Research in Biological Sciences

Mellon College of Science › Biological Sciences › Research

Exploring Life at Every Level

At Carnegie Mellon University's Department of Biological Sciences, researchers delve into the fundamental mechanisms of life — from molecules to ecosystems.

Our faculty lead cutting-edge investigations in biochemistry, bioinformatics, biophysics, biotechnology, cell biology, computational biology, developmental biology, genetics, genomics, molecular biology, neuroscience, proteomics, structural biology and systems biology.

Our interdisciplinary teams push the boundaries of biological understanding to improve health, technology and the environment. Students at all levels are integral to this vibrant research community, gaining hands-on experience and contributing to discoveries that shape the future.

Bioimaging & Imaging Technology

At the core of CMU’s Biological Science’s bioimaging and imaging technology research is the Center for Advanced Biological Imaging Solutions (CABIS). Research here has resulted in many advancements in imaging technologies over the decades. Strengthened by the collaboration with the Department of Chemistry and the University of Pittsburgh, students in bioimaging research will focus on continued improvements in imaging and cellular measurement, such as flow cytometry, and create new technologies, such as protein activation for molecule fluorescence and molecular anchoring strategies, resulting in real-world impact in the medical sciences.

Biomolecular Condensates & Spatial Organization of Cells

Carnegie Mellon researchers investigate how biomolecular condensates — membraneless organelles formed through phase separation — contribute to the spatial organization of cells. These condensates act as dynamic hubs that concentrate specific proteins and nucleic acids, enabling localized biochemical reactions without the need for physical barriers. By combining advanced imaging techniques, computational modeling, and biophysical analysis, scientists explore how these structures regulate processes such as gene expression, signal transduction, and stress response. Their work sheds light on the principles governing cellular compartmentalization and offers insights into diseases where condensate behavior is disrupted, such as neurodegeneration and cancer.

FACULTY: Jonathan Henninger | Tina Lee | John Woolford | Huaiying Zhang | Yongxin (Leon) Zhao

Biophysics, Biochemistry, Structural Biology

At Carnegie Mellon University’s Department of Biological Sciences, faculty conduct interdisciplinary research to solve molecular-level biological problems. Biophysics research utilizes physical principles to explore biological networks and systems. It drives innovation in membrane dynamics, protein folding, cell-size control, and antimicrobial mechanisms, advancing medicine, biotechnology, and fundamental science. CMU’s structural biology researchers uncover the architecture and dynamics of biomolecules to understand their roles in cellular function and disease.

State-of-the-art facilities, including the Bakery Square automated lab, Center for Advanced Biological Imaging Solutions (CABIS), NMR spectrometers, mass spectrometry, calorimetry, fluorescence spectroscopy, and X-ray diffraction, support this research. Collaborations with the University of Pittsburgh’s Biophysics and Structural Biology Program and access to the Pittsburgh Supercomputing Center enhance this work.

Advanced techniques like X-ray crystallography, NMR spectroscopy, cryo-electron microscopy, and computational modeling to visualize proteins, nucleic acids, and macromolecular complexes at atomic resolution, support breakthroughs in enzyme function, drug design, and molecular signaling.

Students in biophysics, biochemistry and structural biology gain hands-on experience in cutting-edge labs and computational techniques. They collaborate across disciplines, departments and institutions like the Pittsburgh Supercomputing Center, benefiting from Carnegie Mellon’s dynamic research environment that fosters innovation and discovery in the world of molecular science.

Cell & Developmental Biology

Researchers at Carnegie Mellon University study cell function and development using advanced tools – many developed at CMU – like live-cell imaging and genetic engineering to investigate membrane formation, cell motility, pattern repair, fate determination and cell death.

Students studying in cell and developmental biology gain hands-on experience, engage in interdisciplinary research, and benefit from CMU’s vibrant and collaborative environment and strong ties to the broader Pittsburgh scientific community.

Cellular-systems Neuroscience

Cellular systems neuroscience research in CMU’s Department of Biological Sciences is part of Pittsburgh’s vibrant and collaborative neuroscience community that includes the neuroscience institute at CMU.

Faculty study the combination of nervous and cellular systems structural and functional properties, signal transmissions, and disorders across multiple levels of analysis to understand investigative topics such as behavior, motor learning, and sensory processing. Set in the interactive environment that CMU offers for research and training, undergraduates, graduate students and postdoctoral researchers benefit from interdisciplinary projects, extensive coursework, journal clubs and seminars.

Many graduate students join the Center for the Neural Basis of Cognition (CNBC), located in the same building (Mellon Institute) as the department. CMU neuroscientists work closely with local experts in systems neuroscience, computational modeling and cognitive science, driving innovation in brain research and education. Learn more about the Systems Neuroscience Research Group at Carnegie Mellon.

Computational Biology & Bioinformatics

Researchers in bioinformatics and computational biology at Carnegie Mellon University’s Department of Biological Sciences integrate biology with big data science, using algorithms, modeling, and machine learning to analyze genomic sequences, cellular imaging, and other complex biological systems.

Supported by the Pittsburgh Supercomputing Center and the Ray and Stephanie Lane Computational Biology Department, collaborative efforts across departments, including computer science, statistics, and engineering, address challenges in genomics, systems biology, and molecular modeling.

This interdisciplinary approach provides students with hands-on experience and prepares them for cutting-edge discoveries in biomedical research, biotechnology, gene regulation, protein structure, systems biology, and personalized medicine.

Evolutionary Biology

Faculty in Carnegie Mellon University’s Department of Biological Sciences have a strong interest in how the environment can lead to changes at the molecular level over time. Activities in the department include the evolution of genome organization and functional diversity, investigating short-timescale changes in microbial pathogens during the progression of disease. Researchers use traditional evolutionary biology methods to assess genetic changes in pathogens, how gains and losses of sequence elements affect gene regulation and how transcriptional regulatory mechanisms have enabled the evolution of phenotypes. A combination of computational and experimental strategies allows CMU scientists to reveal the principles driving biodiversity, genome architecture, and the evolution of complex traits.

FACULTY: Catherine Armbruster | Dannie Durand | Irene Kaplow | Joel McManus | Yongxin (Leon) Zhao

Functional Omics

Faculty in the Department of Biological Sciences study functional omics through advancements in proteomics, genomics, metabolomics, and next-generation sequencing to generate comprehensive datasets that can be mined to understand basic cellular processes and aberrant processes that lead to disease. Omic research activities include genome wide knockouts to study Cholera biofilms, multifunctional analysis to identify regulatory sequences in DNA and RNA, genomics and metagenomics to identify species and physiological diversity in microbial communities, effect of gut microbiota on metabolism and immunity, and prediction of transcriptional regulatory elements in gnomes that have no experimental regulatory data.

Faculty develop innovative computational tools to align and interpret datasets, enabling precise reconstruction of cellular architecture. Experimental labs employ cutting-edge techniques such as live-cell super-resolution imaging and RNA-directed control assays to visualize dynamic processes in real time. This synergy of wet-lab and computational strategies allows CMU researchers to uncover how genes, proteins, and cellular structures interact across space and time, providing insights into development, disease mechanisms, and cellular heterogeneity.

Microbial Pathogens & Microbiome

Faculty in Carnegie Mellon University’s Department of Biological Sciences study microbial pathogens and microbiomes using a combination of molecular biology, genomics, and computational approaches. Their research explores how pathogens like Candida albicans, Streptococcus, Cholera and Pseudomonas aeruginosa interact with hosts and environments, focusing on mechanisms of pathogenesis, antibiotic resistance, and microbial community dynamics. By applying high-throughput sequencing and functional omics, they characterize microbial genomes and transcriptomes to uncover genes involved in virulence and adaptation. Advanced imaging and bioinformatics tools help visualize microbial behavior and model complex microbiome networks, while experimental systems allow manipulation of microbial communities to understand their role in health and disease. This integrative approach provides insights into infection biology, microbiome-driven physiology, and strategies for combating emerging pathogens.

Synthetic and Molecular Biology

Molecular and synthetic biology research at Carnegie Mellon University’s Department of Biological Sciences focuses on gene structure, expression, design genetic circuits and metabolic pathways to improve cell performance and its biological processes.

Faculty use DNA sequencing and molecular tools to study intracellular protein trafficking, cell death, tissue morphogenesis, tumorigenesis, cell signaling, transcriptional networks, and ribosome assembly. Advanced techniques like microscopy, NMR, X-ray crystallography, genomics, proteomics, and mass spectrometry are integrated.

CMU emphasizes interdisciplinary collaboration with Pittsburgh-area groups in prokaryotic, RNA, and yeast genetics. Students gain hands-on experience in a dynamic environment that fosters innovation. Students in molecular and synthetic biology will lead new discoveries in a vast array of fields such as healthcare, industry, and agriculture.

Looking to get into research at an undergraduate level?

CMU offers Faculty Research Focus Groups for undergraduates. Each semester, our faculty host discussions about primary literature and emerging research in different areas of biology. Groups meet about once per month and are open to undergraduate students of any class year. No previous knowledge or experience is necessary.

Why join a faculty research focus group?

Being able to read, understand, and thoughtfully discuss and engage with primary literature is an incredibly valuable skill to develop. Faculty Research Focus Groups provide the opportunity to practice this skill in an informal setting while building relationships with faculty in Biological Sciences.

Contact us to get started!

bio-ungrad@andrew.cmu.edu

Research Centers

Center for Advanced Biological Imaging Solutions (CABIS)

Provides access to instruments for performing a variety of advanced fluorescence microscopy techniques and flow cytometry. In the shared microscopy facility, there are state-of-the-art confocal microscopes, providing one-photon, two-photon confocal, fluorescence correlation spectroscopy (FCS), TIRF, photo-manipulation (activation/switching, ablation, FRAP), Spectra unmixing, and UV uncaging. The center also provides flow cytometry services for cell analysis.

Contact: Aleksandra Klimas

Center for the Neural Basis of Cognition (CNBC)

The Center for the Neural Basis of Cognition (CNBC) is a joint venture of the University of Pittsburgh and Carnegie Mellon University that leverages the strengths of the University of Pittsburgh in basic and clinical neuroscience and those of Carnegie Mellon in cognitive and computational neuroscience. The center supports a coordinated cross-university research and educational program of international stature, formalized in a graduate certificate program that enriches training for students in a wide variety of affiliated Ph.D. programs.

Contact: cnbc@andrew.cmu.edu

Center for Molecular Analysis (CMA)

The Center for Molecular Analysis features modern high-performance analytical instruments for use by the Department of Chemistry, the Department of Biological Sciences, and other departments and centers at Carnegie Mellon. Other research groups outside of the CMU campus may also use the CMA. In addition to the analytical instrumentation, the CMA provides collaborations, analytical assistance, and training. The CMA houses two NMRs, four photon spectrometers, and two mass spectrometers.

Contact: Mark E. Bier, director

Pittsburgh Supercomputing Center

The Pittsburgh Supercomputing Center is a joint effort of Carnegie Mellon, the University of Pittsburgh and the Westinghouse Electric Company. This Center provides cutting-edge computational resources to the national community and advances computational science and computational techniques.

Contact: Barr von Oehsen, director

Machine Learning Department

The Machine Learning Department is a cross-disciplinary center that includes the Departments of Statistics, Computer Science, Robotics, Biological Sciences, Philosophy and Psychology, as well as the Language Technology Institute, the Tepper School of Business and the Center for the Neural Basis of Cognition. Research combines statistics with data mining and machine learning.

Contact: Roni Rosenfeld, department head

Computational Biology Department

The Computational Biology Department at Carnegie Mellon University seeks to realize the potential of machine learning for expanding our understanding of complex biological systems. A primary goal of the department is to develop computational tools that will enable automated creation of detailed, predictive models of biological processes, including automated experiment design and data acquisition. We anticipate that these efforts will not only lead to deep biological knowledge but also to tools for individualized diagnosis and treatment of cancer and other diseases. The Computation Biology Department builds on the strong history of computational and interdisciplinary research at Carnegie Mellon.

Contact: Russell Schwartz, department head

Center for Nucleic Acids Science and Technology (CNAST)

The Center for Nucleic Acids Science and Technology (CNAST) is a community of Carnegie Mellon scientists and engineers unified by interests in the chemistry, biology and physics of DNA, RNA and PNA (peptide nucleic acid). CNAST has three pillars of strength:

RNA Biology
Molecular and Experimental Tools and
Biotech/Nanotech.

We invite you to explore this site to learn more about the cutting-edge research underway in CNAST.

Contact:
John Woolford, co-director
Bruce Armitage, co-director

Center for the Mechanics and Engineering of Cellular Systems (CMECS)

Living systems respond to mechanical signals that influence cell migration, growth and differentiation. At Carnegie Mellon, the Center for the Mechanics and Engineering of Cellular Systems investigates how cells generate, transmit, and respond to mechanical cues at molecular, cellular, and multicellular levels. This research has broad applications in cancer, birth defects, aging, tissue engineering and biological nanomachines. The center leverages CMU’s transdisciplinary strengths in engineering, physics, life sciences and computation to build a collaborative research environment. Students and researchers benefit from cutting-edge tools and partnerships across departments and with the broader Pittsburgh biomedical community.

Contact: Philip LeDuc, director