic stressors. With the funding support, we will examine the relationships between post-transcriptional regulation and stress response, and at the same time generate data sets including isoform-resolved, spatiotemporal atlases of the normal, stressed, …

    Read more
  • July 1, 2021, 12:39 a.m.July

    Lab Receives 7th Percentile for R01 Application

    We are grateful to have received a favorable review for our recent R01 application. We are eager and can't wait to work on the proposed project!

    Read more
  • Feb. 16, 2021, 10:39 p.m.February

    Combining machine learning and targeted mass spectrometry to validate protein isoforms

    Why identify protein isoforms?Alternative splicing plays a very important role in the heart. In a previous work, we found that the heart is one of the examined tissues that are the most affected by alternative splicing (link). Important proteins in the heart that have splice variants include tropomycin 1 as well as titin, the proper splicing of which have been implicated in congenital heart diseases.A current blind spot of alternative splicing research is that most isoforms have been defined only at the mRNA level, and there are not enough technologies that can allow different protein isoforms to be detected. This is important if we want to know whether the spliced isoforms are correctly translated and what their potential molecular functions …

    Read more
  • Oct. 30, 2020, 8:12 p.m.October

    Recent publications October 2020

    Check out some recent publications from our team members:1. "Determining Alternative Protein Isoform Expression Using RNA Sequencing and Mass Spectrometry" in STAR Protocols (Link)This protocol paper led by Erin and Julianna details a step-by-step experimental and computational workflow to identify non-canonical protein isoforms from RNA sequencing and mass spectrometry data.2. "Proteomic Signatures of Acute Oxidative Stress Response to Paraquat in the Mouse Heart" in Scientific Reports (Link)This study by Vishantie, Silas, Cody and others uses quantitative mass spectrometry to explore how the mouse heart and lung respond to acute oxidative stress. See our previous blog entry for more info!3. "A high-stringency blueprint of the human proteome" in Nature Communications (Link)This perspective paper co-authored by Maggie, Sara, and other groups in …

    Read more
  • 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 …

    Read more
  • 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 ( 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 …

    Read more
  • 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”, …

    Read more
  • 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 …

    Read more
  • 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 …

    Read more
  • 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. …

    Read more
  • 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 …

    Read more
  • 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!

    Read more
  • 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 …

    Read more