Anne-Ruxandra Carvunis, Ph.D.

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Dr. Anne-Ruxandra Carvunis is an Assistant Professor at the University of Pittsburgh School of Medicine in the Department of Computational and Systems Biology. Dr. Carvunis identifies as an Evolutionary Systems Biologist and is resolutely interdisciplinary in her research philosophy. She opened her laboratory at Pitt in 2017 with the mandate to uncover the fundamental principles of change and innovation during the evolution of living systems. She is particularly interested in understanding what makes each species unique, including how novel species-specific genes emerge “from scratch”. A broad array of eukaryotic species and lineages are investigated in the Carvunis lab, but their current favorite model system is the budding yeast, whose genome was sequenced over twenty years ago but is still full of surprises.

Traditionally, we think of gene evolution akin to how we think of species evolution: a new gene has descended with modification from an ancestral gene. However, it has become clear over the past decade that completely novel protein-coding genes can also evolve de novo from non-genic sequences. How does this extraordinary transformation take place? How often does it happen? How do the new species-specific genes integrate the pre-existing cellular machinery? What are the physiological contributions of these young coding elements? These are only some of the exciting unanswered questions that Dr. Carvunis tackles in her laboratory.

For Dr. Carvunis, the quest to understand the origins of new genes started with an original hypothesis according to which de novo gene “birth” involves the existence and translation of transitory genetic elements called “proto-genes” (Carvunis et al, Nature 2012). Today Dr. Carvunis and her collaborators are actively pursuing research aimed at understanding the biology of these proto-genes and their evolutionary implications. Some questions require thinking deeply about what “function” and “novelty” mean in the genomic world (Keeling et al, eLife 2019), and how these concepts translate to computational methods for identifying novel sequences (Domazet-Loso, Carvunis et al, Molecular Biology and Evolution, 2017; Vakirlis et al, BioRxiv, 2019a). Other questions require directly testing hypotheses with experiments and following clues from genomics data – here again, surprises abound (Vakirlis et al, BioRxiv, 2019b).

Financial support for Dr. Carvunis’ research on gene birth has been generously provided by the NIH Pathway to Independence Award (K99/R00), the Searle Scholars Award, and most recently the NIH Director’s New Innovator Award (DP2). Dr. Carvunis has also received a number of distinctions including a Medal of honorable doctoral work, the national L’Oreal-Unesco Award for Women in Science, and the Trailblazer award from the Ladies Hospital Aid Society. In addition to her research, Dr. Carvunis co-founded the Pittsburgh Center for Evolutionary Biology and Medicine (CEBaM) to help facilitate research and education in evolutionary medicine. She is also the Associate Director of the Pitt graduate program in Integrative Systems Biology (ISB), which now includes a special track in Evolutionary Medicine.

If you would like to learn more about gene birth, please turn to the extensive review of the field Drs Carvunis and Van Oss wrote and posted to Wikipedia (Van Oss and Carvunis, PLoS Genetics 2019). Have fun!

Hossein Khiabanian, Ph.D.

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Hossein Khiabanian is an Assistant Professor of Pathology in Medical Informatics at Rutgers University. His research focuses on computational biology and cancer genomics, based on the idea that studying complexity, dynamics, and stochastic patterns in biological data is critical for understanding how tumors initiate and evolve. Cancer follows clonal, Darwinian evolution, where, as genetic alterations accumulate, fitter clones dominate, ultimately leading to macroscopic disease. During this process, selective pressures can spur tumor evolution and change its mode of progression, often leading to more aggressive and treatment-refractory disease. It is, therefore, imperative to capture the extent of genomic diversity in the subpopulation structure early in a cancer’s evolution.

Dr. Khiabanian received his Sc.B. in Physics from Sharif University of Technology in Tehran, Iran, where he was born and raised. He moved to the United States in September 2001, and entered Brown University to pursue his childhood dream of studying astronomy. There, under the supervision of Dr. Ian Dell’Antonio, he surveyed and analyzed a uniquely large cosmological datasets, and developed a method to reconstruct multi-resolution maps of galaxy clusters and dark matter structures using week gravitational lensing. During this time, he also attended lectures in genetics and immunology, which motivated him to search for research opportunities in computational biology. Soon after defending his Ph.D., he joined Dr. Raul Rabadán’s group at Columbia University in September 2008, and focused on designing statistical approaches to dissect the cellular and molecular heterogeneity that enables clonal populations to evolve and transform. He developed computational and experimental approaches that led to the discovery of genes implicated in development and disease progression in pediatric and adult leukemias and lymphomas. Specifically, his work revealed that some small mutations present prior to treatment at low abundances infer the same clinical phenotype and poor survival as clonal lesions carried by majority of cancer cells. The results by Dr. Khiabanian and his colleagues strongly suggested that limiting the knowledge of tumor genetics to the dominant clone was not sufficient for accurate prediction of a cancer’s outcome.

In August 2015, Dr. Khiabanian started a tenure-track position at Rutgers Cancer Institute of New Jersey. Since then, his lab has successfully designed statistical, information-theoretic approaches to analyze high-throughput, high-depth sequencing data to especially address the challenges in careful interpretation of clinical sequencing results. These methods aim to resolve genomic heterogeneity in both tumor and non-tumor cell populations, which may confound distinguishing subclonal tumor alterations from those possibly originating from the non-tumor component in the microenvironment. Recently, Dr. Khiabanian led an analysis of a large dataset from patients with solid tumors (Severson et al. Blood 2018), which showed that some detected mutations arose from hematopoietic cells infiltrating the tumor microenvironment. In addition to the presence of mutations associated with coexistent hematological malignancies such as myeloproliferative neoplasms (Riedlinger et al. JAMA Oncology 2019), some mutations were detected due to an age-related condition known as clonal hematopoiesis of indeterminate potential (CHIP). This work raised the hypothesis that CHIP exhibits a distinct genomic landscape when enriched in tumor microenvironment and may evolve under solid tumor treatment. Dr. Khiabanian’s lab has been testing these hypotheses and developing computational methods to study tumor evolutionary patterns supported by an R01 award from the National Cancer Institute, three pre- or post-doctoral fellowships from the New Jersey Commission on Cancer Research, an institutional grant from American Cancer Society, and more recently a Translational Grant from the V Foundation. Since joining Rutgers, the Khiabanian lab has contributed to more than 20 publications including the lead or corresponding role in 12 research articles, reviews, and pre-prints.

Dr. Khiabanian is also passionate about bridging communication barriers between computational and clinical fields and building a pathway for quantitative researchers to become translational scientists. He has organized multiple multidisciplinary meetings at Rutgers, NYU, and Columbia, and has mentored graduate students and postdocs with backgrounds in physics, engineering, informatics, and medicine. He has also made an effort to promote interdisciplinary collaborations as well as pre-print and open-access publishing through his participation in the eLife Community Ambassador program, and by providing opportunities for junior scholars to participate in the peer-review process as an academic editor for the journal PeerJ.

Because of his graduate training in physics and cosmology, Dr. Khiabanian gravitates towards putting current research in genomics in the broader historical context of advancements in science. The study of astronomy was marked by important paradigm shifts based on precise observations that were interpreted by the quantitative language of mathematics and geometry. With the advent of high-throughput sequencing methods, genomics has moved into an era that is characterized by vast amounts of unbiased data. The field has embarked on a path to uncover important insights into tumor pathogenesis and its evolutionary dynamics with the goal of helping design potentially more effective therapeutic approaches for the treatment of cancer. Dr. Khiabanian is excited for the opportunity to be a part of these efforts, and is looking for graduate students and postdocs to join this work. You can find more information about the Khiabanian lab at khiabanian-lab.org or on Twitter at @HKhiabanian.

 

Megan Killian, Ph.D.

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Dr. Megan Killian is an Assistant Professor in the Department of Biomedical Engineering at the University of Delaware. Dr. Killian’s laboratory studies the mechanisms of adaptation and growth of musculoskeletal tissues and joints (e.g., tendon-bone attachment; hip joint) with the goal of leveraging these mechanisms to improve orthopaedic healing and regeneration. To address these challenges, Megan has developed several small animal models to study the onset and progression of mechanically-induced joint disorders. The Killian Lab approaches this problem from an engineering, physiology, and clinical perspective and uses a wide range of tools and techniques such as mechanical testing, optogenetics, transgenic mouse models, and engineered materials to study healing and regeneration.

Megan is a native Michigander and grew up downriver from Detroit in a small, rural town where her father was a steelworker and mother was a tax accountant. Megan was the first in her family to attend a 4-year college and received a B.S. in Biomedical Engineering from Michigan Technological University. At Michigan Tech, Megan was a three-sport athlete (XC, Nordic skiing, and Track and Field) and learned to ski when she joined the team. Her participation in NCAA endurance sports strengthened her interest in movement science and biomechanics. She then pursued her interests in biomechanics at Montana State University, where she completed a M.S. in Exercise Science and Human Movement Biomechanics with Michael Hahn (now Associate Professor and Director of the Bowerman Sports Science Clinic at the University of Oregon). Her interests in biomechanics were strengthened even more, and she returned to Michigan Tech for a Ph.D. in BME with Tammy Haut Donahue (currently the founding chair of BME at the University of Massachusetts Amherst).

Upon completing her Ph.D. in 2010, Megan moved to Saint Louis, Missouri, where she was a postdoctoral fellow in the laboratory of Stavros (Steve) Thomopoulos in Orthopaedic Surgery at Washington University School of Medicine. Her research focused on rotator cuff development and degeneration, and she worked closely with orthopaedic surgeons to develop new animal models of joint instability and degeneration.  Her work in this area earned her the Ruth L. Kirschstein National Research Service Award (F32) and the Children’s Discovery Fellowship.

Megan started her laboratory as an Assistant Professor of Biomedical Engineering at the University of Delaware in 2016 where she continues work in these areas. She was the Co-Chair of the Gordon Research Seminar on Musculoskeletal Biology and Bioengineering in 2016 and a member of the Advocacy Committee for the Orthopaedic Research Society. In 2017, she received a K12 from the Interdisciplinary Rehabilitation Engineering Research Career Development Program. She attended the Training in Grantsmanship for Rehabilitation Research in 2018 and was awarded an R03 from NICHD in 2018 to study the contributions of skeletal muscle loading during rotator cuff maturation and healing. She has also received funding from University of Delaware Research Foundation, Delaware Center for Translational Research, Delaware Biosciences Center for Advanced Technology Applied Research Collaborations, and Delaware Rehabilitation Institution COBRE. In 2018, she was awarded the Journal of Orthopaedic Research Early-Career Award for her work in hip instability.

Megan is passionate about increasing the engagement of women in STEM fields, especially orthopaedics and engineering, which was a major draw for her to UD (which is the headquarters for The Perry Initiative, an outreach program for high school and medical school women aimed at encouraging women to pursue careers in engineering and orthopaedic surgery). Megan’s mentoring style follows principles of the growth mindset and her laboratory is populated with engaged graduate and undergraduate students from diverse educational backgrounds. This diversity brings an array of perspectives and expertise to her research group. She has hosted four high school students and five REU students for summer research and has mentored undergraduate students at UD from a diverse set of majors, including Nursing, Animal Biosciences, Neuroscience, Biomedical Engineering, Biology, Political Science, and Mechanical Engineering.

She is also a peer mentor through UD and led a team of all-women STEM faculty through the UD Faculty Achievement Program. As an active member of New PI Slack, Megan initiated the New PI Slack Faculty Success Program and has organized seven small writing and mentoring groups, which are modeled after the National Center for Faculty Development and Diversity Faculty Success Program “Bootcamp” approach.

For more information about Dr. Killian and her work, find her on Twitter at @megankillian and her website here: https://killianlab.com/

 

 

Katherine Aird, Ph.D.

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Dr. Katherine Aird is an Assistant Professor at Penn State College of Medicine in the Department of Cellular & Molecular Physiology. Her lab is broadly interested in understanding how cellular metabolism regulates cancer initiation and progression with the ultimate goal of exploiting these pathways for new therapies. Dr. Aird’s work has been funded by the NCI, DoD Ovarian Cancer Research Program, W. W. Smith Charitable Trust, and Sandy Rollman Ovarian Cancer Foundation.

Dr. Aird was born in Saudi Arabia, where she lived until she was 6. After moving to Virginia and then Ohio, she began middle school in New Dehli, India. During this time, she developed a passion for science and was especially interested in infectious disease since diseases like leprosy were something she saw on a daily basis. After finishing high school in Singapore,  she attended Johns Hopkins University for her undergraduate degree so that she could have first-hand research experience. During that time, she studied susceptibility to tuberculosis with Dr. Yuka Manabe, which solidified her resolve to obtain a PhD.

For her PhD studies, Dr. Aird moved to Duke University. While she remained interested in infectious disease, she also explored other areas of biomedical science during her rotations. During one particular rotation on cancer biology in Dr. Gayathri Devi’s lab, she was intrigued by the mechanistic cell biology puzzles that remain to be solved in cancer cells. She stayed on in this lab and identified multiple new mechanisms of therapeutic resistance of inflammatory breast cancer (IBC) cells. In 2008, she received a DoD Predoctoral Fellowship from the Breast Cancer Research Program to study mechanisms of resistance to HER2 targeting agents in IBC.  Importantly, her work revealed a new mechanism of action of the HER2 kinase inhibitor lapatinib through increased reactive oxygen species, which suggested that patients taking this drug should not combine it with antioxidants.

Dr. Aird then joined Dr. Rugang Zhang’s lab at Fox Chase Cancer Center, and later moved with him to The Wistar Institute, for her postdoctoral studies. During her interview, Dr. Zhang spoke about From that day on, Dr. Aird has been fascinated by senescence as a biological process and has worked towards discovering how senescence plays a role in both cancer initiation and response to therapy. During her postdoctoral work, she discovered that suppression of nucleotide metabolism is both necessary and sufficient for oncogene-induced senescence. Her work was the first to describe upregulation of a metabolic pathway that could completely overcome senescence and induce proliferation. This work formed the foundation for her K99/R00 Pathway to Independence Award.

In late 2016, Dr. Aird started her independent lab at Penn State College of Medicine. Her love for senescence and excitement about the growing cancer metabolic field has given her a unique niche. The aims to understand the metabolic differences between normal, oncogene-induced senescent, and tumor cells with the overall goals of: 1) elucidating the earliest events in tumorigenesis: and 2) exploiting these pathways for new cancer therapies. For instance, her lab discovered a metabolic pathway through wildtype IDH1 that is upregulated in ovarian cancer compared to normal cells-of-origin. Inhibition of IDH1 in ovarian cancer cells induced senescence through a metabolic-epigenetic axis. This work was recently published in Molecular Cancer Research where it will be highlighted in the August issue. In another project that was recently accepted at Cell Reports and currently available on bioRxiv, Dr. Aird’s lab discovered that the cell cycle inhibitor p16 has a non-canonical role in nucleotide metabolism. They found that suppression of p16 increases nucleotide metabolism to bypass oncogene-induced senescence through regulation of mTORC1. This is one of the first studies to describe a role for p16 outside of the cell cycle. These projects have led to multiple new insights into the ways cells use metabolites and activate metabolic pathways early in transformation. The lab is following up on these studies to determine whether inhibition of these pathways in pre-clinical models results in decreased tumor burden. The next big challenge the Aird lab plans to tackle is whether these metabolic changes alter the tumor microenvironment and how that affects cancer initiation and response to therapy.

Dr. Aird is also passionate about mentoring the next generation of scientists and has been nominated by her postdoctoral fellow for Outstanding Mentor through the PSU Postdoctoral Association. She is the Associate Director for Professional Development for the Penn State College of Medicine Postdoctoral Society and aims to help postdocs develop critical professional skills for the transition to the next phase of their career. Her dedication to her trainees is also evident in their fellowship success rate- both her first graduate student and first postdoc are independently funded through an NCI F31 and Penn State Cancer Institute Fellowship, respectively. You can find more information about open positions and the lab’s projects at airdlab.com. Follow Dr. Aird on Twitter @airdlab.

Joel D. Boerckel, Ph.D.

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Dr. Joel D. Boerckel is an Assistant Professor at the University of Pennsylvania, with joint appointments in the Departments of Orthopaedic Surgery and Bioengineering. His lab seeks to understand how mechanical cues influence embryonic development and to apply these principles to regenerative medicine.

The Boerckel lab’s philosophy is that, if one wants to build a tissue, they should look to how the embryo builds that tissue. Thus the lab seeks to recapitulate embryonic development for tissue regeneration. The Boerckel lab’s work focuses on the mechanosensitive transcriptional regulators Yes-associated protein (YAP) and Transcriptional co-activator with PDZ motif (TAZ) in mechanotransduction, morphogenesis, growth, adaptation, and repair. In addition, his lab seeks to develop new tissue engineering strategies for challenging injuries. The Boerckel Lab uses a combination of engineered matrices and bioreactors to study mechanisms of cell mechanotransduction, genetic mouse models to study development and disease, and mouse and rat models to study repair and regeneration.

Dr. Boerckel was born in Jerusalem, Israel, and spent his childhood in La Paz, Bolivia, before moving to Illinois, USA, at age 12. He received his B.S. in Mechanical Engineering from Grove City College in 2006, and his M.S. and Ph.D. degrees, also in Mechanical Engineering, from the Georgia Institute of Technology in 2009 and 2011, respectively. On entering graduate school, he was intent to work on biomechanics and swore never to work on cell biology or signaling. However, in his doctoral work, with Robert Guldberg at Georgia Tech, he discovered that mechanical forces when applied during tissue regeneration can dramatically influence neovascularization, i.e., the formation of new blood vessels. This led him to an interest in understanding how blood vessels form, and he pursued postdoctoral training in endothelial cell biology with Paul DiCorleto at the Cleveland Clinic. There, as a Ruth L. Kirschstein NRSA Fellow, he uncovered a non-canonical role for the MAP kinase phosphatase, MKP-1, in angiogenesis. By serendipity, he also made a new mouse model that happened to have an embryonic-lethal phenotype. Though he has yet to finish and publish this work, this observation led to hours on a microscope looking at embryos. He was immediately hooked, and knew he had to spend the rest of his career studying development.

Coincidentally, as Dr. Boerckel was preparing to transition to a faculty position, a friend from church and also a postdoc at CCF, Munir Tanas (now Assistant Professor of Pathology at the University of Iowa), discovered that genetic defects in the Hippo pathway effectors, TAZ and YAP, cause the vascular sarcoma EHE. One evening over Belgian beers, Tanas mentioned: “This pathway does everything you’re interested in.” In that moment, Boerckel abandoned every idea he’d proposed in his chalk talks to pursue these fascinating proteins.

Dr. Boerckel set up his lab at the University of Notre Dame in 2014 to study YAP/TAZ signaling in bone and blood vessel development, and in 2017 he moved the lab to the McKay Orthopaedic Research Laboratory at the University of Pennsylvania. His lab was the first to identify the roles of YAP and TAZ in bone development (Kegelman+ 2018).  They discovered a mechanism in endothelial cells by which YAP and TAZ are not only activated by the cytoskeleton, but also drive a transcriptional program that feeds back to modulate cytoskeletal tension to enable persistent cell motility (Mason+ 2019). Just this month, they published a paper in Science Translational Medicine which shows how in vivo mechanical forces are required to mimic embryonic development for regeneration of large bone defects (McDermott+ 2019). His laboratory is supported by the American Heart Association, the Penn Center for Musculoskeletal Disorders, and the Center for Engineering Mechanobiology at Penn, and was recently awarded two R01 grants from the National Institutes of Health to continue this work on mechanobiology of bone development and development-inspired tissue engineering.

Dr. Boerckel is passionate about trainee career development and is looking for PhD students, postdocs, and other researchers looking to chase interesting questions in a dynamic and supportive environment. You can find more about the lab at http://www.med.upenn.edu/orl/boerckellab/, hear about his work in person at the 48th International Musculoskeletal Biology Workshop in July where Dr. Boerckel will be presenting thanks to an Alice L. Jee Young Investigator Award, and follow Dr. Boerckel on Twitter at @jboerckel.

Maitreyi Das, Ph.D.

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Dr. Maitreyi Das is an Assistant Professor at the University of Tennessee, Knoxville in the department of Biochemistry and Cellular & Molecular Biology. Dr. Das’s lab is interested in understanding the intracellular signaling patterns that determine cell polarization. To this end, she studies cell polarization events during cell shape establishment and during cytokinesis. Her research is funded by the National Science Foundation (NSF).

Dr. Das grew up in Mumbai, India. She got her Bachelor’s degree in Microbiology from Mumbai University and her Master’s in Biochemistry from M.S. University of Baroda, India. She received her PhD in 2004 from the Indian Institute of Technology, Mumbai in Biosciences. She then moved to Helsinki, Finland to study cell cycle in fission yeast in the lab of Prof. Tomi Makela. She continued her study of fission yeast in the lab of Prof. Fulvia Verde at the University of Miami where she studied cell shape control. As a postdoc, Dr. Das discovered how the conserved NDR kinase maintains cell shape in fission yeast. She also demonstrated how cells establish and maintain their shape via oscillatory dynamics of active Cdc42, a small GTPase central to polarization. In 2013 she started her own lab where she studies fundamental mechanisms that promote cytokinesis and polarized cell growth in fission yeast. When not in the lab she loves to spend time with her husband and young son.

Research in Dr. Das’s lab mainly focuses on the regulation of the small GTPase Cdc42. Cdc42 is a master regulator of cell polarization in most eukaryotes. While the role of Cdc42 in cell shape establishment is well documented, it was previously unclear why cells activated Cdc42 at the division site during cytokinesis. Dr. Das and her lab discovered that Cdc42 was regulated by a unique spatiotemporal activation pattern via its distinct regulators, which in turn regulated distinct steps of the cytokinesis process. This work was published in the journal Molecular Biology of the Cell and given the novelty of the work, it was also selected as an editor’s highlight in the American Society of Cell Biology newsletter.

More recently, Dr. Das’s lab has shown how endocytosis is critical for the later steps in cytokinesis. They found that Cdc42-mediated endocytosis ensures that proteins are uniformly organized along the actomyosin ring to promote centripetal furrow formation. This research was published in the Journal of Cell Science and also highlighted in the same issue.

In addition to these publications, Dr. Das’s lab has also published two preprints in BioRxiv. In the first preprint, her lab has discovered a novel crosstalk between two activators for Cdc42. They find that these activators regulate each other to fine tune Cdc42 activation during cell polarization and cytokinesis. This research provides much needed insight into the significance of multiple activators for Cdc42.  In the second preprint, they have shown how one of the Cdc42 activators, Gef1 is localized to its functional sites. While both the activators for Cdc42 localize to the same sites of function, this research shows that the activators are regulated by different mechanisms

Apart from her research, Dr. Das is also actively involved in outreach to both young investigators and society at large. Her lab is very diverse with students and trainees from different parts of the world, and two of her graduate students hold NSF graduate research fellowships. Dr. Das was also awarded a supplement to fund a professional development seminar series for graduate students. In this series, Dr. Das invited experts from diverse careers to provide the students with an insight into different career options (academic and non-academic) after obtaining a PhD degree. This seminar series was very well received and has been highlighted here and here.

To learn more about Dr. Das’s research, please visit her website here, and you can also follow Dr. Das on Twitter at @DasLab_Pombe.

Stephanie C. Hicks, Ph.D.

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Stephanie Hicks is an Assistant Professor in the Department of Biostatistics at Johns Hopkins Bloomberg School of Public Health. She is also a faculty member of the Johns Hopkins Data Science Lab and co-founder of R-Ladies Baltimore, a local chapter of a global organization to promote gender diversity in the R programming community. Her research interests are at the intersection of statistics, genomics, and data science. Broadly, she is focused on two major areas of research: (1) data science education and (2) developing statistical methods, tools, and software for the analysis of genomics data to improve quantification and our understanding of biological variability. In March 2019, she was highlighted in AMSTAT News along with 28 women to celebrate women in Statistics and Data Science for Women’s History Month.

Dr. Hicks grew up in a small town in North Louisiana and received her B.S. in Mathematics from Louisiana State University. Afterwards, she moved to Houston, Texas to complete her M.A. and Ph.D. in the Department of Statistics at Rice University under the direction of Marek Kimmel and Sharon Plon (@splon). She completed her postdoctoral training with Rafael Irizarry (@rafalab) in the Department of Data Sciences at Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health. Her postdoctoral work was awarded a K99/R00 grant from the National Human Genome Research Institute (NHGRI) (@genome_gov) to develop statistical methods for the normalization and quantification of single-cell RNA-Sequencing data.

Single-cell RNA-Sequencing (scRNA-seq) data has become the most widely used high-throughput method for transcription profiling of individual cells. This technology has created an unprecedented opportunity to investigate important biological questions that can only be answered at the single-cell level. However, this technology also brings new statistical, computational and methodological challenges. To address these challenges, Dr. Hicks develops methods to address technical variability in single-cell data, methods for fast and scalable methods for clustering single-cell data, develops open-source, practical, reproducible, single-cell workflows to help researchers analyze their own data. She actively contributes software packages to the open-source and open-development R/Bioconductor software project and became involved in one of the 85 one-year projects to develop Collaborative Computational Tools partnering between the Chan Zuckerberg Initiative (CZI) and the Human Cell Atlas (HCA). With other Bioconductor developers, Dr. Hicks will create the infrastructure and tools needed to analyze potentially billions of single cells in the HCA within Bioconductor, which has been highlighted at Rice University and Johns Hopkins.

In addition, Dr. Hicks is passionate about identifying better ways to improve data science education, which she teaches at Johns Hopkins Bloomberg School of Public Health and previously taught at Harvard T.H. Chan School of Public Health.  An increase in demand for statistics and data science education has led to changes in curricula, specifically an increase in computing. While this has led to more applied courses, students still struggle with effectively deriving knowledge from data and solving real-world problems. To address this, her approach includes not only defining innovative frameworks to teach students to make important connections between the scientific question, data, and statistical concepts that only come from hands-on experience analyzing data, but also how to define the field from first principles, namely the elements and principles of data analysis, based on the activities of people who analyze data with a language and taxonomy for describing a data analysis in a manner spanning disciplines. Finally,  she is building the openDataCases community resource of case studies that educators can use in the classroom to teach students how to effectively derive knowledge from data.

Dr. Hicks is also actively working on creating a children’s book featuring trailblazing women in statistics and data science (stay tuned for updates!). She is most proud of her family — her incredibly supportive husband, Chris, and two beautiful boys. In many talks that she gives, Dr. Hicks talks about non-work–related things, such as her own hobbies or her family, as a way to normalize the stigma of work-life balance in academia. She strives hard every day to find that work-life balance and wants students to know you can absolutely have a great family life and be successful in academia.

You can find out more about the lab (and open postdoctoral scientist positions) at https://www.stephaniehicks.com/join/ and you can follow Dr. Hicks on Twitter @stephaniehicks.

Chiara Manzini, Ph.D.

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Dr. M. Chiara Manzini is an Assistant Professor at the George Washington University in the GW Institute for Neuroscience and the Department of Pharmacology and Physiology. The main goal of her research is to bridge the genetics and mechanisms of disease to identify genes that are essential for human brain function and to define the molecular causes of neurodevelopmental disorders. Her work focuses on how specific perturbations of intracellular signaling regulate neuronal differentiation and circuit formation and how disruption of signaling mechanisms leads to disorders such as intellectual disability (ID) and autism. The Manzini lab combines human genetics with molecular, cellular, and behavioral approaches in murine and zebrafish models to link human genetics to neuronal cell biology and animal behavior.

Dr. Manzini was initially trained in Human Genetics at the University of Pavia in Italy, then received her Ph.D. in Neurobiology and Behavior at Columbia University working with Dr. Carol Mason. Her doctoral studies in neuronal cell biology explored how brain circuits are assembled during development in both normal mice and mouse models of neonatal epilepsy. With this combined expertise, she then joined Dr. Chris Walsh’s group at Boston Children’s Hospital/Harvard Medical School to identify and characterize novel disease genes mutated in brain malformations and ID. Her postdoctoral work focused on highly heterogeneous genetic disorders affecting cognitive function and caused by recessive mutations to discover true loss-of-function phenotypes that could be tractable in animal models.

In her independent research laboratory, Dr. Manzini conducts two major projects stemming for her postdoctoral work. One main area of research is congenital muscular dystrophies (CMDs) associated with ID and brain malformations. CMDs are debilitating pediatric disorders often severely affecting brain development. Understanding the additional role of genes mutated in CMD in the brain is critical for therapy development and for affected families. Severe ID will continue to negatively affect care and quality of life, even when muscle function is improved by new therapeutic approaches. Dr. Manzini has led multiple studies to identify novel genes and mutations for CMD and her group has developed zebrafish models to determine how different mutations affect the brain and muscle. This work has been funded by the Muscular Dystrophy Association, the March of Dimes and pilot projects from the Clinical and Translational Science Institute at Children’s National.

A second focus of the Manzini lab is the role of intracellular signaling in cognitive function. After identifying mutations in CC2D1A in ID and autism spectrum disorder, she became interested in the function of this gene because of its role in several pathways important for neuronal differentiation. Preliminary studies from her group and others have led to the hypothesis that CC2D1A is a scaffold protein regulating the localization of intracellular signaling to membranes and that it may do so in a sex-specific manner. Mice lacking Cc2d1a show striking male bias in behavioral deficits and male-specific molecular changes, that could inform us of why autism appears to be more prevalent in boys. Understanding how CC2D1A functions may explain how male bias is established in autism spectrum disorder and other neurodevelopmental diseases. This project has been funded through a K99/R00 award and an R01 grant from the National Institutes of Health.

Dr. Manzini is very excited to be moving to Rutgers-Robert Wood Johnson School of Medicine in summer 2019, to expand the lab and develop new projects in neurodevelopmental disorders affecting cognitive function. Her group is looking to welcome students, postdoctoral fellows, and research assistants who like to work in a multidisciplinary environment and are excited about translational research. Dr. Manzini is passionate about trainee career development and has been working with the Society for Neuroscience as a member of the Professional Development Committee to publish multiple resources for students and postdocs to aid career transitions and improve the mentor-mentee relationships.

You can find more about the lab at www.manzinilab.org and follow Dr. Manzini on Twitter at @MChiaraManzini. Also, take a look at some of the career development toolkits Dr. Manzini helped develop at SfN on transitions from PhD to Postdoc and transitioning out of your Postdoc.

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.