The Bartesaghi Lab

Nanaline H. Duke Building
Room 132G
307 Research Drive
Durham, NC 27705

Lab Members

Alberto Bartesaghi, PhD (Associate Professor)

Alberto received his PhD in Electrical and Computer Engineering from the University of Minnesota in 2005. He was an Associate Scientist at the National Cancer Institute at the National Institutes of Health, Bethesda, MD between 2005 and 2018 and became an Associate Professor of Computer Science and Biochemistry at Duke University in 2018. His lab develops computational methods to solve the structure of large macromolecular complexes by single particle cryo-electron microscopy, cryo-electron tomography and sub-volume averaging. He is also interested more broadly in machine learning, computer vision, image processing, and high-performance computing.

Ye Zhou, PhD (Research Associate)

Ye has worked on cryo-EM/ET data analysis and algorithm development since joining the Bartesaghi lab in 2018. He received his PhD from the University of Chinese Academy of Sciences where he studied the functional and structural mechanism of GPCRs. Combining his Biochemistry and Molecular Biology backgrounds with his expertise in methods and software development, he performs structure determination and analysis using both single particle cryo-EM and cryo-ET, focusing on developing algorithms to achieve high resolution and decipher the biological heterogeneity of biomolecules. He likes nature and enjoys visiting the beautiful wild fields and water areas of NC.

Jeff Martin, PhD (Research Associate)

Dr. Martin works to support researchers and their research by developing a wide variety of software packages that can be shared with and used by other researchers in academia and industry. During his graduate studies at Duke, he studied algorithms for protein structure determination and protein design and implemented them using high-performance computing -- particularly multi-core parallelism, cluster parallelism, and general-purpose GPU computation.

Hsuan-Fu Liu (PhD candidate, Biochemistry)

Hsuan-Fu Liu received his BS and MS degrees in Biotechnology from National Chiao Tung University in 2016. He is currently a PhD student in Biochemistry at Duke University. In the Bartesaghi lab, he specializes in image processing for cryo-electron tomography to determine macromolecular structures in situ. Additionally, he is also interested in developing scalable software applications to handle the large amounts of data generated by modern imaging sensors.

Abigail Watson (PhD student, Biochemistry)

Abigail is pursuing a PhD in Biochemistry with the Bartesaghi Lab. She came to Duke from Versiti Blood Research Institute where she investigated integrins 𝛼iib𝛽3 and 𝛼5𝛽1. Prior to her position at Versiti, Abigail was at the University of Wisconsin – Madison where she studied bacterial DNA repair proteins using X-ray crystallography and got her BS in Biochemistry. Abigail’s interest in cryo-ET brought her to the Bartesaghi Lab. She hopes to improve methods for visualizing membrane protein complexes in near native environments. This is important because these complexes are notoriously difficult to purify and reassemble in vitro while holding many secrets about cell and organelle interactions.

Laura He (PhD student, Computer Science)

My current research focuses on how we can use deep learning and image processing approaches to achieve high-resolution reconstruction in the context of noisy and missing information from cryo-EM and cryo-ET data. More broadly, I'm interested in creating new data visualization tools that leverage my background in machine learning, signal and image processing, and statistical methods to help address structure and modeling challenges in the biomedical sciences. I received my BSc degree in Electrical and Computer Engineering from the University of Toronto in 2022.

LAB AFFILIATIONS

Alumni

  • Qinwen (Wendy) Huang (Computer Science, PhD, 2023), now at Bain & Co
  • Jessica Tiu (Computer Science, MSc, 2023)
  • Soumya Bodavula (Computer Science, BSc, 2022)
  • Justin Mandel (Computer Science, summer intern, 2022)
  • Jonathan Piland (Biomedical Engineering/ECE, spring/summer intern, 2022)
  • Yeongjoon Lee (Biochemistry, rotation, 2022)
  • Ruth Parsons (Biochemistry, rotation, 2021)
  • Xiaochen Du (Chemistry, undergraduate, 2021), now at MIT
  • Daniel Wesenberg (Biochemistry, rotation, 2020)
  • William Luqiu (Computer Engineering, BSc, 2019)
  • Niven Singh (Computational Biology & Bioinformatics, rotation, 2019)
  • Brandon Dopkins (Biochemistry, rotation, 2019)
  • Nikhill Pulimood (Computer Science, BSc, 2018), now Software Engineer AI Network Analytics at Cisco