SCSAP MEMBER PROFILES
April Kriebel, Ph.D., Postdoctoral Fellow, University of Michigan
Bio: April Kriebel defended her doctoral dissertation in the Department of Computational Medicine and Bioinformatics March 11, 2024. She joined Dr. Joshua Welch’s laboratory in 2020, and her dissertation work was focused on developing computational methods for integrating molecular and anatomical data with spatial transcriptomics. She is an alumna of the Genome Science Training Program and an F-31 recipient.
Her first project as a graduate student focused on the development of UINMF, a single-cell dataset integration algorithm that could integrate datasets using both shared and unshared features. This algorithm proved especially advantageous when integrating scRNA-seq datasets with spatial transcriptomic datasets that often measured fewer genes. Genes not captured during the spatial transcriptomic protocol but were measured in the scRNA-seq data could now be leveraged when integrating the two datasets, leading to the identification of more refined cell type distinctions within the spatial transcriptomics data. LEARN MORE HERE
Arul Chinnaiyan, M.D., Ph.D., Director, Michigan Center for Translational Pathology, S.P. Hicks Endowed Professor of Pathology, Investigator, Howard Hughes Medical Institute, American Cancer Society Research Professor, University of Michigan
Bio: Dr. Chinnaiyan is a molecular pathologist and physician scientist at the leading edge of translational cancer research and precision oncology. He is an Investigator of the Howard Hughes Medical Institute, American Cancer Society Research Professor, and Director of the Michigan Center for Translational Pathology. He has received several honors including the Paul Marks Prize for Cancer Research and the NCI Outstanding Investigator Award; he was also inducted into the AACR Academy Class of 2020. He is a member of the American Society for Clinical Investigation, Association of American Physicians, American Academy of Arts and Sciences, National Academy of Inventors, National Academy of Medicine, and the National Academy of Sciences. Most recently he was awarded the 2022 Sjöberg Prize for cancer research by the Royal Swedish Academy of Sciences. LEARN MORE HERE
Bio: Dr. Chapkin is an NIH/NCI R35-Outstanding Investigator Awardee and an American Association for the Advancement of Science (AAAS) Fellow. He has made highly significant precision medicine related contributions including seminal cancer prevention strategies to delineate host responses to environmental (diet-derived) and endogenous (gut microbial) bioactive agents.
With training in nutrition and cancer cell biology, Dr. Chapkin has served as the Deputy Director of the NIH/NIEHS P30 Center for Translational Environmental Health Research at Texas A&M University; Chair of the American Institute for Cancer Research (AICR) Study Section Panel; and is a past President of the Sigma Xi Texas A&M University Chapter. LEARN MORE HERE
SINGLE CELL DATA SCIENCE CORE WEBSITE
Bio: Dr. Fadhl Alakwaa is a faculty member at the University of Michigan, Ann Arbor. His research focuses is on the extraction of biological insight from big data and the development of a data-driven approach for personalized medicine using multi-omics data and modern machine learning algorithms. He developed many bioinformatics pipelines for analyzing multi-omics data such as transcriptomics, metabolomics, microbiome, proteomics, and single-cell omics data. He leads multi-disciplinary projects and has more than 8 federal and non-federal grants as co-I. Dr. Alakwaa has more than 10 years of experience teaching and mentoring undergraduate and graduate students and he got nominated as an outstanding UROP mentor for the 2020-2021 academic year
Bio: Dr. Ying Ma is an Assistant Professor at the Department of Biostatistics and the Center for Computational Molecular Biology at Brown University. Her research interests focus on developing efficient statistical learning methods to address a variety of biological problems and computational challenges in genomics and genetics. These challenges typically arise with the high-dimensional data generated by rapidly evolving sequencing technologies, e.g., single-cell RNA-seq (scRNA-seq), and spatially resolved transcriptomics (SRT). With the emergence of these large-scale data, she has been continually motivated to develop tailored statistical models to advance our understanding in cellular heterogeneity, tissue organization, and the underlying mechanisms of various types of cancers. Besides her genomics research, she also works on genetic risk prediction and polygenic risk score problems in large biobanks such as UKBiobank, and MGI.
Antonio Morales-Hernández, Ph.D., University of Michigan
Bio: Antonio Morales-Hernández joined the laboratory of Drs. Pedro Fernández-Salguero and Jaime Merino, where he earned his PhD in Biochemistry, Molecular Biology, and Genetics at the University of Extremadura (Spain). His PhD project focused on the function of the dioxin receptor in cell differentiation and lung regeneration. While pursuing this work, he received excellent training in molecular biology, genetic mouse modeling, cell differentiation and trafficking and the relatively unexplored and exciting field of transposable elements (TEs). This work piqued his interest in Stem Cell Biology and so he decided to pursue further training in this area and therefore joined Dr. Shannon McKinney-Freeman’s laboratory at St. Jude Children’s Research Hospital for his postdoctoral training. Since then, he gained expertise in hematopoietic stem cell (HSCs), what has allowed him to develop his own research program focused on elucidating GPRASP gene expression refines HSCs functional heterogeneity along with side projects focused on general HSCs biology and B cell lymphomagenesis.
Learn More:
Umich Profile: https://dent.umich.edu/directory/antmor
Lab Website: https://dent.umich.edu/research/morales-hernandez-lab
Andreas Patsalos, M.S., Ph.D., Postdoctoral Research Fellow, Nagy Lab, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital
Bio:
- Undergraduate Studies: Studied biology at the University of Crete, focusing on the immune system’s control of physiological and pathological processes. Conducted research on 3D chromatin organization and epigenome in primary thymocytes.
- Graduate Studies: Pursued Master’s and Ph.D. degrees at the Medical Schools of the University of Crete and the University of Debrecen. Research focused on transcriptional regulation, acute inflammation, and skeletal muscle regeneration. Identified critical regulatory axes and pathways controlling repair-macrophage phenotypes and the communication between myeloid cells and muscle progenitor cells.
- Postdoctoral Studies: Joined Prof. Laszlo Nagy’s lab at Johns Hopkins University to examine the immune system’s role in dystrophy-related delays in muscle repair using high-dimensional omics and described the concept of “regenerative inflammation”.
- Current Focus: Applying knowledge gained from studying tissue repair and regenerative inflammation to drug discovery. Aim to develop novel immunomodulatory therapeutics for Duchenne Muscular Dystrophy.
Assistant Professor, Department of Environmental Health Sciences, University of Michigan School of Public Health
Lab Website: https://dogoodspilab.
J. Michelle Kahlenberg MD, Ph.D., Department: Internal Medicine and Dermatology
Bio: Dr. J. Michelle Kahlenberg MD, PhD is the Giles G. Boles MD and Dorothy Mulkey MD Research Professor of Rheumatology Associate Professor (soon to be Professor as of 9/1/2023) of Internal Medicine and Dermatology at the University of Michigan. She is the Vice Chair for Basic and Translational Research for the Department of Internal Medicine. Her clinical work is centered on the care of complicated lupus patients, including those with refractory skin disease. Her combines translational approaches using patient samples and murine models to uncover the mechanisms that drive lupus and other autoimmune diseases. In particular, she is focused on unraveling the pathogenic mechanisms in cutaneous lupus, the factors that drive photosensitivity, and how skin inflammation can influence systemic lupus activity. To learn more about her visit:
Xin Luo,Ph.D., Department: Computational Medicine and Bioinformatics
Bio: My current research direction is about cell-cell communication and single-cell analysis. I will work on single-cell multi-modality integration in the future. Spatial single-cell analysis interests me a lot as spatial-level cell-cell communication has a lot to explore.
Joshua Sodicoff, B.S.E. , Department: Computational Medicine and Bioinformatics
Bio: In my current role, I am developing a methodology for cell type deconvolution of heterogeneous tissue for application to large scale spatial transcriptomic data collected on the murine brain. Determination of the distributions of both well characterized and novel types identified with scRNA-seq data will allow for integration with physiological data and inference on the impact of present fine tissue structures. More generally, I am interested in the spatial organization of biological structure as a manifestation of the emergent properties of small-scale biochemical and genetic interactions with applications in microbial ecology and evolutionary biology.
Mohammad Faisal Syed, Ph.D., Department of Neurosurgery; Department of Cell and Developmental Biology; and Rogel Cancer Center, University of Michigan Medical School
Research Interests: We will use multimodal approaches; single-cell RNA-seq (scRNA-seq), mass cytometry (cytometry time-of-flight (CyTOF) immune phenotyping), and multiplex imaging to discover the spatial phenotypic signatures of the tumor microenvironment in brain tumors.
Yuji Mishina, Ph.D., William R. Mann Professor of Dentistry, School of Dentistry
Bio: Dr. Mishina’s laboratory is interested in functions of BMP signaling during bone development/remodeling and craniofacial development. Several specific projects include mechanisms of how osteoclasts regulate osteoblast functions in a spatiotemporal manner as a downstream event of BMP signaling, cell fate specification mechanisms in cranial neural crest cells towards chondrogenic lineage, impacts of nanofibrous biomaterials as stem cell niche, identification of crossover points between BMP signaling and mechanosensing for bone homeostasis, and investigation of cellular mechanisms of heterotopic bone formation to identify therapeutic options. We fully utilize genetically modified mouse lines in combination of cellular and molecular approaches including single-cell omics to uncover the above mentioned mechanisms.