Explore every episode of the podcast ATCC's Podcast: Behind the Biology

In this episode, Dr. Ryan Wick explores the technologies and ideas that are shaping the future of microbial genomics. Dr. Wick discusses how advances in machine learning have dramatically improved the accuracy of next-generation sequencing, helping scientists translate complex electrical signals into reliable DNA sequences. He explains the differences between traditional computational approaches and modern AI-driven methods, highlighting how improvements in algorithms and biochemistry have worked together to advance long-read sequencing. Looking ahead, Dr. Wick shares his perspective on emerging opportunities in metagenomics, eukaryotic genome assembly, and the continued evolution of tools designed to make genomic analysis more accurate and accessible.

In this episode, Dr. Ryan Wick discusses the path that led him into bioinformatics and the technologies that have shaped his work in bacterial genomics. Dr. Wick shares how an early interest in biology evolved through careers in healthcare software and science education into a passion for programming and computational biology. He explains how that journey led to the development of a tool that helps scientists visualize genome assembly graphs, and later a hybrid assembler that combines short- and long-read sequencing data to create complete bacterial genome assemblies. Dr. Wick also explores how advances in next-generation sequencing, machine learning, and bioinformatics algorithms have improved the accuracy and accessibility of genome assembly.

In this episode, Dr. Ryan Wick to explore the tools and ideas that have shaped modern bacterial genome assembly. Dr. Wick explains how his bioinformatics tools used for bacterial genome assembly help scientists turn sequencing reads into complete, usable genomes. He breaks down the unique challenges of genome assembly and why bacterial isolates are especially well suited to hybrid approaches that combine short- and long-read data. Throughout the conversation, Dr. Wick emphasizes the importance of choosing the right tool for the right scientific question, noting that every assembly method has strengths, limitations, and intended use cases.

Tune in, to hear Dr. Scott Nguyen explore what it means to trust scientific data while still questioning it carefully. Dr. Nguyen shares a memorable comparison between bioinformatics and storm chasing. In both cases, he explains, you look at data, interpret clues, make predictions, and understand that the information may not be perfect. For storm chasing, that might mean comparing radar images with what you can see in the sky. In genomics, it means checking sequencing results with other tools, understanding how the experiment was run, and making sure the conclusions are supported. The conversation also touches on imposter syndrome and how learning to trust the scientific process can help build confidence. Dr. Nguyen’s storm-chasing example is connected back to his work with genomic data, showing how curiosity, caution, and experience all play a role in good science.

Listen in, as Dr. Scott Nguyen continues the conversation by looking at how sequencing data becomes something scientists can actually use. Dr. Nguyen explains that biological data should not be interpreted on its own. To understand what a genome sequence really means, scientists need to consider where the sample came from, how the experiment was performed, what tools were used, and what limitations may exist. He then shapes the discussion around the bigger picture: bioinformatics is not just about running data through software — it also requires judgment, context, and careful review.

In this episode, Dave Yarmosh sits down with Dr. Scott Nguyen to introduce the world of biocuration and why it matters in modern biology. Dr. Nguyen explains that biocuration is all about making sure scientific data is connected to the right information. In sequencing work, that means confirming that a genome is matched to the correct strain and that the strain’s background details, or metadata, are accurate. He breaks down why this matters: even the best sequencing data can become confusing or misleading if it is not connected to the right biological context. Dr. Nguyen closes by discussing how scientists need a clear starting point for understanding how careful data organization supports trustworthy science.

What’s next for microphysiological systems? In this episode, Dr. Carolina Lucchesi shares her perspective on how these technologies are advancing toward broader adoption in research and drug development. She discusses the potential of patient-derived models to support personalized medicine, the integration of experimental and in silico approaches, and the hurdles that remain in scaling and automation. The conversation also examines the role of MPS in improving safety and predictability—from early drug screening to infectious disease research—while offering a realistic outlook on their future impact.

What drives a scientist to rethink how we model human biology? In this episode, Dr. Carolina Lucchesi shares how her career evolved from animal-based research to pioneering work in organ-on-a-chip systems. She discusses the technical challenges she helped solve, the growing importance of microphysiological systems in drug discovery, and how ATCC is working to bring greater consistency and trust to these emerging models. The episode also highlights the role of diverse cell sources in building more representative and predictive research systems.

In this episode of Behind the Biology, Dr. Carolina Lucchesi explores microphysiological systems (MPS)—advanced bioengineering devices designed to mimic key organ or tissue functions in a more physiologically relevant way than traditional 2D culture, while offering a more human-relevant alternative than many animal models in specific contexts. Dr Lucchesi digs into what it takes to build and run MPS in practice: choosing materials (and understanding tradeoffs like small molecule absorption), selecting the right cell source (primary cells, organoids, iPSC derived cells, or cell lines), accounting for organ specific mechanical forces (like shear stress), and managing biological complexity across multiple cell types, media, and timelines. The episode closes with how cross industry collaboration and protocol harmonization can improve reproducibility and make data more comparable across platforms.

In this episode, Frank Simione explores the future of ATCC. Frank highlights the transformation initiated by Dr Raymond Cypess and continued by Dr Ruth Cheng, which required ATCC to operate more like a business to achieve financial stability. Frank suggested that ATCC's future lies in vertical growth through revolutionary advancements and major technological innovations, similar to venture capital strategies, to ensure sustainable growth. They acknowledged that while contracts, outbreaks, and pandemics are unpredictable, ATCC is well-prepared to handle such events. Standards will remain integral to ATCC's operations, and David expressed excitement about ATCC's role in developing standards, particularly in bioinformatics.

In this episode, David Yarmosh welcomes Frank Simione back to discuss ATCC's evolution from relying on government subsidies to securing government contracts, a shift initiated in the 1990s under Dr. Raymond Cypess's leadership. The discussion also covers ATCC's unique market position, the importance of preserving materials like the Zika virus, and ATCC's role as a patent depository, starting in 1949 and becoming the first International Depository Authority in 1981.

In this episode, Frank Simione, often referred to as the ATCC historian, discusses the rich history of the organization. Frank, who boasts a 42-year tenure with the organization, shares insights from his time as the Director of Standards, overseeing the development and recognition of standards by ANSI. He also touches on the role of the Biological Standards Institute and ATCC's mission to provide standardized biological materials, such as the E. coli strain used in antibiotic susceptibility testing. Frank delves into ATCC's early history, highlighting key figures like Lore Rogers and the organization's journey from the American Museum of Natural History to becoming an independent entity in 1947.

Join in, to hear Dr. Ruth Cheng, CEO share her vision for ATCC’s future, emphasizing the need for organizational agility, calculated risk-taking, and alignment with the pace of scientific progress. She highlights recent initiatives like the partnership with Align to Innovate to develop digital data reference standards and outlines plans to expand ATCC’s global footprint. Dr. Cheng discusses investments in cutting-edge technologies such as microphysiological systems, single-cell sequencing, and high-resolution imaging. Reflecting on her legacy, she expresses a desire to ensure ATCC remains mission-driven and relevant for the next century, while encouraging future leaders to embrace challenges and stay grounded in their values.

Listen in to hear Dr. Ruth Cheng dive into the pivotal career moments that shaped her leadership style and strategic mindset. She recounts leading a therapeutic delivery project at Boston Scientific that she ultimately chose to terminate—an experience that taught her the value of recognizing failure early and reallocating resources wisely. At Smith & Nephew, she embraced a high-stakes strategic planning role without prior experience, relying on mentorship and collaboration. Dr. Cheng also discusses ATCC’s evolution from 2D to advanced 3D cultures and the growing need for standards that support complex biological research, especially in the era of personalized medicine and engineered biology.

Tune in to hear Ruth Cheng, CEO of ATCC, reflect on her personal and professional journey during the organization’s centennial year. From a childhood fascination with science sparked by a high school teacher to leadership roles in biotech startups, Ruth shares how her identity as a scientist continues to shape her leadership. She discusses the importance of innovation, adaptability, and diverse perspectives in STEM leadership, and reaffirms ATCC’s mission to support scientific discovery through reliable, reproducible biological materials. Ruth also explores how diversity in leadership helps combat confirmation bias and fosters a culture of curiosity and long-term thinking.

In this engaging conversation, Rebecca Bradford shares her passion for travel and how it influences her leadership at ATCC. She outlines a bold vision for the future, emphasizing the importance of a new biomanufacturing facility aimed at revitalizing domestic production and supporting health needs. Becky highlights the facility's design for sterility and efficiency, as well as the challenges of weather and material availability. With a focus on collaboration with big pharma and rigorous standards, she reflects on her leadership philosophy and personal goals. Her commitment to innovation and quality promises a significant impact on ATCC's future.

In this episode of 'Behind the Biology', Rebecca Bradford, senior vice president of ATCC Federal Solutions, shares her leadership philosophy and career journey. She discusses the evolution of her management style from team-focused approaches to strategic decision-making as her responsibilities grew. Becky reflects on overcoming imposter syndrome through mentorship and the importance of asking questions to engage others. Her love for travel has also shaped her perspectives, emphasizing the need for adaptability in the biotech field. The conversation concludes with her insights on the future of biotech and the necessity for customization in scientific advancements.

In this episode, Becky Bradford, a senior vice president at ATCC, shares her inspiring journey from a science-loving child in Oklahoma to a leader in biomanufacturing. With over twenty years of experience, she reflects on her early career during the human genome sequencing boom and her diverse background in various biology fields. Becky emphasizes the importance of operational knowledge, quality materials, and educational opportunities in advancing her career. She highlights ATCC's commitment to quality and adaptability in responding to health crises, showcasing the significance of resilience in biosecurity. Her story illustrates the vital role of science in national preparedness and global health.

In this episode, Dr. Aaron Cypess discusses the future of brown adipose tissue (BAT) and white adipose tissue (WAT) research at the NIDDK, focusing on three pillars: integrative physiology, noninvasive imaging, and clinical trials. First, there's integrative physiology, where scientists use cell lines to dig into how fat cells work, how they burn energy, and how they respond to obesity treatments. Then there's noninvasive imaging—think PET-CT and MRI—which helps researchers actually see where fat is in the body and how active it is. And finally, clinical trials are testing treatments like mirabegron to see if they can activate brown fat and boost metabolic health. Dr. Cypess highlights the importance how taking this combined approach to studying BAT and WAT physiology can open doors to real, meaningful benefits to patients.

In this episode, Dr. Aaron Cypess discusses two pivotal moments that led him to change his approach to research. Initially planning to major in biology, he was encouraged to study chemistry, which provided a strong foundation in precision and quantitative analysis. During his endocrinology fellowship, Dr. Cypess shifted his focus to clinically relevant research, leading to his entry into the Clinical Investigator Training Program. This program allowed him to leverage his dual MD and PhD training to study human brown adipose tissue (BAT). Dr. Cypess also reflects on the pressures of being a physician-researcher and how the supportive environment at the NIH's NIDDK has enabled him to continue his impactful research. He highlights the benefits of the NIH's collaborative environment and resources, such as the NIH Clinical Center and the post-baccalaureate fellowship program, which have been instrumental in his research on BAT and its implications for human health.

In this conversation, Dr. Aaron Cypess discusses his research on brown adipose tissue (BAT), an organ that burns fat to generate heat. Initially thought to be present only in small mammals and young children, functional BAT was discovered in adult humans in 2009, spurring global research into its potential for treating obesity and metabolic diseases. Dr. Cypess explains the differences between BAT and white adipose tissue (WAT), and how BAT communicates with other tissues through hormones. Dr. Cypess then focuses on BAT's role in diabetes and obesity, highlighting the collaborative environment that supports his research.

In this episode, David Yarmosh and Briana Benton discuss the future of the ATCC Genome Portal, focusing on upcoming data types and platform enhancements. Benton reveals that by the end of 2025, researchers will gain access to methylation data for the bacteriology collection with future plans to annotate virology genomes, integrate antimicrobial susceptibility data, and enable advanced search features such as taxonomy browsing and gene-based queries. As the portal evolves into a dynamic “digital twin” platform, it will offer more than genome sequences, incorporating valuable metadata like microscopy images and QC results. Benton underscores the pivotal role of customer feedback in driving these innovations and highlights ATCC’s Supporting Membership, which expands data accessibility to researchers beyond those purchasing physical products. With a vision to establish the portal as a trusted, comprehensive reference for authenticated microbial data, ATCC continues to advance reproducibility and innovation in biological research.

In this episode, David Yarmosh and Briana Benton revisit the origins and evolution of the ATCC Genome Portal, tracing its journey from an ambitious research concept in 2017 to a groundbreaking resource for high-quality, traceable genomic data. Benton shares how early internal research proposals—including her push for long-read sequencing and Dr. Marco Riojas’ vision for sequencing ATCC’s collection—laid the foundation for the portal. Their work, along with challenges in microbiome research where public genome assemblies failed to match known inputs, underscored the need for a reliable genomic resource. Launched in 2019 with just 250 genomes and basic sequencing tools, the portal has since expanded to over 5,500 genomes, backed by automation, a larger team, and advanced sequencing capabilities. The portal is continually evolving and now includes data from bacteriology, virology, mycology, and protistology collections, all accessible via a secure REST-API. Looking ahead, ATCC plans to enhance the portal with methylation data, expanded annotations, and additional QC-related metadata, striving to create a comprehensive “digital twin” of each organism to reinforce scientific reproducibility and informed decision-making.

In this episode, Briana Benton presents the ATCC Genome Portal, which was launched in 2019 to offer researchers high-quality, traceable genome data directly associated with physical materials in the ATCC collection. Benton explained that each genome published on the portal is produced entirely in-house, adhering to ISO 9001 standards from strain cultivation to final genome assembly. With over 5,500 genomes currently available and new additions made quarterly, the portal aims to eventually encompass ATCC’s entire collection. The portal’s distinctive value lies in its unparalleled traceability, including documentation of storage conditions and equipment used, which ensures scientific reproducibility and reliability. While the portal does not provide analytical tools, Benton emphasized that ATCC’s mission is to supply authenticated, reproducible data, enabling researchers to utilize their preferred tools for analysis.

In this episode, Dr. Nilay Chakraborty discusses the newly launched MicroQuant portfolio by ATCC, which consists of quantitated microbial reference materials designed to simplify quality control testing. These materials are essential for ensuring the safety and efficacy of products across various industries, including food, cosmetics, and pharmaceuticals. The portfolio includes 12 products that meet stringent regulatory requirements, focusing on ease of use and delivering consistent results in terms of colony-forming units (CFU). They highlight the importance of regulatory guidelines and how the portfolio addresses both known pathogens and adventitious agents. The conversation emphasizes the engineering innovation behind MicroQuant, which reduces preparation time from two weeks to less than a minute, offering significant cost savings and logistical benefits. The portfolio is designed to reduce genetic drift risks and ensure consistency in QC testing, with potential for future expansion based on customer input.

Dr. Chakraborty continues his discussion on cryobiology, focusing on the innovative ThawReady™ Assay Ready Cells that his group developed. He explains that traditional cryopreservation methods cause cellular injuries that manifest when cells are thawed, leading to delayed functionality. ThawReady™ Assay Ready Cells are designed to minimize these injuries, allowing immediate use after thawing and reducing the time and effort required for cell culture. Dr. Chakraborty goes on to discuss the strategic approach ATCC took, leveraging advanced omics technologies to understand and mitigate cellular injuries. The conversation also covers the broader implications of this technology, including cost savings and enhanced efficiency. Dr Chakraborty concludes the discussion by highlighting the importance of compatibility with new characterization technologies and the need for standardization.

In this episode Dr. Nilay Chakraborty, head of the Cryobiology Research and Development Department at ATCC, explains his group's focus on creating innovative technologies and products involving ATCC's organisms and cell lines. Dr. Chakraborty stresses the overall aim to improve the delivery and format of these materials to better serve customers. He then discusses the challenges of managing ATCC's extensive catalog and the importance of cryopreservation in maintaining the bioactivity of biological materials. The conversation highlights the complexities of cryopreservation, the need for different preservation recipes, and the expansion of their R&D unit to include specialized manufacturing. Dr. Chakraborty then explores the intricacies of freezing biological materials and opportunities for improving preservation processes. He also shares his background in engineering and its application to cryobiology, emphasizing the development of platform technologies and the importance of understanding biology at a deeper level for more effective preservation solutions.

Join in, to hear Dr Jesse Boehm discuss the convergence of advancements that are making precision medicine more effective for a larger percentage of patients. He touches on how access to molecular profiling has become more widespread and affordable, allowing more patients to get detailed molecular information about their tumors. Dr. Boehm then mentions how new types of chemistry and drug development are making it possible to target a wider range of cancer proteins. He goes on to describe how innovations in biopsies enable real-time monitoring of tumors, providing a comprehensive molecular portrait of the tumor’s evolution. Overall, Dr. Boehm is optimistic that these and the other advancements that he discusses will significantly improve the outcome for most cancer patients within the next few decades.

In this episode, Dr Jesse Boehm relates his inspiring journey into the world of translational research. Dr Boehm focuses on how his laboratory engineered solutions to complex biological problems, particularly cancer. He stresses the importance of working alongside cancer patients, sharing a very personal story and the impact it had on his perspective. Thanks to this perspective, Dr. Boehm encourages cancer scientists to consider urgency and patient impact of their research.

In this episode, Dr. Jesse Boehm discusses the importance of collaboration in cancer research. Dr. Boehm touches on some of the partnerships that he has been involved in, such as the large collections of organoids and cell models in the Human Cancer Models Initiative. Although logistical and bureaucratic can challenge these cross-institutional partnerships, Dr. Boehm shares the key ingredients that make collaboration more feasible. Dr Boehm also notes that the urgency seen during the recent pandemic should be applied to cancer research to drive significant progress.

In this episode, David Yarmosh and Tasha Santiago-Rodriguez delve into their unexpected journeys into bioinformatics and data science. Tasha shares her transition from wet lab work to data science, emphasizing the importance of reproducibility and proper experimental controls in microbiome research. Finally, Tasha reflects on her work with ancient DNA and microbiomes, viewing it as a way of revealing history and making history by uncovering details about ancient cultures.

Here, Nick Greenfield discusses the evolution of One Codex from a microbiome analysis company to an integrated end-to-end provider. Greenfield brings up a few ideas that he has been incubating, particularly around large language models and data visualization. In a discussion about the future of One Codex, Greenfield shares upcoming changes to his organization’s business model. He also remarks on the challenges of maintaining and updating their database due to the constant changes in taxonomy.

In this episode Nick Greenfield, the founder of One Codex, discusses his transition from a background in environmental studies and international relations to establishing a microbiome company. He touches on his experience entering a contest by the Defense Threat Reduction Agency in 2013, aimed at developing better metagenomics algorithms. Despite not winning, the positive feedback on their prototype’s ease of use revealed a market gap. This led to the creation of One Codex. Greenfield further expostulates on the challenges and lessons learned during the construction of the first metagenomic database for One Codex.

In this episode Nick Greenfield, the founder of One Codex, describes his organization’s evolution from a microbiome analysis company in 2014 to a full-service microbial company. Mr. Greenfield shares his transition from CEO to board chair, reflecting on the early days of One Codex when there was no market. He also emphasizes the company’s focus on reducing complexity for the user, providing a high-quality result, and making new types of data more accessible for a large audience. Mr. Greenfield then shares some of One Codex’ positive contributions to the biological community and the general market.

In this episode, James Crill delves into the future of microbial forensics, emphasizing the importance of fully vetted databases for microbial forensics and the impact of rapid technological advancements. Mr. Crill discusses the evolution of sequencing technologies, from large laboratory equipment to more mobile and efficient technologies. He underscores the urgency for data validation and authentication due to the influx of diverse data and the ongoing changes in sequencing technologies. Crill closes by discussing the importance of studying microbial forensics and microbial communities, emphasizing the need for continued research and development of new techniques in this field.

In this episode, James Crill discusses his unconventional career path, highlighting his transition from healthcare to academia and research. He underscores the importance of adaptability, hard work, and openness to new opportunities in shaping one’s career. Mr. Crill’s experiences in various roles, from industry to academia, and the challenges faced during these transitions are discussed. He then focuses on the influence of his previous roles in government and industry on his current work and the unique challenges presented by mobile lab deployment.

In this episode, Jamie Crill discusses his research focus of microbial forensics, particularly the origins of bacteria and yeast. Join us as we engage discussion about how to use microorganisms to determine if a crime was a biological one, or if these microbes can clarify when and where a person has been recently. Additionally, Dr. Crill will discuss what the current methods are for determination, and what it's like to teach these skills to graduate students.

In the third episode in this series, Dr. Birgitt Schuele shares her insights on the current state and future directions of this field, from diagnosis and care to mechanisms and treatments. She also tells us about her own work on using machine learning to study mouse behavior in the dark, and creating 3D organ models from stem cells to simulate drug responses. She explains how these technologies can help us understand our own biology better, and reduce the need for animal models and human trials. She also discusses the challenges and limitations of creating a simulated human that can capture the complexity and diversity of individual biology.

In this second episode of the series, Dr. Birgitt Schuele discusses how the study of Parkinson’s disease has transformed over the years, from gel bands done by hand to modern sequencing technologies. Dr. Schuele then detours to how we as scientists recognize research in today’s big data biology. We also find an answer to the question “what does a researcher gain through personal interactions with their patients?” Join us in our conversation to hear Birgitt’s take on these topics and more!

We kick off this season of ATCC’s podcast with insights from Dr. Birgitt Schuele on Parkinson’s disease. In this episode, she discusses the physical and cognitive changes brought on by the disease, and zeros in on some of the genetic components. Dr. Schuele then talks about her current focus of research, the role of alpha synuclein in the onset and progression of Parkinson’s. She touches on some of the daunting challenges that researchers face when looking for biomarkers and druggable targets to treat the disease. Finally, Dr. Schuele goes back to her roots to share with us how she ended up studying this devastating neurodegenerative disease.

In the final episode of season one of ATCC’s podcast, John Bagnoli peers into the future of bioinformatics and describes the challenges that are likely to appear along the way. He’ll explore important questions such as: Will bench scientists become the bioinformaticians as the bioinformaticians transition into software development? Will machine learning and robotics replace humans in the laboratory all together? Listen in, to hear John’s surprising answers.

In this episode ATCC’s John Bagnoli reminisces about his role in the response to the 2014 Ebola virus epidemic in western Africa. Mr. Bagnoli does a deep dive into the challenges that he faced while running a biosafety level 4 laboratory in a shipping container. He then pivots to discussing how these experiences have informed his management style, giving Bagnoli a new appreciation for logistics, communication, teamwork, and patience.