NEWS
2026
Professor Trey Ideker appointed Director of the Big Data Institute, Nuffield Department of Medicine, University of Oxford (March 9, 2026)
The Big Data Institute brings together researchers from diverse disciplines to harness large, complex, and heterogeneous biomedical data sets that offer unprecedented opportunities to improve human health worldwide.”
Trey Ideker, PhD is a Visiting Member at the Ellison Medical Institute, Ellison Medical Institute (January 23, 2026)
We’re excited to see how this collaboration will strengthen our drug discovery and development programs and bring us closer to our mission: delivering more effective, personalized treatments and improving outcomes for our patients.”
2025
The U.S. just bet $1 billion that AI supercomputers can turn most cancers from ‘death sentences’ to ‘manageable conditions’ within 8 years, Fortune Magazine, Eva Roytburg (October 28, 2025) [View PDF]
Called the ‘DREAM complex,’ these proteins may determine how fast humans age, Earth.com, Jordan Joseph, Oct 2, 2025
DREAM complex acts as master brake on DNA repair, where higher activity steadily increases mutations and accelerates aging.
UCSD researchers are featured in final teams of international cancer competition, San Diego Union-Tribune, Oct 1, 2025
Ludmil Alexandrov and Trey Ideker are on teams exploring mutational signatures and AI-human collaborations for cancer care.
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.
Human Cell Maps Uncover Insights in Pediatric Bone Cancer, Genetic Engineering and Biotechnology News, Apr 10, 2025
Researchers have identified mutated proteins strongly linked to bone cancer by constructing a multimodal map of human subcellular architecture.
The 43rd Barcelona BioMed Conference explores the potential of Artificial Intelligence to transform biomedical research, Institute for Research in Biomedicine | IRB Barcelona, Apr 2, 2025
Between 31 March and 2 April, IRB Barcelona, supported by the BBVA Foundation, hosted the 43rd Barcelona BioMed Conference, entitled “AI in Drug Discovery and Biomedicine”. Held in the emblematic Casa de Convalescència in Barcelona, and organized by Dr. Patrick Aloy (IRB Barcelona) and Dr. Trey Ideker (UC San Diego, US), the conference gathered 150 international researchers to explore the potential of artificial intelligence (AI) to transform Drug Discovery.
A Comprehensive Map of the Human Cell. UC San Diego Today, Susanne Clara Bard, April 9, 2025
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).
Biological aging may not be driven by what we thought, Live Science, Feb 13, 2025
What drives aging? A new study draws a line between random genetic mutations and predictable epigenetic changes used to measure biological aging.
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
UC San Diego Ranks 7th in the World for Most Influential Researchers, UC San Diego today, December 4, 2024
Dr. Ideker has been selected as a 2023 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.
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
Jacobs School researchers named most highly cited in the world, Jacobs School of Engineering, November 17, 2023
Yet again, 16 faculty and researchers at the UC San Diego Jacobs School of Engineering were named among the world’s most influential in their fields in this year’s Clarivate listing of Most Highly Cited Researchers in the World.
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
Interview with Dr. Trey Ideker: Mapping the Circuitry of a Cancer Cell, National Cancer Institute (.gov), Nov 24, 2022
In this interview, Dr. Trey Ideker discusses systems biology and his CSBC research as co-director of the Cancer Cell Map Initiative (CCMI).
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
16 Jacobs School researchers among most highly cited in the world, Jacobs School of Engineering, November 22, 2022
A remarkable 16 faculty and research scientists at the UC San Diego Jacobs School of Engineering are among the world’s most influential researchers in their fields, according to the 2022 Clarivate listing of Most Highly Cited Researchers in the World. The list highlights individuals at universities, research institutes and commercial organizations who have demonstrated a disproportionate level of significant and broad influence in their field of research.
Bioengineering, bioinformatics graduate students selected as Siebel Scholars. Jacobs School of Engineering, September 22, 2022
Yue Qin, Graduate Student in the Ideker Lab, has been honored as a 2023 Siebel Scholar. The Siebel Scholars program recognizes the most talented students in the world’s leading graduate schools of business, computer science, bioengineering and energy science.
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
Interview with Dr. Ideker and Yue Qin. “Revealing a Cell’s Components through Artificial Intelligence” AZO Life Sciences (23 Dec 2021)
In this interview, we speak to Professor Trey Ideker and Yue Qin about their latest in cell biology and how artificial intelligence could be used to discover new components within cells.
10 Jacobs School faculty among 2021 list of most highly cited researchers in the world, Jacobs School of Engineering, November 30, 2021
View all 2021 Clarviate Web of Science Highly Cited Researchers
AI-Based MuSIC Reveals Previously Unknown Cell Components. GEN (29 Nov 2021)
The structure of the cell, and its components, have largely been explored through methods such as protein fluorescent imaging and protein biophysical association. Now, researchers have combined microscopy, biochemistry, and artificial intelligence techniques to advance the understanding of the cell by revealing previously unknown cell components…. Multi-Scale Integrated Cell (MuSIC), is described in Nature, in the paper, “A multi-scale map of cell structure fusing protein images and interactions.”
What is in our cells?, Healthcare-in-europe.com, Nov 27, 2021
Most human diseases can be traced to malfunctioning parts of a cell — a tumor is able to grow because a gene wasn’t accurately translated into a particular
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.
Using a new artificial intelligence identifying method, researchers at UC San Diego and its collaborators have taken what may turn out to be a significant leap forward in the understanding of human cells, according to a report published Wednesday. The pilot study — which combines microscopy, biochemistry techniques and artificial intelligence in a technique known as Multi-Scale Integrated Cell — revealed around 70 components contained within a human kidney cell line, half of which had never been seen before.
We Might Not Know Half of What’s in Our Cells, New AI Technique Reveals. UC San Diego News Center (24 Nov 2021)
See also: Phys.Org, Nanowerk, SciTech Daily, ScienceDaily, The Medical News, Neuroscience News, Science Blog, Laboratory Equipment.
Artificial intelligence-based technique reveals previously unknown cell components that may provide new clues to human development and disease
Investigators Aim to Identify New Treatment Targets with Cancer Cell Map Initiative. OncLive (16 Nov 2021)
The Cancer Cell Map Initiative, developed by investigators at the University of California San Francisco and the University of California San Diego, has successfully charted how hundreds of genetic mutations involved in breast cancer and cancers of the head and neck affect the activity of proteins that ultimately lead to disease.
Dog Years to Human Years: Your Canine’s Lifespan Explained. Newsweek (7 Nov 2021)
Whether you’ve got a puppy or an older pooch in your household, it is natural to wonder how to translate their age from dog years to human years. Historically, there have been various myths which claim to have the answer to this equation. One of these suggests that to find out a dog’s age, you simply multiply it by seven to reveal its human equivalent. But, how accurate is this really?
Studies Delve Deep into the Protein Machinery of Cancer Cells. National Cancer Institute, Cancer Currents Blog (4 Nov 2021) [PDF]
A team of researchers has used advanced technologies and computational techniques to identify the interactions among proteins that commonly form in head and neck and breast cancer cells. They also created a map of how the interacting proteins—also called protein complexes—function in key communication networks, or pathways, in those cells.
Uncovering Key Interactions Between Cancer-Driving Proteins, Technology Networks, Oct 19 2021
The CCMI aims to transform the field of cancer drug discovery by uncovering the molecular networks underlying the disease.
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)
UC San Diego ‘Cancer Cell Mapping’ Research May Improve Chemotherapy. Times of San Diego (2 Oct 2021)
Researchers at UC San Diego and UC San Francisco have mapped out how hundreds of mutations involved in two types of cancer affect the activity of discrete groups of proteins that are the ultimate actors behind the disease, reports published Friday revealed. The work points the way to identifying new precision treatments that may skirt side effects common with much current chemotherapy.
The effort, dubbed Cancer Cell Mapping Initiative, is led by Trey Ideker, professor at UCSD School of Medicine and Moores Cancer Center, and Nevan Krogan, director of the Quantitative Biosciences Institute at UCSF, who are co-senior authors on a set of three related studies that describe the map.
From COVID to cancer, gene-mapping tool could ‘revolutionize’ treatment, UCSF studies say. Danielle Echeverria, San Francisco Chronicle (2 Oct 2021) [PDF]
New research by UCSF and UC San Diego scientists involving techniques also deployed to fight COVID-19 has the potential to revolutionize cancer treatment by creating opportunities for more precision treatments, they say — which can be far less harmful than chemotherapy.
The collaborative effort — called the Cancer Cell Map Initiative — found that mapping the protein disruptions caused by DNA mutations, rather than just the mutations themselves, is very useful for grouping different kinds of cancer-causing mutations together. That opens up the opportunity to create precision treatments that can target groups of mutations, rather than just one.
On Thursday, the group released three papers in the journal Science describing how the maps work for breast cancer and cancers of the head and neck.
In-Depth Cancer Protein Mapping Project Sheds Light on Disease Processes, Clinical Omics, Oct 1, 2021
An in-depth project mapping cancer-causing gene mutations to their encoded proteins and also tracking protein-protein interactions in cancer has allowed University of California scientists to gain new insight into the complex mechanisms of this disease, using head and neck cancer and breast cancer as specific examples.
Published as three papers in the current issue of Science and led by researchers Trey Ideker, University of California San Diego (UCSD), and Nevan Krogan, University of California San Francisco (UCSF), the project used proteomic mass spectrometry and also computer-based data integration to map linked proteins found in cancer cells. They also used a statistical model of mutation to assess which proteins are “under strong mutational selection and in which cancer types,” explain the authors.
Looking Beyond DNA to See Cancer with New Clarity, UCSF News Room, By Robin Marks, September 30, 2021
Mapping How Mutated Proteins Interact Reveals Previously Unseen Drug Targets. Researchers at UC San Francisco and UC San Diego have mapped out how hundreds of mutations involved in two types of cancer affect the activity of proteins that are the ultimate actors behind the disease. The work points the way to identifying new precision treatments that may avoid the side effects common with much current chemotherapy.
See also:
- 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 , Sept 30, 2021
- First map of proteins in tumour cells pinpoints cancer therapy targets. New Scientist , Sept 30, 2021
Study identifies 579 genetic locations linked to anti-social behavior, alcohol use, opioid addiction and more. Science Daily, Aug 26, 2021
COVID-19: Scientists Identify Human Genes That Fight SARS-CoV-2 Infection, SciTech Daily, April 16, 2021
Research pinpoints interferon stimulating genes that control SARS-CoV-2 replication.
Scientists at Sanford Burnham Prebys have identified a set of human genes that fight SARS-CoV-2 infection, the virus that causes COVID-19. Knowing which genes help control viral infection can greatly assist researchers’ understanding of factors that affect disease severity and also suggest possible therapeutic options. The genes in question are related to interferons, the body’s frontline virus fighters.
The study was published in the journal Molecular Cell.
2020
10 Jacobs School Faculty Named in 2020 List of Highly Cited Researchers, Jacobs School of Engineering, December 8, 2020
Ten professors at the University of California San Diego Jacobs School of Engineering are among the world’s most influential researchers in their fields, according to a new research citation report from the Web of Science Group. The professors, Ludmil Alexandrov, Trey Ideker, Rob Knight, Nathan E. Lewis, Prashant Mali, Ying Shirley Meng, Bernhard O. Palsson, Joseph Wang, Kun Zhang and Liangfang Zhang, are amone 52 professors and researchers at UC San Diego named in the prestigious list of Highly Cited Researchers in 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
UC San Diego Bioengineering Department Makes Strong Showing in List of Highly Cited Researchers Around the World. UCSD Jacobs School of Eng. (Nov. 25, 2019)
- Eleven faculty members and affiliates of the Department of Bioengineering at the University of California San Diego are among the world’s most influential in their fields, according to a new research citation report from the Web of Science Group. UC San Diego played key roles in launching the discipline of bioengineering over 50 years ago, and the new report is yet another indicator that the Department of Bioengineering at the UC San Diego Jacobs School of Engineering continues to shape the future of bioengineering.
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]
Most of the human genome — 98 percent — is made up of DNA but doesn’t actually encode genes, the recipes cells use to build proteins. The vast majority of genetic mutations associated with cancer occur in these non-coding regions of the genome, yet it’s unclear how they might influence tumor development or growth. Now researchers at University of California San Diego have identified nearly 200 mutations in non-coding DNA that play a functional role in cancer. Each of the mutations could represent a new target in the search for cancer drugs. The study is published April 2, 2018 in Nature Genetics.
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)
- Tumor Suppressor Mutations Alone Don’t Explain Deadly Cancer, Jacobs School of Engineering (August 1, 2014)
- Although mutations in a gene dubbed “the guardian of the genome” are widely recognized as being associated with more aggressive forms of cancer, physicians and bioengineers at the University of California, San Diego School of Medicine have found evidence suggesting that the deleterious health effects of the mutated gene may in large part be due to other genetic abnormalities, at least in squamous cell head and neck cancers. The study, published online Aug. 3 in the journal Nature Genetics, shows that high mortality rates among head and neck cancer patients tend to occur only when mutations in the tumor suppressor gene coincide with missing segments of genetic material on the cancer genome’s third chromosome.
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).
In a novel use of gene knockout technology, researchers at the University of California, San Diego School of Medicine tested the same gene inserted into 90 different locations in a yeast chromosome – and discovered that while the inserted gene never altered its surrounding chromatin landscape, differences in that immediate landscape measurably affected gene activity.
The findings, published online in the Jan. 3 issue of Cell Reports, demonstrate that regulation of chromatin – the combination of DNA and proteins that comprise a cell’s nucleus – is not governed by a uniform “histone code” but by specific interactions between chromatin and genetic factors.
“One of the main challenges of epigenetics has been to get a handle on how the position of a gene in chromatin affects its expression,” said senior author Trey Ideker, PhD, chief of the Division of Genetics in the School of Medicine and professor of bioengineering in UC San Diego’s Jacobs School of Engineering.
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)
- Cells Use Mix-and-Match Approach to Tailor Regulation of Genes. Jacobs School of Engineering. (June 16, 2006)
- Pharmaceutical companies are hoping to develop drugs that selectively block the binding of transcription factors to upstream sequences of genes as a way to short-circuit the harmful effects of diseases, and researchers at the University of California, San Diego on June 16 reported new findings that could aid that effort.
- 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)
- UC San Diego’s Entrepreneurism Center Funds Nine New Faculty Projects for Technology Commercialization, Jacobs School of Engineering, (May 22, 2006)
- UCSD’s von Liebig Center for Entrepreneurism and Technology Advancement has awarded approximately $430,000 to nine projects led by faculty from the Jacobs School of Engineering. The projects include a bioengineered treatment for anemia; and a miniature camera for certain types of minimally invasive surgery.
- Cell, Heal Thyself: New systems biology model reveals how cells repair DNA damage, Jacobs School of Engineering, May 18 (2006)
- Researchers at UCSD and three other institutions have described for the first time a web of inter-related responses that cells use to avoid becoming diseased or cancerous after being exposed to a powerful chemical mutagen. The group led by UCSD bioengineering professor Trey Ideker describe in the May 19 issue of Science an elaborate system of gene control that is triggered by chemical damage to DNA.
- 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)
- Two UCSD Bioengineering Professors Recognized as Pioneers in Emerging Field of Comparative Interactomics, Jacobs School of Engineering, March 20, 2006
- Technology Review, MIT’s magazine of technology, has highlighted two bioengineering professors at the University of California, San Diego (UCSD) Jacobs School of Engineering, as pioneers of one of 10 “emerging technologies” that the magazine predicts will soon transform computing, medicine, telecommunications, and business.
- 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)
- Ideker named a Top 35 Innovator Under the Age of 35, MIT 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. (October 15, 2004)
- The David and Lucile Packard Foundation has named Trey Ideker, an assistant professor at UCSD’s Jacobs School of Engineering, as one of this year’s 16 recipients of the Packard Fellowships for Science and Engineering. Ideker and each of the other fellows will receive unrestricted research grants of $625,000 over five years.
- Thinking, Tinkering, Tooling in Systems Biology, Genomics and Proteomics (2004)
- UCSD Undergraduates Participate in Collaborative Studies Abroad on Cyberinfrastructure, Jacobs School of Engineering, July 8, 2004
- Nine undergraduate students from the UCSD Jacobs School of Engineering have arrived in Asia and Australia to conduct collaborative research on a wide variety of topics related to cyberinfrastructure. They are part of a new Pacific Rim Undergraduate Experiences (PRIME) program funded by the NSF. This summer’s host institutions are in Osaka, Japan; Hsinchu and Taipei, Taiwan; and Melbourne, Australia.
- 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)