Anthony Gitter, Ph.D.

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Dr. Anthony Gitter is an Assistant Professor of Biostatistics and Medical Informatics at the University of Wisconsin-Madison and an Investigator at the Morgridge Institute for Research. His computationally-focused lab develops network algorithms to model transcriptomic and proteomic data. They apply these methods to study cellular stress responses, viral infection, and viral-induced cancers. In addition, his lab creates machine learning approaches to determine how to prioritize biological experiments, especially chemical screening for drug discovery.

Dr. Gitter received his B.S. in Computer Science from Arizona State University. His first research experience with Dr. Chitta Baral and Dr. Graciela Gonzalez combined text mining and crowdsourcing to extract protein-protein and gene-disease relationships from biomedical abstracts. During his Ph.D. in Computer Science at Carnegie Mellon University with Dr. Ziv Bar-Joseph, he designed computational methods to interpret changes in gene expression and protein activity through biological networks. His postdoctoral position was joint between Dr. Ernest Fraenkel’s lab at MIT and Microsoft Research New England, directed by Dr. Jennifer Chayes. As a postdoc, Dr. Gitter developed new algorithms to detect different genetic mutations in cancer that have unexpectedly similar consequences. He applied these methods to study pediatric cancer with collaborators at Boston Children’s Hospital and the Broad Institute.

In 2014, Dr. Gitter started his independent lab at the University of Wisconsin-Madison and the Morgridge Institute for Research. As a member of the Rowe Center for Research in Virology at the Morgridge Institute, he enjoys having his computational lab embedded among those of his wet lab collaborators and values using computational predictions to influence experimental design. Dr. Gitter received an NSF CAREER award in 2016 to develop algorithms that infer network models from signaling and transcriptional data collected over time by tracking which cellular events happen before others. For instance, analyzing the timing of phosphorylation changes during cellular stimulus response can predict the direct targets of kinases and phosphatases, as demonstrated in his lab’s recent publication. Similar time series modeling ideas underlie their preprint about predicting transcriptional regulators from pseudotime-annotated single-cell RNA-sequencing data.

Dr. Gitter also recently returned to his roots in crowdsourcing science by joining Dr. Casey Greene in a collaborative review about deep learning in biology and medicine. In a novel form of scientific writing, the open project was written on GitHub and attracted over 40 contributors, including other members of the New PI Slack community. Dr. Gitter has teamed with Dr. Greene and Dr. Daniel Himmelstein to expand this writing approach into the Manubot platform. Ongoing development will make Manubot manuscripts more interactive and more accessible to a non-technical audience.

To learn more about Dr. Gitter’s research, visit his lab website or read about his work in drug discovery or on collaborative writing with Manubot. You can also find him on Twitter at @anthonygitter.

Medha Pathak, Ph.D.

Dr. Medha Pathak is an Assistant Professor of Physiology & Biophysics at the University of California, Irvine. Research in her lab aims to uncover mechanotransduction events that shape cell behavior and fate in neural systems. Her group’s current research focuses on mechanisms by which the mechanically-activated ion channel Piezo1 drives neural stem cell fate. She was recently awarded the NIH New Innovator award and an R01 grant for her research.

Dr. Pathak grew up in India where she received her B.Sc. and M.Sc degrees in Biochemistry and Neuroscience, respectively. After her Masters, she moved to the US to pursue doctoral work with Dr. Ehud Isacoff at UC Berkeley in Biophysics. During her Ph.D., she used simultaneous electrophysiological and fluorescence measurements to determine how voltage activates an ion channel. As a Helen Hay Whitney postdoctoral fellow she transitioned to studying mechanically-activated ion channels responsible for hearing and balance in Dr. David Corey’s lab at Harvard Medical School. After finding that allergies to furry laboratory animal models impaired her ability work in this field, she returned to working in cellular systems during a second postdoc with Dr. Francesco Tombola at UC Irvine. Here, her work on the mechanically-activated ion channel Piezo1 brought to light the channel’s role in determining neural stem cell fate. She started her own lab at UCI in 2016, which focuses on how Piezo1 shapes neural development and repair at a molecular, cellular, and organismal level.

Dr. Pathak is the recipient of several awards including a Helen Hay Whitney postdoctoral fellowship and the NIH Director’s New Innovator award. Her mentoring efforts as a PI have been recognized through a UCI Chancellor’s award for Excellence in Undergraduate Research Mentoring. Her work identifying mechanosensitivity of the voltage-gated proton channel, Hv1, was recognized as the outstanding paper of the year by the Journal of General Physiology. She is an active member of the Physiology and Mechanobiology research communities, serving as a member of the Early Careers Committee of the Biophysical Society and is a recent recruit to the Editorial Advisory Board of the Journal of General Physiology. She recently chaired a multidisciplinary conference on Mechanobiology at UC Irvine.

The Pathak lab takes an interdisciplinary approach to understanding how mechanical forces shape neural events at the molecular, cellular and systems level. Focusing primarily on mechanotransduction through the ion channel Piezo1, the lab develops innovative imaging approaches to follow the channel’s activity in intact cells and tissues over time. Combined with molecular, genetic, and bioengineering techniques in cell culture, mouse models, and human stem cell-derived brain organoids, this approach provides new insights into how cells integrate mechanical information with genetic and chemical cues in development and repair. A recent preprint from the lab uncovered how cell-generated traction forces activate Piezo1 in the absence of external mechanical forces. An unexpected finding in this study is that native Piezo1 channels are mobile, which opens up new mechanisms of Piezo1 mechanotransduction.

The lab welcomes applications for positions at the postdoctoral, graduate and undergraduate levels from trainees who want to be part of an interdisciplinary group that enjoys asking complex questions at the interface of fields. A dedicated mentor, Dr. Pathak says “I believe that success in the lab is most likely when we develop an individualized approach for each member. When trainees join the lab, I work closely with them to identify a research question that best aligns with their research interests and long-term career goals, while leveraging their innate strengths and giving them an opportunity to develop new skills. Our shared goal is to generate novel scientific findings that help each trainee successfully transition to their next career stage. As a multidisciplinary and collaborative group, we are able to support a broad range of research interests.”

You can find out more about the Pathak lab and open positions here, learn about Dr. Pathak’s New Innovator award here, and read a recent interview by Suzan Mazur on Dr. Pathak’s efforts in Mechanobiology here.

Cynthia St. Hilaire, Ph.D.

Cynthia St. Hilaire

Dr. St. Hilaire is an Assistant Professor of Medicine at the University of Pittsburgh in the Division of Cardiology and the Vascular Medicine Institute. Research in her lab focuses on characterizing the underlying pathobiology of vascular disease, concentrating on mechanisms that drive vascular and valvular calcification and remodeling. Her lab’s long-term goal is to dissect the mechanisms that drive the transformation of a healthy vascular cell into a calcifying cell, in order to identify targets for the development of pharmacological therapies. She was recently awarded an R01 to study the mechanisms driving aortic valve calcification.

Dr. St. Hilaire grew up in New Hampshire and is a first-generation college graduate. As a child aspired to be an astronaut until the research bug bit her in high school; she read the book And The Band Played On by Randy Shilts, which chronicled the discovery of the HIV virus and the early days of the AIDS epidemic, and decided she wanted to swap a spacesuit for a biohazard suit.

She majored in Molecular Genetics at the University of Vermont and worked in the laboratory of Dr. Cardy Raper who studied the sex-type signaling in the fungi S. commune. She was involved in a project that characterized the Bβ2 mating-type locus of this mushroom and spent a lot of time switching out a lysine for a leucine in a G-protein coupled receptor. Believe it or not, it was riveting! In 2001, she graduated from UVM and moved to Boston to work in the laboratory of Dr. Elizabeth C. Engle studying the genetic cause of ocular motor neuron disorder at Children’s Hospital Boston. In 2003, she started her PhD training in Biochemistry at Boston University School of Medicine and joined the laboratory of Dr. Katya Ravid where she was first exposed to vascular biology and how adenosine receptor signaling regulates vascular homeostasis. In 2009, she joined the Center for Molecular Medicine at the National Heart, Lung, and Blood Institute at the NIH, under the mentorship of Dr. Manfred Boehm.

At the NHLBI Dr. St. Hilaire and colleagues discovered the genetic cause of the rare disease, Arterial Calcification due to Deficiency of CD73 (ACDC; OMIM #211800), which identified the novel role for the enzyme CD73 and adenosine signaling in vascular calcification. This was the first novel discovery by the nascent Undiagnosed Disease Program, and provided the foundation for her successful application of a K22 NHLBI Career Transition Award. In 2015 Dr. St. Hilaire established her own research group at the University of Pittsburgh in the Department of Medicine in the Division of Cardiology and the Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute.

Dr. St. Hilaire is the recipient of several awards including the Best Peripheral Artery Disease Research Award, NHLBI Director’s Award, and the Orloff Science Award. She is an active member in the Vascular Biology community, serving as an Editorial Board Member of the Journal of the American Heart Association, the co-Chair of the Early Career Committee of the American Heart Association, Council on Arteriosclerosis, Thrombosis, and Vascular Biology (ATVB), the co-Chair of the Women’s Leadership Committee of the International Society of Applied Cardiovascular Biology, and is a member of the ATVB Women’s Leadership Committee.

Dr. St. Hilaire is passionate about training the next generation of scientists and even more passionate about breaking down the barriers and biases that have contributed to the gender and racial disparities seen in academic science and medicine. When not in the lab Dr. St. Hilaire enjoys pretending to have a talent for watercolor painting, yoga, dining, travel, and walking the dog.

You can find out more about the St. Hilaire Lab at www.sthilairelab.pitt.edu and find Dr. St. Hilaire’s publications here.

 

Greg Szeto, Ph.D.

Dr. Szeto is an Assistant Professor of Chemical, Biochemical, and Environmental Engineering at the University of Maryland Baltimore County. His lab uses engineering principles to understand the underlying rules of the immune system. Dr. Szeto’s work is currently funded by the Elsa U. Pardee Foundation, Inova Health System, and the Lupus Foundation of America. He is also a 2018 Public Policy Fellow for the American Association of Immunologists.

Dr. Szeto received dual B.S. degrees in Chemical and Biomedical and Health Engineering at Carnegie Mellon University. He then received his PhD in the Cellular and Molecular Medicine Program at Johns Hopkins University School of Medicine. His PhD work focused on the molecular mechanisms of the antibiotic minocycline as an antiviral in HIV infection and latency, and how it alters the molecular biology of T cell signaling. Dr. Szeto moved to MIT for his postdoc with Dr. Darrell Irvine. During his postdoc, Dr. Szeto diversified his research into immune engineering, including publications on developing new single-cell platform technologies, engineering new therapies using biomaterials and devices, and systems biology of cytokine networks in HIV and cancer. He was funded by an F32 postdoctoral fellowship from the NCI, a fellowship from the Ragon Institute, and 2 MIT Frontier awards. His postdoc work also produced 2 issued patents, 1 of which is currently licensed by SQZ Biotech and Roche for cancer vaccines. Dr. Szeto’s microscopy of microparticle drug delivery to lungs won a 2015 Koch Institute Image Award and 2015 Wellcome Image Award. In 2016, Dr. Szeto started his independent group at UMBC. His lab is currently working on new models of the immune response to traumatic brain injury, drug targets to improve immune infiltration into tumors, non-genetic methods for cell engineering, enhanced drug delivery in cancer and lupus, and predictive modeling of immune system responses. The lab was just awarded an inaugural 2018 Inova Translational Research Fund grant to test their new approach to predicting immunotherapy response in melanoma patients.

In addition to research, Dr. Szeto is passionate about mentoring and teaching. He is deeply committed to training the next generation of scientists to be critical thinkers and scientists as well as communicators who can engage with the public about the scientific process and achievements. Dr. Szeto has trained over 50 undergraduates, grad students, and postdocs who have entered diverse careers including venture capitalists, pharmacists and clinicians, R&D in academia and industry, and numerous ventures outside STEM.

You can find out more about the Szeto lab at http://gregoryszeto.com/

Buck S. Samuel, Ph.D.

The featured outstanding New PI for October 2018 is Buck S. Samuel, Ph.D.!

Dr. Samuel is an Assistant Professor of Microbiology at Baylor College of Medicine in Houston, TX. His lab seeks to understand how gut microbiomes influence host physiology and development. Dr. Samuel’s work is currently funded by a NIH New Innovator Award in which he aims to identify the host genetic pathways that microbes modulate using the simple nematode, Caenorhabditis elegans.

“Interactions with the microbiome impact our health, and if these interactions are disrupted, it can predispose an individual to disease. We want to understand how the microbiome influences health outcomes. By unlocking these genetic pathways we hope to develop strategies for microbiome stewardship that are as individual as we are,” Samuel said.

Dr. Samuel is a first-generation college graduate who received dual B.S. degrees in Microbiology and Molecular Biology and Biochemistry from the University of Idaho, followed by a Ph.D. from Washington University in St. Louis. As a graduate student in the laboratory of Dr. Jeffrey I. Gordon at Washington University, Dr. Samuel contributed to some of the first studies that characterized the human microbiota and helped establish a link between the microbiome and host metabolism. This work was supported by a NSF graduate fellowship and led to multiple first author and collaborative papers. After receiving his Ph.D., Dr. Samuel pursued postdoctoral work with Dr. Gary Ruvkun at Massachusetts General Hospital and Harvard Medical School. In his postdoc, Dr. Samuel was awarded an NRSA from the NIH and a Charles King Trust Fellowship for this work to define the natural microbiome of wild C. elegans, a new paradigm for microbiome research. In 2015, Dr. Samuel started his independent lab at Baylor College of Medicine. The Samuel lab has pioneered the use of C. elegans as a system for host-microbiome interactions and is working with collaborators around the world to develop an extensive set of microbiome resources for the community. You can read more about use of C. elegans in microbiome research here.

In addition to his scientific contributions, Dr. Samuel is a strong advocate for diversity and inclusion in science. “I believe that truly creative solutions grow from diverse perspectives and worldviews. As a community, our science is better for embracing diversity in all of its forms,” said Samuel. He is currently seeking to bring his passion for advocacy to the national stage as a member of the Genetics Society of America Board of Directors [more info here].

Dr. Samuel is also a proponent of open and interdisciplinary science and is leading an effort to overhaul the Immunology and Microbiology graduate curriculum at Baylor College of Medicine. This new curriculum seeks to shed typical didactic classes in favor of more interactive and integrative course work that prepares students for a wide range of scientific careers.

Learn more about Dr. Samuel’s research and open postdoc positions here.

Casey Greene, Ph.D.

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The featured outstanding New PI for September 2018 is Casey Greene, Ph.D.!

Dr. Greene is an Assistant Professor of Systems Pharmacology and Translational Therapeutics in the Perelman School of Medicine at the University of Pennsylvania. He is also the Director of the Childhood Cancer Data Lab for Alex’s Lemonade Stand Foundation.His lab uses computational approaches to develop deep learning methods for large-scale datasets. Dr. Greene’s lab is focused on modeling complex biological systems, which have spanned from zebrafish development to cancer.Dr. Greene is currently funded by grants from National Science Foundation (NSF), the Gordon and Betty Moore Foundation, Alex’s Lemonade Stand Foundation, Pfizer, the Chan-Zuckerberg Initiative, in addition to an R01 from NIH/NIGRI.

Dr. Greene received his B.S. in Chemistry from Berry College. He then received his Ph.D. in Computational Genetics from Dartmouth College. During his Ph.D. studies, Dr. Greene was funded by a highly competitive predoctoral training fellowship from the NIEHS. He was also a finalist for a number of best student paper awards and winner of the Graphics Processing Units (GPUs) for Genetic and Evolutionary Computation Competition in 2009. He then moved to the Lewis-Sigler Institute for Integrative Genomics at Princeton University where he worked as a postdoctoral fellow from 2009-2012. In 2012, Dr. Greene started his independent laboratory at Dartmouth College’s Geisel School of Medicine in the Department of Genetics. In 2014, Dr. Greene was named one of fourteen Moore Investigator in Data-Driven Discovery from the Gordon and Betty Moore Foundation. In 2015, Dr. Greene was recruited to the Perelman School of Medicine at the University of Pennsylvania.

Dr. Greene has many scientific accomplishments. For instance, he, along with Anthony Gitter from the University of Wisconsin, led an open review on deep learning in biology that was authored on GitHub. The full text of the review has been downloaded more than 70,000 times. It was listed in the article, “2017 in news: The science events that shaped the year” from the journal Nature. He states that his accomplishments have been shaped by the “hardworkingpeople that I get to work with and talk to each day about new software, new things we are trying to accomplish, and new discoveries”. Additionally, Dr. Greene’s work has been consistently recognized. He has been invited to give talks around the world and is also an academic editor, associated scientific advisor, or reviewer for many well-known journals. Finally, Dr. Greene is a prolific scientist with nearly 50 peer reviewed research publications in addition to multiple reviews, editorials, and other reports.

Dr. Greene’s lab recently deposited a preprint on bioRxiv where a postdoctoral fellow in his group (Dr. Jaclyn Taroni) demonstrated that performing unsupervised transfer learning enhances the analysis of rare disease datasets. Using both unsupervised machine learning and transfer learning algorithms will be vitally important for analyzing datasets from rare disease where samples are limiting. Using a large, existing dataset to train the model, Dr. Greene’s lab can then use that model to analyze the limited rare-disease data. Using this technique “MultiPLIER”, Drs. Greene and Taroni have begun to better understand the biology of a rare autoimmune disease. You can read the preprint here.

In addition to being an accomplished scientist and passionate mentor, Dr. Greene is dedicated to open science. He provides all of the source code to his lab’s work strives to make research “routinely reproducible”. His lab develops webservers for other scientists to use their algorithms. Dr. Greene believes this will push science forward more efficiently and more rigorously. In fact, he co-founded a research award for this exact purpose: The Research Parasite Award. This award is given annually to scientists that have performed secondary analysis of existing data. To see past winner or apply, please visit the Research Parasite Awardswebsite. He notes: “this is the parasite season, and applications are accepted for this award year until 5PM HST on September 30, 2018. If you share data, don’t miss the Symbiont Awardsfor a chance to win a prize!”

Learn more about Dr. Greene’s research here: http://www.greenelab.com

 

 

 

Jordan Ward, Ph.D.

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The featured outstanding New PI for August 2018 is Jordan Ward, Ph.D.!

Dr. Ward is an Assistant Professor in the Department of Molecular, Cell, and Developmental Biology at the University of California, Santa Cruz. His lab uses a combination of genetics, molecular biology, microscopy, in vitro biochemistry, and genomics to determine how individual, evolutionarily conserved transcription factors regulate distinct gene expression programs. Dr. Ward’s lab is funded by a R00 from NIGMS, which aims to understand how nuclear hormone receptors control molting in both C. elegans and the human parasitic nematode B. malayi. He was also recently selected as a member of the Editorial Board of Micropublications. He is very excited about the potential of this publication format to rapidly disseminate results to the community and to create citable publications from undergraduate research projects.

Dr. Ward received his B.Sc. and M.Sc. in Microbiology from the University of Alberta in Edmonton, Canada. He then received his Ph.D. in Biochemistry from Cancer Research UK/University of London in London, England. During his graduate work, he explored how cells repair mitotic and meiotic DNA damage. This work was extremely collaborative and led to an impressive first, co-first, and 10 middle author publications in four years. Dr. Ward then moved to the University of California, San Francisco for his postdoctoral studies. During his postdoc, Dr. Ward was prolific with 10 peer reviewed publications, including a single author research paper. He also published a single-author perspective during this time on strategies to import tools from C. elegans into parasitic nematodes. He was funded by highly competitive postdoctoral fellowships from the Canadian Institutes of Health Research and the Terry Fox Foundation. In 2014, he was awarded a K99/R00 from the NIGMS. Dr. Ward was recruited as a faculty member to UC Santa Cruz in 2016. There, he focuses on transcription factor regulation of gametogenesis and the nematode molt in the model organism C. elegans.

Dr. Ward was awarded a grant from the National Science Foundation to organize a workshop at the 2017 International C. elegansmeeting designed to educate and promote interactions and collaborations between the parasitic roundworm community and C. elegansresearchers. The workshop included over 70 participants and was so successful that Dr. Ward will organize a similar event in 2019. This workshop personifies Dr. Ward’s excitement for, “understanding how gene regulation controls development and extending these findings into a parasitic nematode.” His review of the workshop can be found here: http://wbg.wormbook.org/2018/07/17/review-of-3rd-parasitic-nematodes-bridging-the-divide-workshop/

In addition to focusing on basic biology that could have a large impact, Dr. Ward is also a dedicated mentor. He says one of his favorite things about being a PI is, “getting to mentor a great group of really smart people.” He enjoys watching his trainees grow, take ownership of their projects, and start to teach him things. His excellent mentorship is evident by the fact that one of his first trainees is funded by a training grant. He is also a strong advocate for diversity in STEM. He works closely with STEM Diversity programs on campus and is dedicated to helping train undergraduate and graduate students from underrepresented minorities.

Learn more about Dr. Ward’s research here: http://www.jordandward.com