NEWS
2025
Fortune, Eva Roytburg (October 28, 2025) [View PDF]
UC San Diego Researchers Shortlisted for International Cancer Competition
UC San Diego Today, Miles Martin (Sept 29, 2025) [PDF]
Twelve teams reached the Cancer Grand Challenges finals, including two with UC San Diego scientists. Dr. Ideker’s Team ‘Biologia Ex Machina’ is developing the next generation of AI-powered co-scientists to revolutionize cancer research.
This Detailed Map of a Human Cell Could Help Us Understand How Cancer Develops
Discover Magazine, Cody Cottier (May 29, 2025) [PDF]
Mapping a human cell gives researchers a view of subcellular architecture and sheds light on how cancer develops
“Digital Tumors” for Precision Oncology: UC San Diego Receives Award from ARPA-H.
UC San Diego Today, Miles Martin (May 22, 2025) [PDF]
Researchers at UC San Diego, led by Professor Trey Ideker, are included in a $142 million initiative from ARPA-H with the goal of creating adaptive and personalized cancer treatments. As part of the new project, Ideker will lead a team developing “digital tumors” to help match patients with the right treatment and predict the evolution of their disease.
UCSD team is part of cutting-edge, nationwide cancer program.
The San Diego Union-Tribune, Paul Sisson (May 23, 2025) [PDF]
Grants will fund use of artificial intelligence to predict cancer evolution during treatment and better match treatments to disease
ARPA-H pioneers game-changing cancer care designed to adapt throughout treatment.
ARPA-H News & Events (May 20, 2025) [PDF]
Selected performer teams will use predictive models to match treatments with changing tumor biology and prevent disease progression
Protein Map Illuminates Hidden Drivers of Childhood Cancer
AACR Cancer Discovery News, Elie Dolgin (April 25, 2025) [PDF]
A high-resolution map of how protein organization inside the cell provides a platform for interrogating the way cancer mutations disrupt entire protein assemblies—not just individual genes. By combining spatial proteomics with pediatric tumor genome data, researchers uncovered 102 previously overlooked cancer drivers, highlighting the power of structural context in interpreting cancer genomes and identifying new therapeutic targets.
A Comprehensive Map of the Human Cell.
UC San Diego Today, Susanne Clara Bard (April 9, 2025) [PDF]
UC San Diego and Stanford University researchers have created a comprehensive map of the human U2OS cell. The map revealed previously unknown functions of proteins including C18orf21 (pictured).
Epigenetic Clocks May Only Be Scratching the Surface of Aging.
SynBioBeta (Jan 21, 2025) [PDF]
UC San Diego researchers uncover a pivotal link between genetic mutations and epigenetic changes, reshaping our understanding of aging
What makes the biological clock tick? La Jolla scientists link two theories on aging.
The San Diego Union-Tribune, La Jolla Light, Ashley Mackin Solomon (Jan 27, 2025) [PDF]
UCSD researchers work to pave the way for new therapies to slow or reverse the process. Zane Koch and Trey Ideker are authors of a study out of the UC San Diego School of Medicine on aging.
Is aging caused by gene expression or mutations? The answer is key to treatment
KPBS Public Media, Thomas Fudge (Jan 27, 2025) [YouTube][PDF]
What do your genes have to do with growing old? Quite a lot. But is it due to the actual DNA, or the way those genes are expressed? KPBS sci-tech reporter Thomas Fudge has more on new research that raises a question that’s key to treating age-related conditions.
Is anti-aging science misguided? ‘Reversing’ your biological clock may be out of reach.
StudyFinds, Steve Fink (Jan 24, 2025) [PDF]
Findings challenge current anti-aging research focused solely on reversing epigenetic changes, as these changes may be symptoms rather than root causes of aging – making the development of anti-aging treatments more complex than previously thought.
New Study Links Epigenetic Changes to Genetic Mutations. There may be negative implications for epigenetic therapies.
Lifespan.io, Arkadi Mazin (Jan 21, 2025) [PDF]
A new paper published in Nature Aging suggests that somatic mutations cause significant remodeling of the epigenetic landscape. The findings might be relevant to future anti-aging interventions.
Why Our Biological Clock Ticks: Research Reconciles Major Theories of Aging.
UC San Diego Today, Miles Martin (Jan 21, 2025) [PDF]
Two major theories of aging both involve DNA, but in very different ways. Researchers at UC San Diego have revealed that these theories may not be so different after all.
Inside the Lab: Researcher Spotlight with Dr. Trey Ideker
UC San Diego, Moores Cancer Center. Izzy Ancharski (Jan 7, 2025) [Vimeo, 15mins]
Trey Ideker, PhD, is a 21-year Professor of Medicine, Bioengineering and Computer Science, and former Chief of Genetics, at the University of California San Diego (UCSD). Additionally, he is Director or Co-Director of the Bridge2AI Functional Genomics Data Generation Program, the Cancer Cell Map Initiative, the National Resource for Network Biology, and the UCSD Graduate Program in Bioinformatics and Systems Biology, all NIH-funded efforts. Ideker’s research laboratory has led seminal studies establishing the theory and practice of systems biology, including systematic techniques for elucidating human cell architecture and its molecular networks.
2024
Dr. Ideker has been selected as a Clarivate Highly Cited Researcher, continuing his ongoing nomination since 2019. This highly anticipated annual list identifies researchers who demonstrated significant influence in their chosen field or fields through the publication of multiple highly cited papers during the last decade. (Published December 2024)
View the complete list of 2023 Highly Cited Researchers HERE
Image credit: UC San Diego
All In. Transforming cancer treatment with artificial intelligence (pgs 12-17)
Delivering Discoveries. Moores Cancer Center Annual Impact Report FY 2024
UC San Diego Moores Cancer Center is committed to supporting patients at every step of their cancer journey. Through innovative research and compassionate patient care, we strive to change the landscape of cancer prevention, detection, and care in San Diego and beyond. Our inaugural annual report features inspiring patient stories, research breakthroughs, community partnerships and more.
Image credit: UC San Diego Health Sciences, generated with Adobe Firefly
How Artificial Intelligence Could Automate Genomics Research. UC San Diego Today, Miles Martin (Dec 2, 2024) [PDF]
Functional genomics seeks to identify what genes do and how they interact. Researchers at UC San Diego have demonstrated that large language models such as GPT-4 could make functional genomics research significantly faster and less laborious than current, non-AI approaches.
See also: Medical Express
Photo credit: iStock/Lillia Bila
$12.7M Grant to Establish New Center to Investigate Genetic Basis of Autism and Schizophrenia
UC San Diego Today, Sara Bock (Oct 10, 2024)
Funded by a California Institute for Regenerative Medicine (CIRM) grant, researchers in the UC San Diego Verge Center aim to uncover the genetic mechanisms behind neuropsychiatric disorders.
CBS8 News San Diego
UC San Diego School of Medicine uses AI to predict which drugs to use to treat cancer patients
CBS8 News San Diego, Abbie Black (Jan 18, 2024) [PDF] [YouTube]
The team published a study in Cancer Discovery that uses artificial intelligence to predict the best treatment for cancer patients.
Why can’t my dog live as long as me? To live for days or for decades? We uncover how an animal’s lifespan is determined.
BBC World Service, CrowdScience (Nov 22, 2024)
[Podcast, 29 mins]
The use of AI for drug discovery results in a more secure and effective treatment of cancer. list23, Claire Reed (May 6, 2024)
Open-Source AI Tool Streamlines Cancer Drug Candidate Generation
AZORobotics, Lexie Corner (May 7, 2024) [PDF]
Simulated Chemistry: New AI Platform Designs Tomorrow’s Cancer Drugs
UC San Diego Today, Miles Martin (May 6, 2024) [PDF]
The new platform helped UC San Diego scientists synthesize 32 potential multi-target cancer drugs. Photo: Study co-author Katherine Licon, photographed here at the bench, is lab manager for the Ideker Lab at UC San Diego, which combines computational and traditional wet-lab techniques to answer fundamental questions about disease biology and discover new ways to enhance precision medicine.
Infusion of Artificial Intelligence in Biology
The Scientist, Meenakshi Prabhune (Feb 23, 2024) [PDF]
With deep learning methods revolutionizing life sciences, researchers bet on de novo proteins and cell mapping models to deliver customized precision medicines. As the AI flood gates open, biology is experiencing a surge of new applications. From synthetic proteins to cell mapping, researchers are using AI to improve precision medicines.
Machine Learning Models Help Predict Medication Responses
NIH, National Cancer Institute, Center for Biomedical Informatics and Information Technology (CBIIT) (Feb 5, 2024) [PDF]
UCSD School of Medicine researchers use AI models to predict chemotherapy treatment responses. The UCSD Guardian, Eru Ishikawa (Jan 29, 2024) [PDF]
Scientists use AI to predict when cancer cells will resist chemotherapy
Interesting Engineering, Sejal Sharma (Jan 18, 2024)
AI points to better and new cancer treatments
Innovators Magazine, Susan Robertson (Jan 18, 2024)
AI Uses Tumor Genetics for Prediction of Treatment Response
Inside Precision Medicine (Jan 18, 2024)
AI Harnesses Tumor Genetics to Predict Treatment Response. There are many paths to cancer resistance; AI can decode them all simultaneously.
UC San Diego Today, Miles Martin (Jan 18, 2024) [PDF]
Cervical cancer, shown here at the cellular level, frequently resists treatment. The researchers’ machine learning algorithm could help scientists better understand why this and other forms of cancer resist chemotherapy.
2023
Congratulations to Dr. Yue Qin!
Dr. Yue Qin has been selected to join the Forbes 30 Under 30, Class of 2023. Read more HERE and HERE. (2023 May 17)
Dr. Yue Qin has been awarded the 2023 UC San Diego Chancellor’s Dissertation Medal for the Jacobs School of Engineering. (2023 May 10)
A New Map Reveals the Complicated World in Which Cells Seek to Repair Damaged DNA
Scott LaFee, UC San Diego Today. (2023 May 22) [PDF]
Image: An artistic rendering of the concept of DNA damage and repair. Numerous diseases are linked to or caused by alterations that affect genomic integrity and the ability of cells to function and divide normally. A process called DNA damage response has evolved to repair errors and mutations. Researchers have produced a new map that more fully captures the complexity of that process.
Smartly Done. Artificial intelligence is on its way to transforming how we understand and treat disease.
UC San Diego Today, Nicole Mlynaryk (2023 May 18) [PDF]
“The same way your Netflix algorithm predicts what movie you should watch tonight, our algorithms will predict what drug is best fit to treat your cancer”. – Trey Ideker
Watch on YouTube
Creating a Meaningful College Experience with Ximena Gonzalez.
University of California Television (UCTV). YouTube. (Jun 29, 2023)
2022
UC San Diego Joins NIH ‘Bridge to Artificial Intelligence’ Program
UC San Diego Today, Nicole Mlynaryk (September 13, 2022) [PDF]
The NIH Common Fund’s initiative will expand the use of artificial intelligence to solve pressing challenges in human health. Researchers at University of California San Diego School of Medicine have been selected to lead components of the National Institutes of Health (NIH) Common Fund’s Bridge to Artificial Intelligence (Bridge2AI) program. Over the next four years, Bridge2AI will award $130 million to accelerate the widespread use of AI in biomedical research and health care
Dr. Trey Ideker is honored to be included in the ISCB 2022 Class of Fellows.
The ISCB Fellows program was created to honor members who have distinguished themselves through outstanding contributions to the fields of computational biology and bioinformatics. Begun in 2009, 2022 marks the 13th anniversary of the program. ISCB will be honoring the 2022 Class of Fellows during the annual ISMB 2022 conference. (April 28, 2022)
How old is your dog in human years? New formula is more accurate than multiplying by 7. The Kelly Cutrara Show, Global News Radio 640 Toronto. (4 Feb 2022)
Radio interview with Trey Ideker & Kelly Cutrara
Scientists develop novel tools to visualize DNA repair.
The Science Advisory Board, Monish Makena (4 Jan 2022)
Researchers can now visualize DNA repair in unprecedented detail using a new high-throughput microscopy technique in combination with machine learning. The methodology, published in Cell Reports on December 28, has led to the identification of new proteins involved in DNA repair.
2021
“Artificial intelligence allows us to see the invisible inside cells” Sciences Et Avenir (27 Dec 2021)
Interview with Dr. Ideker “Revealing a Cell’s Components through Artificial Intelligence” AZO Life Sciences (23 Dec 2021)
Dr. Ideker named on the annual Clarivate™ Web of Science Highly Cited Researchers List 2021 (1 Dec 2021)
AI-Based MuSIC Reveals Previously Unknown Cell Components. GEN (29 Nov 2021)
Shock AI Discovery Suggests We’ve Not Even Discovered Half of What’s Inside Our Cells. Clare Watson. Science Alert. (26 Nov 2021)
UCSD Finds Technique That Could Boost Mapping of Cell Interiors. Times of San Diego (24 Nov 2021).
See also La Jolla Light, Patch.
We Might Not Know Half of What’s in Our Cells, New AI Technique Reveals. UC San Diego News Center (24 Nov 2021)
Investigators Aim to Identify New Treatment Targets with Cancer Cell Map Initiative. OncLive (16 Nov 2021)
Dog Years to Human Years: Your Canine’s Lifespan Explained. Newsweek (7 Nov 2021)
Studies Delve Deep into the Protein Machinery of Cancer Cells. National Cancer Institute, Cancer Currents Blog (4 Nov 2021) [PDF]
Uncovering Key Interactions Between Cancer-Driving Proteins. Laura Elizabeth Lansdowne, Technology Networks (12 Oct 2021) [PDF]
UCSD researchers help map out how cancer mutations affect proteins. Valley News (7 Oct 2021)
Moonshot Project Aims to Understand and Beat Cancer Using Protein Maps. Singularity Hub (5 Oct 2021)
Cancer Cell Map Initiative reveals protein interactions that drive cancer. The Science Advisory Board (4 Oct 2021)
From COVID to cancer, gene-mapping tool could ‘revolutionize’ treatment, UCSF studies say. Danielle Echeverria, San Francisco Chronicle (2 Oct 2021) [PDF]
UC San Diego ‘Cancer Cell Mapping’ Research May Improve Chemotherapy. Times of San Diego (2 Oct 2021)
New map of protein interactions offers opportunity to ‘do such damage to cancer,’ scientists say. FierceBiotech (1 Oct 2021)
In-Depth Cancer Protein Mapping Project Sheds Light on Disease Processes. Clinical Omics (1 Oct 2021) [PDF]
Proteins give a clearer picture of cancer growth. Eileen Drage O’Reilly, AXIOS (30 Sept 2021)
Protein network map uncovers previously unknown cancer drivers. News Medical (30 Sept 2021)
First map of proteins in tumour cells pinpoints cancer therapy targets. New Scientist (30 Sept 2021)
Looking Beyond DNA to See Cancer with New Clarity. Heather Buschman & Robin Marks, UCSF Research News, see also UC San Diego Today (30 Sept 2021)
Study identifies 579 genetic locations linked to anti-social behavior, alcohol use, opioid addiction and more. Science Daily (26 Aug 2021)
COVID-19: Scientists Identify Human Genes That Fight SARS-CoV-2 Infection. SciTech Daily (16 Apr 2021)
2020
52 UC San Diego Researchers Are Named Highly Cited in 2020 Listing. UC San Diego News Center. (23 Nov 2020)
See also: Dr. Ideker named on the annual Clarivate™ Web of Science Highly Cited Researchers™ 2020 list
Old Dogs, New Research and the Secrets of Aging. James Gorman, New York Times (9 Nov 2020) [PDF]
DrugCell: New experimental AI platform matches tumor to best drug combo. ScienceDaily (26 Oct 2020)
Deep Learning Model Could Enhance Cancer Precision Medicine. Health IT Analytics (26 Oct 2020)
New AI Platform Matches Tumor to Right Drug Combination. Med India (23 Oct 2020)
Experimental AI platform predicts best approach to cancer treatment. AZO Life Sciences (26 Oct 2020)
DrugCell: New Experimental AI Platform Matches Tumor to Best Drug Combo. Heather Buschman, UC San Diego Health Newsroom (22 Oct 2020)
How Mass Spectrometry is Accelerating Quantitative Proteomics. Bio-IT World (20 July 2020)
Deep learning takes on tumours. Artificial-intelligence methods are moving into cancer research. Esther Landhuis, Nature, Technology Feature. Vol 580, 551-553 (21 April 2020) [PDF]
Hundreds of Scientists Scramble to Find a Coronavirus Treatment. Carl Zimmer, The New York Times. (17 March 2020) [PDF]
Genes from scratch: Far more common and important than we thought. Science Daily (18 Feb 2020)
Podcast: How old is your dog in human years? Genetic study offers a new way to answer that question. Scientific American (9 January 2020)
How to calculate your dog’s real age. BBC (6 Jan 2020)
2019
Fido’s Human Age Gets New Estimates. Scientific American (27 Dec 2019)
Radio Interview: Measuring A Dog’s Age Is More Complicated Than You Think. KCBS Radio. (14 Dec 2019)
A New Way To Calculate Your Dog’s Age. NPR (7 Dec 2019)
Researchers propose new way to measure dogs’ ages. New York Daily News (7 Dec, 2019)
Scientists have come up with a better way to convert your dog’s age to human years. Washington Post (28 Nov 2019)
A new formula for converting the age of dogs to humans has appeared, how old are 1-year-old dogs? Gigazine (22 Nov 2019)
Convert your dog’s age into human years using this new formula. New Scientist (21 Nov 2019)
Science May Have a Better Way to Translate Dog Years to Human Years. Discover Magazine (20 Nov 2019)
New “dog to human years” calculation more accurately determines when your beloved pet will die. TechBallad (20 Nov 2019), reprinted at AV Club (20 Nov 2019).
Calculate Your Dog’s Age With This New, Improved Formula. Smithsonian Magazine (19 Nov 2019)
Why a dog’s age in ‘human years’ might not be as old as you think. New York Post (19 Nov 2019)
There’s a New Way to Calculate Your Dog’s Age in Human Years. Kelly Conaboy. The Cut, New York Magazine. (19 Nov 2019)
There’s a Better Way Calculate Your Dog’s True Age in Dog Years, Researchers Say. People Magazine (19 Nov 2019)
New way to calculate your dog’s age in human years. That’s Life! (19 Nov 2019)
How old is my dog? Sueddeutsche Zeitung (19 Nov 2019)
The New Formula to Calculate Your Dog’s Age in Human Years. Popular Mechanics (18 Nov 2019)
How old is your dog REALLY in ‘human years’? Researchers come up with a new formula for calculating the ‘true age’ of your canine friend (and it’s not multiplying it by seven). Daily Mail UK (18 Nov 2019)
Your dog’s REAL age in ‘dog years’ revealed (and it’s not their age multiplied by seven). The Sun (18 Nov 2019), see also FOX News, WDRB.
What’s The Real Human Equivalent of Your Dog’s Age? Here’s a New Formula. Science Alert (18 Nov 2019)
Here’s a better way to convert dog years to human years, scientists say. Science Magazine (15 Nov 2019)
Classroom crowdscience: UC students challenged to detect schizophrenia genes. Physorg. (Apr 24, 2019).
Genome-wide analysis reveals new strategies to target pancreatic cancer, Scott LaFee, ScienceDaily (April 4, 2019).
Ribosomal DNA Can Predict an Animal’s Age. Abby Olena, The Scientist Magazine. (Feb 14, 2019). PDF.
2018
- Ideker Lab awarded a Merck KGaA 350 Research Grant to develop an AI for Cancer. LinkedIn, Dec 2018.
Trey Ideker included in new listing of highly cited researchers in the top 1% for their field. 45 UC San Diego Faculty Named Most Influential in Their Fields. Michelle Franklin, UC San Diego News Center. (November 28, 2018)
Watch Video: Dr. Ideker’s keynote talk at The Workshop on the Future of Algorithms in Biology (FAB) 2018. “Towards a structure/function simulation of a cancer cell.” Video recorded at Carnegie Mellon University. (Sept 28, 2018)
Scientists map interactions between head and neck cancer and HPV: Connecting the dots between human papillomavirus and smoking-related cancers. Julie Langelier, Gladstone Press Release. (Sept 12, 2018).
NIH Funds UCSF-led Initiative to Chart a Course Toward New Psychiatric Drugs. Dana Smith, UCSF News Center. (September 05, 2018)
Genetic Mutations of Appendix Cancer Identified, May Impact Treatment. Yadira Galindo, UC San Diego News Center. (August 08, 2018).
Mutations in Noncoding Regions of Human Genome Also Cause Cancer, Study Shows. Patricia Inacio, Myeloma Research News. (25 June 2018) PDF
Gems in the ‘Junk’ – Noncoding mutations found to be a major mechanism in cancer. Rachel Flehunger, DDN News. (7 May 2018). [PDF]
Video: Dr. Ideker’s talk at AACR 2018: “Decoding patient genomes through the hierarchical pathway architecture of the cancer cell“. Trey Ideker. AACR Webcasts. Video recorded at the AACR Annual Meeting 2018 on April 16, 2018. (Chicago, IL)
Researchers Identify Hundreds of Mutations outside of Coding Genes that Influence Tumor Gene Expression. Zvi Cramer, SCI NEWS. (06 Apr 2018)
Cancer Can Be Driven by Noncoding DNA Mutations. Genetic Engineering & Biotechnology News. (Apr 3, 2018)
Even DNA that Doesn’t Encode Genes Can Drive Cancer. Heather Buschman, UC San Diego Health Newsroom. (02 April 2018) [PDF]
Cracking Open the Black Box of AI with Cell Biology. Eliza Strickland, IEEE Spectrum, (13 Mar 2018).
Deep Learning-Based Cell Model May Predict Patient Tumor Cell Growth Someday. Uduak Grace Thomas, Genome Web, (06 Mar 2018). [PDF]
Virtual Cell Can Simulate Cellular Growth Using Machine Learning. Kenny Walter, R and D Magazine (05 March 2018).
How a Yeast Cell Helps Crack Open the “Black Box” Behind Artificial Intelligence. Heather Buschman, PhD, UC San Diego Health Newsroom, (05 March 2018). Reprinted at Phys.Org News (05 March 2018), and Technology Networks (06 March 2018).
Interview with Dr. Ideker: Duke TIP Takes 5 with Distinguished Alum, Trey Ideker. Duke TIP (07 Febr 2018)
2017
- Cell Mapping Initiatives Aim to Uncover Hidden Pathways of Disease. Nicholas Weiler and Bennett McIntosh, UCSF News Center. (15 Nov 2017)
- Frontline Cancer: Genetic background can provide clues about possible future tumors. Dr. Scott Lippman, La Jolla Light, (31 May 2017).
- CRISPR-based mapping of genetic interactions. Ross Cloney, Nature Reviews Genetics 18, 272–273 (2017) doi:10.1038/nrg.2017.25 (03 April 2017).
- Gene Editing Approach Uncovered Cervical Cancer’s Weak Spots. Magdalena Kegel, Cervical Cancer News (27 Mar 2017).
- Watch interview with Dr. JP Shen: Gene editing used to find cancer’s genetic weak spots, Bradley J. Fikes, San Diego Union Tribune, (22 March 2017). [Printed article]
- CRISPR/Cas9 Reveals Cancer’s Synthetic Lethal Vulnerabilities, GEN Genetic Engineering & Biotechnology News Highlights (21 March 2017).
- CRISPR Method Used to Detect Synthetic Lethalities in Cancer. GenomeWeb, (20 March 2017).
- Gene Editing Technique Helps Find Cancer’s Weak Spots. Heather Buschman, UCSD Health Newsroom, (20 March 2017).
- The Siri of the cell – Tech Podcast. Leigh Alexander and Iain Chambers, The Guardian, (9 Mar 2017).
- Massively Parallel Perturbations. Ruth Williams, The Scientist, (1 Mar 2017).
- Ideker Lab awarded the 2017 Roddenberry Prize. The Roddenberry Foundation Announces Winners Of The Roddenberry Prize, $1 Million In Awards. PR News Wire. Feb 8, 2017.
2016
An In Depth Look at the Father of Systems Biology. Mary Chitty, Library Director & Taxonomist, Cambridge Healthtech Institute. Bio-IT World. (28 Nov 2016).
New Bioinformatic Analysis Reveals Role of Proteins in Diabetic Kidney Disease, Yadira Galindo, UCSD Health Newsroom, (15 November 2016).
A Disease of the Genome, Liz Harley, Frontline Genomics Magaine, Issue 10, 17-20, (Oct 2016) [PDF]
Researchers ID Cancer Gene-Drug Combinations Ripe for Precision Medicine, Heather Buschman, UCSD Health Newsroom, (21 July 2016).
Big Data’s Big Implications for Cancer Treatments, Patricia Fitzpatrick Dimond, GEN Genetic Engineering & Biotechnology News, 9 May (2016).
San Diego biotech raises $46 million. Ideaya Biosciences, of La Jolla and South San Francisco, focuses on cancer therapy, Bradley J. Fikes. The San Diego Union Tribune. (2016 May 5)
Biomarker Tracks Accelerated HIV-Associated Aging, National Institute of Mental Health (2016 Apr 21) and AIDS.Gov (2016 Apr 26)
People Who Are HIV-Positive May Be Aging Faster Than Their Peers, Michaeleen Doucleff, NPR Health, 26 April (2016).
HIV Infection Prematurely Ages People by an Average of Five Years, Science Daily, 21 April (2016).
Meet The Author: Andrew Gross, Molecular Cell, Vol 62, 21 April (2016).
NextGen Stars Program, AACR American Assoc For Cancer Research, April (2016). Dr. John Paul Shen presents at the AACR Major Symposium “Modeling the Interface between Cancer Genomics and Drugs”.
UCSF Establishes Quantitative Biosciences Institute: New Research Unit will Identify Opportunities for Disease Treatments Using Computation, Mathematics and Statistics. Jennifer O’Brien, UCSF News Center (16 March 2016)
New Research Unit will Identify Opportunities for Disease Treatments Using Computation, Mathematics and Statistics, Jennifer O’Brien, UCSF News Center, 16 March (2016).
Using Big Data to Chart Cancer’s Hidden Genetic Weaknesses. Nicholas Weiler, UCSF News Center (24 Feb 2016).
Just The FAQs: Connecting Genotype to Phenotype with “Ontotype”, UC San Diego Health Sciences, 24 Feb (2016).
Comparative Genomics: One for all, Duncan T Odom, ELife, 11 Feb (2016).
All’s Well That Scales Well, H Craig Mak, Cell Systems Editorial, Vol 2, Issue 2, p 59. 24 Feb (2016).
GenomeSpace “Recipes” Help Biologists Interpret Genomic Data, Heather Buschman, UCSD Health Newsroom, 20 Jan (2016).
2015
- Three UC San Diego Professors Named AAAS Fellows, Mario Aguilera, UCSD News Center, 24 Nov (2015), and at AAAS.Org, 16 Nov (2015)
- New Biomarkers Might Help Personalize Metastatic Colorectal Cancer Treatment, UCSD Health Newsroom, 17 June (2015) and in ScienceDaily, 17 June (2015)
- UC San Diego, UC San Francisco Launch New Cancer Cell Mapping Initiative, UCSD News Center, 29 January (2015) and in GenomeWeb, 29 January (2015)
2014
- Don’t judge every tumor by its tissue, scientists say, Julia Rosen, Los Angeles Times, 7 Aug (2014)
2013
How cells remodel after UV radiation. Medical Xpress, 19 December (2013) and in Medical News Today, 29 December (2013), ScienceDaily, 19 December (2013), Nanowerk, 20 December (2013), Innovations Report, 20 December (2013), and HealthCanal, 19 December (2013)
Making connections: using networks to stratify human tumors, Benjamin J. Raphael, Nature Methods 10(11):1077-1078 (2013)
“Wildly Heterogeneous Genes”. Scott LaFee, UC San Diego Health Newsroom (16 Sept 2013). Reprinted in Innovations Report (16 Sept 2013) and Science Daily (15 Sept 2013).
Studying Tumor Mutations via a Network Approach, GEN Genetic Engineering & Biotechnology News, 16 September (2013) and in News Medical, 16 September (2013)
Gene networks predict cancer prognosis, Bradley J. Fikes, UT San Diego, 15 September (2013)
Unraveling cancer through network models, Sarah Webb, PhD, BioTechniques, 09 September (2013) [PDF]
Searching for Meaningful Markers of Aging, David Stipp, New York Times, 22 July (2013)
UCSD Study Clarifies Epigenetic Behavior, Bradley J. Fikes, UT San Diego, 04 January (2013)
Automating the construction of gene ontologies. Kara Dolinski and David Botstein, Nature Biotechnology News and Views, (09 Jan 2013)
In Epigenomics, Location is Everything. Scott Lafee, UC San Diego Health Newsroom, (29 Oct 2010).
2012
- Network-Extracted Ontologies Organize Knowledge from Genomic Data, BiotechDaily, 24 December (2012)
- Toward a New Model of the Cell. Scott LaFee, UC San Diego Health (17 Dec 2012).
- Biomarking time: methylome modifications offer new measure of our ”biological” age news, Scott LaFee, UC San Diego Health, (21 November 2012).
- My data are your data, Vivien Marx, Nature Biotechnology, 30, 509–511, 07 June (2012)
- Proteomics: The interaction map. Monya Baker, Nature 484, 271–275 (12 April 2012) doi:10.1038/484271a Published online (11 April 2012).
2011
- La Jolla Research and Innovation Summit Connects Business and Academia, Tiffany Fox, April 25 (2011)
- Digging Deeper, Seeing Farther: Supercomputers Alter Science, John Markoff, The New York Times, April 26 (2011)
- Study shows how stress causes extensive genetic rewriting, Kristen Bole, PHYSORG.com, (12 Jan 2011) andUCSF News Center (12 Jan 2011).
- Rewiring makes the difference. Andrea Califano, Molecular Systems Biology 7(463); doi:10.1038/msb.2010.117, (18 January 2011).
2010
- UC San Diego Receives $6.5M to Decipher Protein Interactions, Steve Sinovic, San Diego Business Journal, December 13 (2010)
- Scientists Map Genetic Network’s Response to DNA-Damaging Agents, Steve Sinovic, San Diego Business Journal, December 3 (2010)
- Scientists Map Changes in Genetic Networks Caused By DNA Damage, Scott LaFee, UC San Diego Health (02 Dec 2010).
- UCSD Gets $6.5M NIH Grant to Fund New Network Biology Center, GenomeWeb Daily News, November 2 (2010)
- Stanford, UCSD Biologists Take Plunge Into Arpanet-Style Project with Sage Bionetworks, Luke Timmerman, Xconomy — Seattle, October 6 (2010)
- UCSD awarded $15.4 million for systems biology research, La Jolla Light, October (2010)
- New Center Looks at How Human Systems Function or Fail. Scott Lafee, UC San Diego Health Newsroom, (29 Oct 2010).
- Researchers Map Thousands of MAPK Protein Interactions. Debra Kain, UC San Diego Health (20 Sept 2010).
- Neither models nor miracles: a look at synthetic biology, Robert Fortner, Ars Technica, August 24 (2010)
- Life Science Technologies: Protein-Protein Interaction Technologies Toward a Human Interactome, Jeffrey M. Perkel, Science, July 23 (2010)
- Researchers Create Atlas of Transcription Factor Combinations. Debra Kain, UC San Diego Health (05 March 2010).
2009
- Search for pathway-level biomarkers, Amy Swinderman, Drug Discovery News, August (2009)[Print version]
- More harm than good?, Justine Davies, The Guardian, June 23 (2009)
- Amid Efforts to Give Foods More Antioxidant Punch, Mysteries Remain, Jennifer LaRue Huget, The Washington Post, June 2 (2009)
- Oxidative stress may extend lifespan, The Times of India, May 29 (2009)
- How Oxidative Stress May Help Prolong Life. Scott LaFee, UC San Diego Health. (28 May 2009)
2008
- UCSD’s Ideker Seeks Contributors for ‘Clearinghouse’ of Network Models, Vivien Marx, October 17 (2008)
- Primetime for Protein Arrays, Jeanene Swanson, Genome Technology, July/August (2008)
2007
- Networking, protein style, Nicola McCarthy, Nature Reviews: Cancer, December (2007)
- Using Molecular Pathways to Assess Cancer Patients, Katherine Bourzac, Technology Review, October 17 (2007)
- What Can Systems Biology Do for You? Four computational modeling strategies and the data that build them, Jeffrey M. Perkel, The Scientist, March (2007)
- Friendster for Proteins, Robert Langreth and Matthew Herper, Forbes, March 12 (2007)
2006
- Scientist to Watch. Trey Ideker: Navigating Deep Waters, Ishani Ganguli, The Scientist, Oct (2006)
- Making Inroads on Malaria: MS and Other Analytical Methods Aid the Detection and Understanding of the Persistent Parasite Plasmodium. Tom Hayden, Analytical Chemistry, August 1 (2006)
- How Cells Thwart Cancer: A systems biology map of cells’ responses to DNA damage could provide valuable clues to discovering new cancer drugs. Katherine Bourzac, Technology Review, May 25 (2006)
- Cell, Heal Thyself: New systems biology model reveals how cells repair DNA damage, Jacobs School of Engineering, May 18 (2006)
- By creating maps of the body’s complex molecular interactions, Trey Ideker is providing new ways to find drug, Jon Cohen, Technology Review, Mar 20 (2006)
- 10 Emerging Technologies Report: Comparative Interactomics, Technology Review, Feb 21 (2006)
2005
- Two UCSD Bioengineering Professors Recognized as Pioneers in Emerging Field of Comparative Interactomics, Jacobs School of Engineering, Nov 2 (2005)
- Malaria Parasites ‘Wiring’ May be Key, The San Diego Union Tribune, Nov 3 (2005)
- Researchers Develop New Method To Find Deadly Malaria Parasite’s Achilles Heel, ScienceDaily, Nov 2 (2005)
- TR35: Technology Review’s top 35 innovators under the age of 35, Technology Review, Oct (2005)
- UCSD Bioengineering Professor Trey Ideker Named Top 35 Young Scientist By MIT’S Technology Review Magazine, UCSD News, Sept 6 (2005)
- Mapping ‘circuitry’ of yeast genes using technique that could be applied to humans, Medical News Today, May 7(2005)
- Researchers Map ‘Circuitry’ of Yeast Genes Using Technique That Could be Applied to Humans, Science Daily, May 6 (2005)
- Examination of Internal ‘Wiring’ of Yeast, Worm, and Fly Reveals Conserved Circuits, Science Daily, Feb 8 (2005)
2004 and prior
- UCSD Bioengineering Professor Wins 2004 Packard Foundation Fellowship, Jacobs School of Engineering, Oct 15 (2004)
- Thinking, Tinkering, Tooling in Systems Biology, Genomics and Proteomics (2004)
- UCSD and SDSC to Host RECOMB Computational Molecular Biology Meetings, Jacobs School of Engineering, Mar 23 (2004)
- PATHBLAST: Software Tackles Protein Pathways, Whitehead Institute for Biomedical Research, Sept 25 (2003)
- Hot Papers: Yeast Pushes the Proteomic Envelope, Mignon Fogarty, The Scientist, July 28 (2003)
- Data Explosion: Bringing Chaos to Order with Bioinformatics, Charles W. Schmidt, Environmental Health Perspectives, May (2003)
- Integrating the Pieces of Systems Biology, Beth Schachter, Genomics and Proteomics, June (2003)
- “The Path Not Taken”, Edward M. Marcotte, Nature Biotech, July (2001), pp.626-627
- ISB Scientists Have Their Work Cut Out, John S. MacNeil, Genome Web, May (2001)