Columbia University Bio Bytes
By Columbia Sys Bio Initiative
Welcome to Bio Bytes, your starting point for all things Systems Biology. Tune in for interviews with prominent scientists working at the intersection of Biology, Engineering, Medicine, Computer Science, and Mathematics.
Bio Bytes 27: Microbial Systems and Synthetic Biology with Harris Wang
In which Harris Wang, associate professor of Systems Biology at the Columbia University Irving Medical Center, and Vaibhav discuss the application of systems and synthetic biology to the study of microbial communities. He describes the motivation and application of many of his group's seminal contributions (MAGE, CAGE, MaPS-seq), the various use cases of synthetically minimal genomes and engineered bacteria, and closes with some advice for young scientists and trainees.
November 19, 2021
Bio Bytes 26: Precision Medicine with Adam Bass
In which Adam Bass, oncologist and inaugural director of the Columbia Center for Precision Cancer Medicine, discusses the relevance of genomic science and treatments informed by sequencing in modern cancer medicine. Among other things, Vaibhav and Adam discuss current standards of care involving sequencing, the importance of first-principles understanding and research in advancing medicine, and what the future of precision medicine might look like.
November 7, 2021
Bio Bytes 25: Engineering Chromatin, DNA Databases, and Neurodevelopmental Organoids with Albert Keung
In which Albert Keung, Assistant Professor in the department of Chemical and Biomolecular Engineering at North Carolina State University, shares many insights on Synthetic Biology. He touches on synthetically perturbing the chemical makeup of chromatin, designing and using DNA databases to store digital information, and the challenges and promise associated with developing cerebral organoids.
September 17, 2021
Bio Bytes 24: Gut Microbiome Biotechnology with Zack Abbott
In which Aaron speaks with Zach Abbott, PhD, about his company ZBiotics. ZBiotics is a biotechnology start-up that is focused on engineering microorganisms for consumer benefit. Aaron and Zach talk about the company’s current product, a genetically engineered probiotic designed to breakdown acetaldehyde, a toxic byproduct of alcohol. Additionally, Zach offers insight on his transition from completing a PhD to the biotech start-up space.
March 27, 2021
Bio Bytes 23: Machine Learning and Structural Biology with Mohammed AlQuraishi
In which Vaibhav speaks with Dr. Mohammed AlQuraishi, an Assistant Professor of Systems Biology at the Columbia University Irving Medical Center, about using machine learning to predict protein structure. Among other things, they discuss the direction of algorithmic development in computational structure prediction, from neighborhood-based assembly of peptide fragments to modern applications of Deep Learning in structural modeling. They discuss the features of physical priors and discuss approaches in computationally optimizing protein-energy state predictions, taking into account the difficulties associated with the many local minima in an energy function. Throughout this discussion, Mohammed contextualizes the intuition behind the methods used by Deep Mind with their developments of AlphaFold.
March 13, 2021
Bio Bytes 22: Aneuploidy and Cancer Biology with Alison Taylor
In which Vaibhav speaks with Dr. Alison Taylor, an Assistant Professor of Pathology and Cell Biology at the Columbia University Irving Medical Center, about her research on the role of aneuploidy (abnormal numbers of chromosomes) in cancer. Among other things, they discuss the basic mechanisms of aneuploidy, the ways in which it can favor cancer development, and contemporary approaches in chemically targeting aneuploid cells. Alison explains her group's models for studying aneuploidy and their new computational genomics efforts as well. She concludes by discussing ongoing projects in her lab and some pressing questions about genome integrity in cancer initiation and progression.
February 27, 2021
Bio Bytes 21: Antiviral Drug Development with Dr. Alex Chavez
In which Aaron speaks with Alex Chavez, MD-PhD about antiviral drug development. They discuss chemical strategies for protease inhibitor development and the details and rationale of a novel assay that allows for early validation of candidate drugs. Additionally Alex discusses newer collaborations he is engaged in to build cellular resistance to damaging radiation.
February 20, 2021
Bio Bytes 20: Orthopedics and Regenerative Biology Research with Stavros Thomopoulos
In which Josh speaks with Stavros Thomopoulos, PhD about biomechanical engineering at the tendon-bone interface. Dr. Thomopoulos is the director of the Caroll Laboratories for Orthopedic Surgery and the Vice Chair for Basic Science Research in Orthopedic Surgery at the Columbia University Irving Medical Center. Among other things, they discuss the challenges of attaching a tendon to a bone and stem cell-based regenerative medicine to improve healing in orthopedic injuries, such as those to the rotator cuff.
February 12, 2021
Bio Bytes 19: Molecular Cardiology with Andy Marks
In which Josh explores the intersection of molecular biology, structural biology, and cardiology with Dr. Andrew Marks. Dr. Marks is the Chairman of the Department of Physiology at Columbia Medical School, the Founding Director of the Wu Center for Molecular Cardiology, and a professor of Physiology and Cellular Biophysics and Medicine. Among other things they discuss his critical development of the rapamycin coated drug eluting stent, his past and current work on Ryanodine receptors, and the multi-system impact of defective Ryanodine receptors.
February 3, 2021
Bio Bytes 18: Genome Topology and Leukemia with Aaron Viny
In which Vaibhav and Dr. Aaron Viny (a clinician scientist and assistant professor at Columbia) discuss the role of Cohesin complexes in 3D genome organization and how spatiotemporal irregularities in higher order genetic structures lead to blood cancers. They talk about the importance of linage commitment and how a disorganized genome can prevent it. Aaron concludes with a discussion of his experience as a physician-investigator and meeting (now president-elect) Joe Biden.
November 10, 2020
Bio Bytes 17: Epigenome Editing and the Neuroepigenome with Shawn Liu
In which Vaibhav and Shawn Liu (The Joan and Paul Marks, MD ’49 Assistant Professor of Physiology and Cellular Biophysics at CUIMC) speak about the specifics of epigenome editing, from selecting the right model cells, to tool design, to loci considerations for editing experiments and much more. They also touch on how neurons are methylated during memory acquisition and the potential for in vivo neuroepigenome editing. Find out more about Shawn's work here: https://epibrain.info
September 1, 2020
Bio Bytes 16: The Power of Single Cell Data Analysis with Dana Pe'er
In which Dana speaks with Vaibhav and Jason about the principles of single cell analysis and informatics challenges associated with it. Among other things, they discuss manifolds and data topology, Bayesian approaches and considerations in prior distribution selection in biology, matrix factorization and imputing missing cell states with graphical walks through phenotypic space, and the utility of diffusion components when Principal Component Analysis is insufficient. Dana concludes with some advice for young people interested in Systems and Computational Biology.
June 5, 2020
Bio Bytes 15: Small Molecule Perturbation, Ferroptosis, Computational Chemistry, and COVID-19 treatments with Dr. Brent Stockwell
In which Vaibhav and Dr. Stockwell talk about how using small molecule screening helped uncover pioneering details about Iron influenced cell death (Ferroptosis), the therapeutic context for Ferroptosis, and ligand prediction with computational chemistry. They conclude with some discussion about Dr. Stockwell's current collaborative SARS-CoV2 antiviral efforts.
May 17, 2020
Bio Bytes 14: Quantifying and Representing Genetic Variation with Dr. Tuuli Lappalainen
In which Dr. Lappalainen speaks to Vaibhav and Mona about a variety of topics including her latest paper in Science, the various considerations one needs to make when interpreting statistical genomic data, and a graphical representation of genomes as opposed to the traditional linear model.
May 8, 2020
Bio Bytes 13: CRISPR-Cas13 and Using Deep Learning to Model Gene Regulatory Networks with Dr. Xuebing Wu
In which Vaibhav, Jason, and Professor Xuebing Wu discuss the mechanism and applications of CRISPR-Cas13 and how deep learning might be used to model a unified gene regulatory network.
April 12, 2020
Bio Bytes 12: All About Coronavirus with Dr. Vincent Racaniello (Part 2)
In which Vaibhav and Professor Racaniello continue to speak about the epidemic timeline, the use and biology of Anti-Malaria drugs against COVID-19, single cell and CRISPR based antiviral studies, and other topics, like how strong immunity to the virus is (once developed).
March 25, 2020
Bio Bytes 11: All About Coronavirus with Dr. Vincent Racaniello
In which Vaibhav speaks to Vincent Racaniello, professor of Virology at Columbia University, about the science behind the current Coronavirus (SARS-CoV-2). Among other topics, they discuss the origins of the virus and the rationale behind current retroviral drug based approaches to treat patients.
March 25, 2020
Bio Bytes 10: Dr. Elham Azizi Part 2
In which Vaibhav and Dr. Azizi continue their discussion on using machine learning to integrate various data modalities into sensible probabilistic and statistical models to better understand cancer genetic networks.
January 31, 2020
Bio Bytes 9: Dr. Elham Azizi Part 1
In which Vaibhav and Dr. Elham Azizi discuss the role of machine learning, AI, and data modeling in cancer biology.
January 31, 2020
Bio Bytes 8: Dr. It'sik Pe'er Part 2
In which Vaibhav and Jason talk to Dr. Pe'er about the central goals of Systems Biology, the projects that he's most excited about, and what sorts of coursework students should complete to prepare themselves for getting into the field
December 28, 2019
Bio Bytes 7: Dr. It'sik Pe'er Part 1
In which Vaibhav and Jason talk to Dr. It'sik Pe'er, Associate Professor of Computer Science with cross-affiliation in the Systems Biology department, about his current projects and the emergence of computational biology
December 28, 2019
Bio Bytes 6: Dr. Sam Sternberg - Part 2
In which Vaibhav and Jason talk to Dr. Sternberg about how computational power is advancing his work with CRISPR
December 22, 2019
Bio Bytes 5: Dr. Sam Sternberg - Part 1
In which Vaibhav and Jason speak with Dr. Sam Sternberg about his work at the forefront of CRISPR tools development
December 22, 2019
Bio Bytes 4: Chao Lu
In which Vaibhav speaks to Dr. Chao Lu, Assistant Professor of Genetics and Development at CUMC, about his work in the field of Epigenetics and how computation is accelerating progress in discovering novel targets for therapy.
April 16, 2019
Bio Bytes 3: Raul Rabadan
In which Miriam Interviews Dr. Raul Rabadan about the role of computing in Systems Biology, his journey as a theoretical physicist from CERN to the Institute for Advanced Studies in Princeton, to Columbia's Systems Biology Department, and why now is the time to be excited about Systems Biology.
April 10, 2019
Bio Bytes 2 with Nicholas Tatonetti
In which Miriam speaks to Dr. Nicholas Tatonetti, Herbert Irving Assistant Professor of Biomedical Informatics, about his research regarding EHR, his children's book Toshi Builds Consensus, and much more!
April 2, 2019
Podcast 1: Understanding Systems Bio, Synthetic Bio, and Computational Bio, and Bioinformatics
In which Miriam, Allison, and Vaibhav go over similarities and differences between Systems Bio, Synthetic Bio, and Computational Bio, and Bioinformatics.
March 21, 2019
In which we introduce ourselves, give a brief overview of Systems Biology, and discuss the potential of the field.
March 13, 2019