IQ Biology

BioFrontiers Institute and IQ Biology alum, Joey Azofeifa (Arpeggio Bio), Raises $3.2 Million in Seed Funding and is Named to the 2020 Forbes 30 Under 30 List in Healthcare

Anonymous — Wed, 15 Jan 2020 23:51:42 +0000

BioFrontiers Institute and IQ Biology alum, Joey Azofeifa (Arpeggio Bio), Raises $3.2 Million in Seed Funding and is Named to the 2020 Forbes 30 Under 30 List in Healthcare Anonymous (not verified) Wed, 01/15/2020 - 16:51

Arpeggio Bio, a preclinical company whose technology provides a mechanistic understanding of how drugs work, today announced that it has closed a $3.2 million seed financing round, which was oversubscribed by over $2 million. Funding will support the ongoing development of a nascent RNA drug screen.

“We’re excited to have the support of our investors to allow us to continue our mission of helping bring new therapies to patients with epigenetically-driven diseases,” said Joey Azofeifa, Ph.D., Founder and CEO, Arpeggio.

Since inception in 2018, Arpeggio has partnered with over twenty biotech and pharmaceutical companies — including four of the world’s top ten — to uncover new insights into their therapeutics. Arpeggio’s early market traction and progress led it to be selected for the prestigious Y Combinator’s (YC) Summer 2019 batch, which provides emerging startups with funding and mentorship. Following a successful program tenure, Dr. Azofeifa’s YC Demo Day pitch attracted distinguished investors to lead a funding round, including Khosla Ventures, FundersClub, Fifty Years, TechU, and YC.

Arpeggio has built an automated system that collects information about which genes turn on or off for hundreds of time points beginning in the minutes following drug treatment in preclinical models. Using algorithms originally developed for financial forecasting, Arpeggio reconstructs the biological network a drug affects and identifies the genes critical for the success or failure of a drug. This new kind of data allows for the elucidation of novel drug and disease mechanisms, supporting development of safer, more effective therapies by understanding drug effects before they’re given to patients.

The company's platform analyzes its time-series RNA profiles using proprietary machine learning algorithms developed by Dr. Azofeifa. Driven by Arpeggio’s success, Dr. Azofeifa was recently named to the 2020 Forbes 30 Under 30 List in the Healthcare category, recognizing him as one of the country’s top young entrepreneurs.

Arpeggio's technology combines a proprietary biological assay and machine learning algorithms that, together, enable rapid, high-resolution snapshots of cellular dynamics following drug treatment. These snapshots are then analyzed to reveal the biological networks that determine a drug’s function and guide therapeutic development. To learn more, www.arpeggiobio.com

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A Summer Internship Where Only the Cows Obey Traffic Signals

Anonymous — Wed, 13 Nov 2019 20:37:08 +0000

A Summer Internship Where Only the Cows Obey Traffic Signals Anonymous (not verified) Wed, 11/13/2019 - 13:37

Lindsay Diamond

IQ Biology graduate student, Taisa Kushner, spent her summer as a Microsoft Research intern in Bangalore, India, working on a global mental health platform.

Can you tell us about your internship experience at Microsoft Research?

I interned at Microsoft Research (MSR) in Bangalore, India this past summer. MSR is under the umbrella of Microsoft, but it is separate from Microsoft corporate, where they do product development and engineering. The work that comes out of MSR does influence products at Microsoft, but MSR is focused on basic research and functions more like academia than industry. MSR has multiple labs throughout the world, and each lab focuses on a different broad area. The Bangalore lab houses their "Tech for Emerging Markets" (TEM) group, which does computational social science, fieldwork, and tech development focused on working with and for individuals in developing countries. I have been interested in the work coming out of the TEM group for a couple of years and applied to be a Ph.D. intern at the lab. Luckily, after a few rounds of interviews, I got the position!

I worked with Dr. Amit Sharma in the TEM group, whose primary research focus is on causal inference and the societal impact algorithmic interventions can have. My project centered around a global mental health platform, Talklife, which seeks to provide a peer-to-peer support network for individuals suffering from psychological distress. When considering interactions on this platform, some end up being helpful, while others are not. Broadly, my work this summer focused on answering the questions, "What makes a certain series of interactions helpful to users?" And, "Are there actions individual users can take to improve their experience on the platform?"

What surprised you about the experience?

I knew MSR functioned more like academia than industry, but I was surprised by the extent to which there is not any hierarchy. Everyone is very humble despite being brilliant. The lab director, Sriram Rajamani, is very kind and collaborative. Despite being busy, he takes time to get to know everyone, including all the interns. I was able to have lunch with Sriram and discuss research ideas for my work back here in �鶹ӰԺ. I appreciated being treated as a research equal by all the full-time researchers.

Did your IQ Biology experience play a role in this experience?

Yes! It is such an interdisciplinary environment. For my project, in particular, we had to communicate with the company Talklife, which provided us with data, physicians from both the US and India, and other researchers who work on societal differences in mental health care and communication across the US and India. Through IQ Biology, I have gained a skill set of being able to effectively communicate with people from different backgrounds and also critically think through all of the aspects of a research problem. For this project, I had to consider how to identify causal relations within the data (math), identify and understand biases that might be present in the data (health care, social science), how to think about and handle them, and how to bridge computational work with medical care. With mental health, in particular, the stigmas are very different in the US and India, and people utilize different words and descriptions to discuss symptoms and how they manifest. You need to understand the human aspect of these nuances to deal with the data effectively.

Would you recommend doing a summer internship as part of grad school? Why/Why not?

Yes, 100%. Working at MSR is still very academic-focused rather than a traditional industry internship, so I can only speak to my experience. Still, I appreciated the opportunity to branch out from my doctoral research, which focuses on artificial pancreas controllers for individuals with type-1 diabetes. I had a lot of freedom to explore the data, and I learned techniques in causal inference, natural language processing, and I learned about how mental health care differs across the globe, which I feel will be beneficial to future work I do.

I would also recommend doing research in an eastern setting, if possible. I thought the experience provided a critical exposure to have as a researcher. I appreciated the opportunity to hear about the differences in culture and opinions and the needs of people in India. MSR brings in a lot of collaborators, and the Bangalore lab does a significant amount of social science focused on working with impoverished people across India, in their language. MSR identifies the needs they have in terms of life stressors and how technology may help rather than taking research done in the west and assuming other people want the same thing.

Did anything happen during your internship outside of the research/work experience that made an impression on you? Any lessons learned while abroad?

MSR brings in lots of researchers and doctoral interns from across the world. As a result, I was able to befriend people who come from different backgrounds. I appreciated embedding into the Indian culture through working and living there rather than just as a tourist. One of the other interns, who is a professor at the University of Cincinnati, is originally from the Indian state of Kerala. I visited her family's rubber and pineapple farms and experienced parts of India that I don't think I would otherwise get to see.

What will happen to the work you were doing during your experience?

We have submitted a paper on the work, and we have a second paper in progress. Related work on the project is being continued at MSR now, and I'm assuming they will have new interns on the project in the future. If anyone wants to talk more about the project or my experience, I'd be happy to connect!

Did this experience affect your current career plans?

It was very helpful in making me feel more competent as a researcher, which is nice to be able to say. I feel like I was able to approach a pretty loosely defined project and complete a substantial amount of work on it. I had a lot of independence in the process, along with excellent mentoring, which made it a great experience overall. In terms of working at MSR again, I would love to work at MSR Bangalore, though there is a lot about living in India that would be tough long-term. It's also a challenging position to obtain.

What is your favorite memory from this experience?

Oh, so many! All of the people I was able to meet and befriend. Everyone was so kind and welcoming. I learned so much about India, the local politics, climate problems, and social structure. It was fascinating to see US news from the Indian perspective and to listen to the thoughts and opinions of people who are not from the west.

We did have one very ridiculous series of events where we almost got stuck in the Indian Himalayas and, as a last resort effort, ended up going to Kashmir during the peak in military occupation and unrest surrounding the split of the state and removal of article 370. This adventure involved classic Indian twelve-passenger van travel for 17 hours straight with people I had never met. The van was a classic sight: completely falling apart, the exhaust poured in from the gear shift, yet it was decorated with LEDs and cheesy phrases. We had tea in the middle of nowhere in Kashmir at 2:00 am. I genuinely thought we would fall off the mountainside on this incredibly steep and narrow dirt path, and we had a run-in with the Indian Army 30km outside of Srinagar when our driver didn't have his driver's license. Thankfully, they let us through because we all had our proper documents.

I miss being in Bangalore with its almost 13 million people living there. It was overwhelming at times, but by the end, I loved it. I enjoyed being able to safely walk around at any time and see people congregated around tea shops and street food at all hours of the day. It's a lively city. The cows wandering the streets are also very fun. They are the only ones who obey traffic signals.

The Interdisciplinary Quantitative (IQ) Biology Ph.D. Certificate is designed for students interested in gaining interdisciplinary quantitative skills, while also joining a network of interdisciplinary faculty and peers across our eleven partner departments.

IQ Biology graduate student, Taisa Kushner, talks about her summer as a Microsoft Research intern in Bangalore, India, working on a global mental health platform.

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Chris Smith (IQ Biology): Evolution Meeting

Anonymous — Wed, 26 Jun 2019 20:47:51 +0000

Chris Smith (IQ Biology): Evolution Meeting Anonymous (not verified) Wed, 06/26/2019 - 14:47

Chris Smith

I just got back from the Evolution Meeting in Providence and I’m full of information and ideas for research. I had the opportunity to reconnect with past colleagues and meet some new people. Other CU �鶹ӰԺ folks attended, including the labs of Dan Doak, Nancy Emery, Nolan Kane, Stacy Smith, and Scott Taylor (sorry if I missed any others).

Although most of the research represented at Evolution is empirical research on understanding and preserving biodiversity, many attendees were excited to discuss methods. In particular, producing large amounts of DNA sequencing data - both empirically, and using computer simulations - is no longer limiting in many cases. Therefore, the challenge of developing theory and methods for analyzing these data has received more attention in recent years.

Highlighting a couple of talks I thought were memorable: Paul Hohenlohe (U. Idaho) described the array of reduced representation sequencing approaches that are available and important trade-offs among them. Adam Jones (also U. Idaho) used simulations to see if and how pleiotropy and epistasis affect scans for loci involved in adaptation; he reported that pleiotropic effects don’t really affect outlier scans and that some important loci are still detected in the presence of genetic interactions. Zach Gompert (Utah State) presented a cool approach for quantifying fluctuating selection.

My presentation was part of the session on Population Genetics Theory, which is too broad of a name for the session because the talks were each focused specifically on inferring historical population sizes and admixture. Multiple speakers used ancient DNA to infer population history and used computer simulations to validate their approach. Other speakers, including myself, were trying to “break” commonly used tools that infer population history, to understand which parameters and data work best, or worst.

On a fun note, we got to see the “WaterFire” event in downtown Providence next to the convention center. This event is a big deal. There were thousands of attendees packed onto bridges and standing in the park along the river. Leading up to, and during the event, large amplifiers played music covering a range of- and alternating dissonantly between- intense classical music, tribal music, country music, and horns. At dusk, they lit small bonfires floating on the river. That’s it.

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Kristin Powell Serves on Interdisciplinary Teaching, Research and Creative Work Committee

Anonymous — Tue, 26 Feb 2019 07:00:00 +0000

Kristin Powell Serves on Interdisciplinary Teaching, Research and Creative Work Committee Anonymous (not verified) Tue, 02/26/2019 - 00:00

Academic Futures

Jim White, interim dean of the College of Arts and Sciences, today announced the composition of the Interdisciplinary Teaching, Research and Creative Work committee, which he chairs. The committee will explore what the campus needs to effectively embrace interdisciplinarity in both education and scholarship.

“Interdisciplinarity is a theme that recurs strongly in the life of the CU �鶹ӰԺ campus,” said White. “It is a key recommendation of the Academic Futures Committee, the subject of a variety of Academic Futures white papers and of conversations within academic units and during last year’s town halls. I’m looking forward to the committee taking on a topic with such strong implications for our teaching, research and creative work.”

White said the campus “is at a watershed moment in which we can consider the full potential of interdisciplinary research while removing barriers to interdisciplinary teaching and creative work.”

“This is the right moment, and this committee has the right people, to take on these vital and exciting questions,” White said.

The committee will begin its work this spring and is expected to deliver its recommendations to campus on Sept. 1, 2019.

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Research here could speedup clinical trials around Type 1 diabetes

Anonymous — Thu, 06 Dec 2018 07:00:00 +0000

Research here could speedup clinical trials around Type 1 diabetes Anonymous (not verified) Thu, 12/06/2018 - 00:00

Josh Rhoten

Researchers at CU �鶹ӰԺ have developed virtual clinical trials for an artificial pancreas that could significantly improve treatments for those with Type 1 diabetes by tailoring medical devices and speeding up trials.

The work was done through a four-year, $600,000 award from the National Science Foundation and was headed at the CU �鶹ӰԺ College of Engineering and Applied Science by Sriram Sankaranarayanan, an associate professor and the Roubos Engineering Endowed Faculty Fellow in the Department of Computer Science. Sankaranarayanan said the project has led to research papers in journals and conferences across many disciplines and created numerous areas of collaboration between his group, chemical engineers, mathematicians, statisticians, biologists and physicians focused on the treatment of Type 1 diabetes.

“Type 1 diabetes is one of the few diseases where the treatment could be technological, so it sits at the convergence of health, human behavior, computer science and mathematics. It’s a really interesting sweet spot for us to explore and a field that has grown a lot since we started the work,” he said.

There were many collaborators on the project, including other faculty at CU �鶹ӰԺ, researchers from the Rensselaer Polytechnic Institute (RPI) in New York, the Barbara Davis Center at the University of Colorado Anschutz Medical Campus and the Stanford University Medical Center. The project also involved CU computer science PhD student Taisa Kushner.

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Barn swallows may indeed have evolved alongside barns, humans

Anonymous — Tue, 30 Oct 2018 06:00:00 +0000

Barn swallows may indeed have evolved alongside barns, humans Anonymous (not verified) Tue, 10/30/2018 - 00:00

Cay Leytham-Powell

As humans evolved and expanded, so too did barn swallows, new research from CU �鶹ӰԺ suggests

The evolution of barn swallows, a bird ubiquitous to bridges and sheds around the world, might be even more closely tied to humans than previously thought, according to new study from the �鶹ӰԺ.

Chris Smith (left) and Rebecca Safran (right) re-examined the evolution of barn swallows and found that they may indeed have evolved alongside barns. Photographs courtesy of Rebecca Safran and Patrick Campbell/�鶹ӰԺ.

The research, published this week in Molecular Ecology, offers preliminary insight suggesting that the barn swallow and its subspecies evolved alongside—but independently from—humans. These new results make it one of the only known species, in addition to microscopic organisms like bacteria or viruses, to have developed in such a way, upending previous assumptions that barn swallows evolved prior to human settlement.

“Humans could be a really big part of the story,” said Rebecca Safran, a co-author of the study and an ecology and evolutionary biology (EBIO) associate professor at CU �鶹ӰԺ. “There’s very few studies that can point to the exact influence of humans, and so here, this coincidence of human expansion and permanent settlement and the expansion of a group that relies really, really heavily on humans is compelling.”

Barn swallows are found across the northern hemisphere and are characterized by their mud-cup nests that are built nearly exclusively on human-made structures. Despite their prevalence, however, not much is known about their evolutionary history, the timing of their expansion from northern Africa (where they originated) or how the six subspecies evolved so physically and behaviorally different yet remain almost genetically identical.

Previous studies published in the Proceedings of the Royal Society of London and Molecular Phylogenetics and Evolution looked into these questions and found that the different subspecies split early, well before human settlement.

This new study, however, gave the topic a fresh look by examining the whole genome of 168 barn swallows from the two sub-species farthest apart on an evolutionary scale: H. r. savignii in Egypt (a non-migratory species that lives along the Nile) and H. r. erythrogaster in North America (a species found throughout North America that migrates seasonally to South America).

Barn swallow subspecies are found throughout the northern hemisphere. Barn Swallow illustrations courtesy of Hilary Burn, and map courtesy of the Safran lab.

These data—which are on the order of 100,000 times bigger than the previous dataset used—were then analyzed with more sophisticated computational resources and methods than previously available. This allowed researchers to get a more complete picture that places the timing of barn swallow differentiation or speciation (i.e., when the barn swallow subspecies separated) closer to that of when humans began to build structures and settlements.

“The previous studies were playing with the idea of potential impact on population sizes due to humans,” said Chris Smith, a graduate student in EBIO and the Interdisciplinary Quantitative Biology program, and the study’s lead author. “Our results suggest a much more substantial link with humans.”

These new preliminary findings also suggest that this evolutionary link may have been forged through a “founder event,” which is when a small number of individuals in a species take over a new environment and are able to expand their new population there thanks to an availability of resources and an absence of competitors. For barn swallows, this event may have occurred rapidly when they moved into a new, relatively empty environment: alongside humans.

“Everyone is always wondering how do you study speciation? It’s been viewed as this long-term, million-year (process), but in barn swallows, we are not talking about differentiation within several thousands of years,” said Safran. “Things are really unfolding rather rapidly.”

Smith concurred: “It’s interesting to study speciation in the beginning steps.”

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World Congress of Biomechanics – Dublin, Ireland

Anonymous — Wed, 24 Oct 2018 16:53:57 +0000

World Congress of Biomechanics – Dublin, Ireland Anonymous (not verified) Wed, 10/24/2018 - 10:53

Kristin Calahan

This summer, I had the opportunity to present my research at the 2018 World Congress of Biomechanics in Dublin, Ireland. As the premier meeting worldwide in the field of biomechanics, this was an incredible opportunity to network with scientists in this field, both within my subfield of biomechanics and far outside of it. I especially enjoyed this aspect of the conference because as an IQ Biology student I am intrigued by interdisciplinarity and the intersection of biology and mechanics at different length scales.

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IQ Biology Program Wins IGERT

Anonymous — Tue, 13 Jan 2015 07:00:00 +0000

IQ Biology Program Wins IGERT Anonymous (not verified) Tue, 01/13/2015 - 00:00 BioFrontiers

BioFrontiers Institute's IQ Biology program wins National Science Foundation Grant

The BioFrontiers Institute’s Interdisciplinary Quantitative Biology Certificate Ph.D. (IQ Biology) program recently was awarded a $3 million grant from the National Science Foundation’s Integrative Graduate Education and Research Traineeship (IGERT) program. These funds will be spent over the next five years on supporting the students in the IQ Biology program in their work toward advanced interdisciplinary degrees in the biosciences.

IGERT is the National Science Foundation’s flagship interdisciplinary training program, educating U.S. Ph.D. scientists and engineers by building upon their disciplinary knowledge with interdisciplinary training. One of the goals of the IGERT program is to give students the personal and professional skills to succeed in 21^stcentury careers. Since 1998, the IGERT program has given 278 awards to top institutions throughout the country and provided funding for approximately 6,500 graduate students.

“The IGERT grant will allow us to expand our IQ Biology program beyond the successful foundation we have already built,” said BioFrontiers Director Tom Cech. “It is imperative that we train students to go beyond the limits of their academic departments and explore other research areas to develop solutions. The IGERT grant is giving us the resources to continue this program and confirms our belief that interdisciplinary education is a valuable component in training our future educators, scientists and engineers.”

The IQ Biology Program

The IQ Biology program is the graduate education arm of the BioFrontiers Institute. The program was designed to give graduate students the opportunity to earn a Ph.D. in one of eight academic departments:

Applied Mathematics
Chemistry and Biochemistry
Chemical and Biological Engineering
Computer Science
Ecology and Evolutionary Biology
Mechanical Engineering
Molecular, Cellular and Developmental Biology
Physics

In addition to an advanced degree, students are also immersed in an interdisciplinary culture where they gain additional skills in computational biology and mathematics, and complete lab rotations in areas outside their field of study. IQ Biology faculty members are active in interdisciplinary research themselves and offer a unique perspective to students wanting to prepare for careers in education or industry that demand a multi-disciplinary approach.

IQ Biology’s first class of nine students completed their first year of the pilot program in May and will be joined by a new class of seven students this fall. They entered CU-�鶹ӰԺ as interdisciplinary scholars and will continue to refine their training in their selected majors after their first year. Distinguished Professor of Chemistry and Biochemistry, Tom Cech is the current principal investigator of the program, and he is joined by the following co-principal investigators:

Kristi Anseth, Distinguished Professor of Chemical and Biological Engineering
Meredith Betterton, Associate Professor of Physics
Robin Dowell, Assistant Professor of Molecular, Cellular and Developmental Biology
Manuel Lladser, Assistant Professor of Applied Mathematics

CU and NSF's IGERT Program

NSF funded the IQ Biology program, in part, because of the flexibility it gives graduate students who want to cross-train in multiple disciplines, and customize their education to meet their individual education and research goals. The state of Colorado has benefited greatly from IGERT grants. The University of Colorado has had four other IGERT-funded programs:

The Graduate Training in Optical Sciences and Engineering (OSEP 2), led by Professor of Physics and JILA Fellow at CU-�鶹ӰԺ, Dana Anderson, implemented a new graduate training program in optical science. Students in the program produced an ultrastable atomic force microscope for studying proteins.
The Interdisciplinary Graduate Education in Computational Optical Sensing and Imaging (COSI) program, led by Professor of Electrical and Computer Engineering at CU-�鶹ӰԺ, Rafael Piestun, focused on using interdisciplinary approaches to develop instrumentation and algorithms that use optical forces to manipulate particles, molecules and atoms.
The Carbon, Climate and Society program, led by Professor of Geological Sciences and Director of the Institute of Arctic and Alpine Research at CU-�鶹ӰԺ, James White, used interdisciplinary education approaches to better train graduate students on the carbon cycle, climate change and human interactions with the environment.
The Sustainable Urban Infrastructure-Integrating Engineering, Planning, Policy, Health and Human Behavior Perspectives, led by Professor of Civil Engineering and Director for the Center of Sustainable Infrastructure Systems at CU Denver, Anu Ramaswami, addressed the interconnections between infrastructure engineering, urban planning, public policy, health and human behavior that need to be explored to design effective and sustainable urban infrastructure systems.

Additional IGERT grants have been awarded to Colorado State University and Colorado School of Mines.

�鶹ӰԺ the BioFrontiers Institute

The BioFrontiers Institute began in 2003 as a grassroots effort between University of Colorado scientists to break down academic barriers and work across disciplines on significant challenges in biotechnology and biosciences. The Institute is led by Nobel Laureate Tom Cech and Chief Scientific Officer Leslie Leinwand, and includes faculty members from across CU. In addition to research and its applications, the BioFrontiers Institute is also focused on educating the next generation of interdisciplinary scientists, beginning with its Interdisciplinary Quantitative Biology graduate certificate program. The IQ Biology program allows students to work toward a degree in one of eight academic departments, while receiving collaborative opportunities and research experience across many disciplines.

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