Aysegul Ors, Ph.D.
Aysegul Ors, Ph.D. uses single-cell transcriptomic and multi-omic assays to study the role of transcriptional, genetic and epigenetic heterogeneity in tumors. She’s interested in uncovering the role of heterogeneity in tissue transformation and tumor progression in hormone responsive cancers such as breast cancer. Previously, she studied the role of histone variants in the epigenetic regulation of transcription and mitosis. Aysegul conducted her graduate research in the Institute of Advanced Biosciences at the University of Grenoble, France and received her Ph.D. in molecular biology and genetics from Bilkent University in Ankara, Turkey.
Cigdem Ak, Ph.D.
Cigdem Ak develops and applies novel machine learning algorithms to understand complex systems in life sciences. Her main research interest is designing theoretical and computational approaches to learn good feature representations for the joint analysis of heterogenous sources of data to explore mechanisms of cancer biology. She is currently integrating novel, scalable, and interpretable machine learning solutions into understanding single cell analysis, at CEDAR. Besides cancer, she also works on modeling spatiotemporal dynamics of COVID-19 with location-specific demographic and socioeconomic characteristics. Cigdem Ak has a Ph.D. in Computational Sciences and Engineering from Koc University, and an M.Sc. in Mathematics from École Normale Supérieure de Lyon.
Carlos Origel, Ph.D.
Carlos Origel joined CEDAR as a postdoctoral researcher after working as a postdoctoral fellow in the Frock Lab at Stanford School of Medicine, where he focused on elucidating the mechanisms of DNA repair in cells using high-throughput sequencing platforms. Carlos received his Ph.D. degree in Biochemistry and Cell Biology from Rice University in Houston, Texas. His doctoral thesis focused on developing a gene expression reporter platform to study stress-response signaling pathways in mammalian cells. He has expertise in cell biology, cell engineering, synthetic biology, and protein expression. At CEDAR, Carlos will work on the impact of ATR-Chk1 signaling pathway in oncogenesis through epigenetic reprogramming.
Danielle Konetski, Ph.D.
Danielle (Dani) joined CEDAR in 2018 following the defense of her Ph.D. in chemical engineering at the University of Colorado Boulder. Her graduate studies focused on developing a photo-controllable synthetic cell membrane as part of an artificial cell collaboration. Here she is leveraging her experience in microfluidics fabrication to develop and implement organ-on-a-chip systems to study the relationship between tumorigenesis and gut dysbiosis.
Ece Eksi, Ph.D.
Ece Eksi, Ph.D., is a postdoctoral scholar at CEDAR. She works on understanding the molecular and cellular heterogeneity in localized prostate cancer. She is specifically interested in revealing the systemic changes that occur in the gene regulatory networks of epithelial and stromal cells in prostate tumors. Dr. Eksi is merging single-cell sequencing with multiplex imaging to study the bidirectional interactions between cancer and neuronal, as well as neuronal and immune cells. In parallel, she develops liquid biopsy tools to stratify prostate cancer patients with localized disease into further risk groups. She received her Ph.D. in Molecular, Cell and Developmental biology from the University of Illinois at Chicago.
Joséphine Briand, Ph.D.
Joséphine Briand obtained her Ph.D. from the University of Nantes, France in December 2019, titled "Glioblastoma and Epigenetics: from prevention to new treatments discover". In her previous lab, her research was mainly about microRNA (circulating and in exosomes), microRNA methylation and DNA methylation. In CEDAR she will work on microRNA in liquid biopsies in order to find new biomarkers of cancer development. She also would like to participate in new technologies development
Kemal Caglar Gogebakan, Ph.D.
Kemal Caglar Gogebakan is a health economist and population health scientist who primarily focuses on cancer screening and control policies. At CEDAR, Kemal works on developing microsimulation models to project the impact of early detection technologies on the incidence and mortality rates of melanoma, lung, ovarian and pancreatic cancers; implementing statistical methods for cancer screening modelling; and estimating costs of cancer care and screening via large population-based sources of data.
Mike Brasino joined CEDAR as a postdoc in 2018 after completing his Ph.D. and a postdoc at the University of Colorado at Boulder. There he focused on genetically engineering bacteriophage (viruses that infect bacteria) to act as biosensor platforms and modified proteins with non-natural amino acids to better target therapeutics to tumors. He has brought his skillset in synthetic biology and protein engineering to CEDAR, where he is investigating the use of engineered bacteria to detect cancer.
Riccardo Carloni joined CEDAR as a postdoc in 2021 after completing his Ph.D. in physical and organic chemistry from the universities of Urbino and Alcalá. He works on the synthesis and application of dendritic polymers to treat early forms of cancer. He’s interested in the formulation of novel warheads and linkers for antibody-drug conjugates, focusing on their structure-activity relationship. In his previous lab, Riccardo worked on the physicochemical characterization of novel nanomaterials for biomedical applications.
Ryan Mulqueen joined CEDAR as a postdoc in 2021 after completing his Ph.D. at the Molecular and Medical Genetics Program at OHSU, defending his work on novel single-cell omics assays for the interrogation of cortical development. He uses single-cell multiomic approaches to assess heterogeneity across early stages of cancer. During his time at CEDAR, he is developing new protocols to measure methylation, chromatin structure and transcription all within a single-cell. This multifaceted approach, applied across tumor microenvironments, will improve understanding for hormone responsive breast and prostate cancers.
Sila Ozdemir, Ph.D.
Sila Ozdemir is a computational biologist and her main research interests are molecular modeling and molecular dynamics simulations of biomolecules such as proteins and their complexes. She is interested in predicting protein-protein interactions as well as studying their stability and dynamics. At CEDAR, Sila Ozdemir is currently implementing her expertise in modeling and simulation to predict interaction mechanisms of protein complexes playing major roles in the early stage of the cancer upon oncogenic mutations. She is also working on drug discovery to inhibit protein-protein interactions. She has a M.Sc. degree in Molecular Biology and Genetics from Bilkent University and Ph.D. degree in Chemical and Biological Engineering from Koc University, Turkey.
Justin Plaut, Ph.D.
Justin Plaut, Ph.D. works on the delivery of oncolytic viruses using nanoengineered scaffolds and is an expert at characterizing biological samples via atomic force microscopy. He is also interested in applying aptamer technology to early cancer detection. Plaut has a Ph.D. in bioengineering from the University of California, San Diego.
Sinan Sabuncu, Ph.D.
Sinan Sabuncu has been a postdoctoral scholar at OHSU for 2 years, where he specialized on bio-spectroscopy and bio-inorganic chemistry. At CEDAR, Sinan focuses on combining his spectroscopy and nanotechnology background with developing early cancer detection technologies. For this purpose he is mainly working on two projects. The first project is focusing on cancer biomarker amplification using ultrasound and gas-stabilizing nanoparticles for minimally invasive biopsy of prostate cancer. The second is about understanding the role of extracellular vesicles during initial carcinogenic events.
Spandana Naldiga, Ph.D.
Spandana earned her Ph.D. from University of Connecticut, where she worked on understanding the mutagenesis of damaged DNA replication in human cells. At CEDAR, she is working on understanding the early biology of the small cell lung cancer incidence in humans using molecular biology and advanced microscopy techniques. She is passionate about the field of cancer cell reprogramming and its probable influence in the initiation of different cancers.
Yahong Wen, Ph.D.
Yahong Wen is interested in utilizing single cell sequencing and bulk sequencing platforms to understand the progression of early breast cancer. Prior to joining CEDAR, Yahong was a senior scientist in industry who developed cell-based assays for preclinical screening of anti-cancer drugs. She received her Ph.D. in Biochemistry from Indiana University Bloomington and her postdoctoral training in colorectal cancer research at Washington University in St. Louis.
Departed CEDAR Postdocs
Marilynn Chow-Castro joined CEDAR in December 2017. She has a Ph.D. in Cancer Biology from Oregon Health & Science University and a MS in Biology from the University of the Pacific. At CEDAR, she applied her research experience in Biology to build a 3D ex vivo organoid system derived from primary human lung cells. She and her multidisciplinary team used this model system to interrogate and target the critical mechanisms that initiate small-cell lung cancer. Marilynn also diversified her skillset through other research-related activities, including project facilitation, professional development program management, and clinical needs assessment. She departed CEDAR in June 2021 to serve as an Alliance Manager for the Knight Cancer Institute.
Canan Schumann joined CEDAR in June 2020. At CEDAR, Canan worked on nanoparticle formulation and graphene-based biosensor development. He has worked on nanoparticle formulations that have led to formulations for stage 4 ovarian cancer therapy and cancer-based muscle wasting (cachexia). He specialized in RNA-based gene therapies being delivered with various nano based materials and platforms (lipids, polymers, and iron oxide particles). Canan has also helped develop theranostic dual imaging/therapy platforms for breast and prostate cancers. He worked. at the interface of biology and chemistry and considers himself an application scientist, having the ability to pull materials and concepts from numerous fields of science and re-engineering them to solve new and novel problems. He departed CEDAR in April 2021.
André Walcott joined CEDAR in July 2019. He received his B.A. in Neuroscience from Bowdoin College and his Ph.D. in Behavioral Neuroscience at Oregon Health & Science University. At CEDAR André worked on creating pathways for interns to gain access to CEDAR and developed professional/career development programming for all trainees within CEDAR. Additionally, the main focus of André’s work was to make sure that CEDAR is a diverse, equitable, and inclusive place for all its trainees and staff (through program and policy development). He departed CEDAR in March 2021 to join OHSU's Research and Innovation Office.
Josiah T. Wagner joined CEDAR in September 2017. He was interested in developing highly accurate liquid biopsy biomarker panels for non-invasive detection of early disease. Josiah’s work at CEDAR focused on using molecular profiles of cell-free RNA/DNA and metabolites to classify patient plasma and urine samples. Previously, he worked on identifying sources of genetic and physiological variation that contribute to extreme stress tolerance in vertebrates. He received his doctorate in biology from Portland State University in 2015. He departed CEDAR in January 2021 to serve as Clinical Genomic Senior Scientist at Providence Health Systems.
Katie Baker joined CEDAR in January 2019. She used sequencing technology for both early biology and liquid biopsy applications. She completed her Ph.D. in Pathology at the University of Washington’s Molecular Medicine and Mechanisms of Disease Program, where she characterized precancerous mutations using duplex sequencing. She departed CEDAR in January 2021 to serve as a Medical Science Liaison at Natera.
Daniel Heineck joined CEDAR in March 2017. He focused on developing and integrating microfluidic assemblies on super-resolution microscope systems, and supporting efforts towards integrating diagnostic workflows onto dielectrophoretic chip systems. He received his Ph.D. from the University of California San Diego. He departed CEDAR in October 2020 to serve as a Process Scientist with Biological Dynamics.
Sarah Barnhill joined CEDAR in August 2018. Sarah’s work at CEDAR focused on using bottom-up approaches to build scaffolds for collecting and analyzing cancer biomarkers. She aimed to use her expertise in synthetic/biopolymer nanostructure hybrids to develop advanced technologies that reliably capture specific markers, such as circulating DNA and RNA, with high selectivity and efficiency. Sarah earned her Ph.D. in Chemistry from the University of California San Diego. She departed CEDAR in May 2020.
Asia Mitchell joined CEDAR in February 2019. Asia applied her expertise in cancer genomics and bioinformatics on two CEDAR projects. She supported biomedical informatics and data engineering needs of the Healthy Oregon Project (HOP), and curated germline variants in DNA damage repair genes to determine their influence on lung cancer risk in smokers. She received her Ph.D. from OHSU. She departed CEDAR in September 2019.
Sejung (Sam) Kim
Sejung (Sam) Kim joined CEDAR in September 2017, At CEDAR, Sam focused on synthesizing/self-assembling nanomaterials and understanding how these structures can effectively be interacted with biological materials in cancer environment toward early cancer detection and treatment. Sam received his Ph.D. in Materials Science and Engineering from the University of California San Diego. He departed CEDAR in July 2019 to serve as a Staff Engineer at Samsung.
Jesus Bueno Alvarez
Jesus Bueno Alvarez joined CEDAR in November 2017. Jesus worked on flow, electrical and heat transfer modeling using commercial software. He also assembled and tested electrokinetic-microfludic devices and quick prototyping of microfluidic devices for bone marrow on a chip, tissue and cell staining. He earned is Ph.D. in Computational Mechanics from the University of A Coruna and the University of California San Diego. He departed CEDAR in May 2019 to serve as a Senior Research and Development Engineer for Leonyte Biosystems.
David Edwards joined CEDAR in September 2018. He worked to develop a core infrastructure for writing support at CEDAR. His work on scientific communication, writing education, and community outreach aimed to accelerate the time to manuscript publication, share compelling research stories with the public, and strengthen CEDAR’s communication with key stakeholders and the broader community. In 2018, he earned his Ph.D. at Oregon Health and Science University, where he studied under Dr. Jeffrey Tyner. Before that, he earned Bachelor’s degrees in Creative Writing and in Molecular Biosciences/Biotechnology from Arizona State University. He departed CEDAR in May 2019 to serve as a Medical Writer and Publications Manager for Exact Sciences.
Augusta Modestino joined CEDAR in July 2017. Augusta worked on development of technologies to enable early cancer, by on-chip isolation and characterization of exosomes, cfc-DNA-RNA from blood samples. Additionally, she developed an assay to rapidly measure proteolytic activity as a means for detection of early pancreatic and colorectal cancer. She earned her Ph.D. in Bioengineering and Biomedical Engineering from the University of California San Diego. She departed OHSU in May 2019 to serve as a Senior Scientist/Manager at Leonyte Biosystems.