​My passion for scientific research started the day I saw fungal spores under a microscope. It was my sophomore year in college in a plant pathology class. By the end of that semester, I was an intern in the plant pathology lab. I got my undergraduate degree in Agricultural Engineering, and my interests were applied field research in crop protection and crop health. Little did I know that a decade later I would be making a career move to be a computational biologist.
 
During my PhD, I transitioned from the field research setting to computational biology. I studied the host-pathogen interactions of a soil-borne fungal pathogen of bermudagrass using transcriptomics. It was my introduction to the world of omics and bioinformatics. As I had no background in this area, my biggest challenge yet was to learn bioinformatics tools. I was privileged to have taken two courses at Cold Spring Harbor Laboratory, where I learned computer programming (Python), sequencing technologies, and analyses of omics data. I just fell in love! But, it took a while to become efficient in my data analyses. I started to “get it” when I was approaching the end of my PhD.
 
One month before graduating with my PhD, I came to the University of Arizona in June 2019 to attend the first FOSS (Foundational Open Science Skills) course offered by the CyVerse. Every single day during FOSS I learned new skills that I could apply to improve my data analyses. The most important tool for me  was my code notebook and at FOSS I learned how to develop scripts with RStudio and integrate them with Git. Further, I learned about principles of FAIR data and reproducibility with Git, Jupyter and Rmarkdown. I was also amazed by all the resources CyVerse offers like the Discovery Environment and the Atmosphere (their cloud-computing platform) because it was so easy to use. The people behind the CyVerse are committed to open science and to help researchers, which is very motivating and inspirational for me. I just wish I had taken FOSS at day one of my PhD!
 
I joined the Tfaily lab (Environmental Science-Res) in October 2019. Currently, my main research focus is to develop data analyses pipelines for a variety of research projects. We use a combination of microbial genomics, metabolomics, geochemical and isotopic techniques to understand carbon cycling, soil organic matter composition and climate change in many ecosystems like peatlands, desert, and the tropical rainforest at the Biosphere 2. Pretty soon, I will be expanding our research to agricultural systems to study the role that agricultural management practices play in the soil and plant microbiome, and how those practices affect soil organic matter degradation and formation using the unique and modern techniques that our lab specializes in.
 
My path into computational biology has had many ups and downs. Nonetheless, this experience gave me strength and confidence to not be afraid to get out of my comfort (research) zone. I really enjoy the challenges that computer programming brings to my day-to-day life. I have become highly enthusiastic in sharing my vulnerability, knowledge and collaborating with researchers to help them understand bioinformatics tools and be more efficient in their data analyses.
 
 

Much of my research is built on the idea that data has structure or “shape” and this shape helps us understand the data. For example, voting records may be clustered by party affiliation. In particular, the shapes I am most interested in are topological, like circles or voids (like the inside of a balloon). Detecting and measuring these types of shape can be difficult if the data is complex, that is, there are lots of different components (like many genes for many patients) or it changes over time (like a flock of birds). 

As an illustration, suppose we have a set of points arranged very roughly in a circle. On their own, it’s just a bunch of points, but we can intuitively detect the structure, or how they interact with each other,  by blurring our eyes until the points all merge into a ring. As a postdoctoral researcher in the Mathematics Department of the University of Arizona, my research uses math that makes this structure detection process precise for much more complicated data that evolves over time. This helps answer fundamental questions about the systems the data came from.  For example, with collaborators, I find defects and measure order of arrays of nanodots as they form on semiconductors to better understand the process for potential in manufacturing. I characterize the roughness of snowfields as they melt to better estimate their energy transfer which is used in climate models. In another project we are studying the patchiness of coral reefs to better predict recovery and catastrophic reef loss. I love that math allows me to work on such a wide variety of scientific applications. 

In addition to research, I have had the opportunity, with some colleagues in the math department, to launch a Women in STEM Mentorship Project this fall. This is a peer mentoring program for first year women in STEM majors. I am passionate about mentoring and making pathways for a more diverse STEM workforce. 


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​Human beings are now collecting data at an astounding rate in almost every process that we are involved in, from astronomy to social media to medicine.  But what do we do with all this data?  How do we draw meaningful conclusions from it?  How can we find structure within it?  How can we even use the data for computations when we can’t access it all at once?

My research is in the mathematical foundations of analyzing large-scale, high-dimensional data.  Dimensionality of data can be described as the number of parameters used to describe it.  For instance, an image from our phones has over 10 million pixels, each of which has a red, green, and blue color value.  Such an image can then be thought of as having 30 million parameters to describe it.  But if we just chose random values for colors at each pixel we would not end up with a meaningful picture to the human eye.  Thus, we might expect that real photos can be described by many fewer parameters.

I am interested in the complementary tasks of designing methods which find low-dimensional structure within high-dimensional data, and designing methods which can reduce the dimensionality or complexity of data in a way that is interpretable and faithful to what is there.  I have applied such methods to tasks in Computer Vision, like segmenting motions of objects moving in videos and in facial recognition from images. I have also worked with a Postdoc in Medical Imaging on a method to find the smallest number of parameters that governs, say, MRI images.
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Here at the University of Arizona I am fortunate to be among a tremendous group of interdisciplinary faculty and have had many fruitful collaborations with members of the Data Science Institute as well as Mathematicians, Statisticians, and Computer Scientists in the TRIPODS program.  TRIPODS stands for Transdisciplinary Research in Principles of Data Science, and is an NSF-funded initiative designed to bring together researchers from these three fields to work on foundational problems that arise in analyzing data. Sharing common interests but a diverse perspective has brought a lot of great work from the program, and will continue to advance scientific understanding of data analysis moving forward.

​Microbes are present everywhere, from the barren Atacama Desert to the mucous lining of our lungs and guts. Their interactions in the environment and within their hosts fascinate me, which has lead me into the field of microbial ecology.
For my graduate studies, I worked with Dr. Raina Maier at the University of Arizona focusing on the role of microbes in phytostabilization of mine tailings, which are the waste left behind after ore extraction. The goal of phytostabilization is to utilize a plant cover to sequester metals in the root zone and prevent wind erosion. We aimed to assess the feasibility of direct-planting with a compost amendment into highly acidic and toxic metal-contaminated mine tailings that were susceptible to wind erosion and transport into the nearby town. Specifically, my project was to examine how plant-associated bacteria immobilized metals, such as As and Pb, while also contributing to plant health and soil development. I found that while compost amendment and plants increased the pH of the tailings substrate and abundance of plant-growth-promoting bacteria and heterotrophs in the beginning, over time, the tailings returned to acidic conditions dominated by autotrophs as the compost either eroded away or was used up, restricting the presence of beneficial bacteria to ‘islands’ surrounding the plants. Because plants need beneficial bacteria in the bulk soil to recruit from, this indicated unsustainable plant establishment and lack of healthy soil development. To support me in my graduate studies, I had the honor of being awarded the NSF Graduate Research Fellowship.
In my current postdoc position with Drs. Donata Vercelli and Fernando Martinez at the Asthma and Airway Disease Research Center, I have shifted from the environment to the host microbiome by exploring how gut and lung microbiota are associated with asthma. In one of my projects, we use a germ-free mouse model to study the role of the gut microbiome in asthma development. We have discovered that mice receiving fecal transplants from Amish farm children, who have extremely low rates of asthma, protect from experimental asthma while fecal transplants from Hutterite farm children, who have high rates of asthma, do not. This reveals the important role of the gut microbiome in asthma development, which is likely driven in part by microbially-produced metabolites. For this work I was awarded the ATS (American Thoracic Society) Science and Innovation Center Abstract Award. For my other project, I have characterized the sputum microbiome of adult subjects from the Children’s Respiratory Study (CRS) to examine how lower respiratory infections in childhood and smoking can impact adult lung microbiome. We hope that the results could shed light on the potential role of the lung microbiome in the development of asthma and perhaps even chronic obstructive pulmonary disorder (COPD). During this time, I was supported by the NIH T32 Postdoctoral Research Fellowship.
In my next postdoc adventure, I am excited to join Drs. Laura Meredith and Malak Tfaily at Biosphere 2 to explore the rainforest soil microbiome’s response to drought in the WALD (Water Atmosphere and Life Dynamics) experiment. Overall, I enjoy identifying patterns in microbial ecology using creative approaches, whether by linking the environmental or host microbiomes to geochemical or immunological data, or combining multiple ‘omics datasets. While I’m not working, I enjoy taking time off to run and ride bikes through the beautiful Tucson desert.
 

​I have specialized in studying traumatic brain injury and Alzheimer’s disease research for the last 8 years. My goal is to determine the role of chronic increases of inflammation after brain injury and how it may induce dementias like Alzheimer’s disease. Traumatic brain injury remains a national health concern. Though fewer people are dying from brain injury, the effects of chronic brain injury on cognition and other behavioral outcomes still remain largely unknown. Chronic brain injury has similar pathologies and behavioral outcomes as many neurodegenerative diseases, including Alzheimer’s disease. Alzheimer’s disease is the most common form of dementia and there is no way to prevent or slow down the progression of the disease. One aspect of both brain injury and Alzheimer’s disease that holds true in almost all cases is an increase in both peripheral and central inflammation. Discovering the effects of inflammation on brain circuitry and behavioral outcomes after brain injury can answer mechanistic questions on how Alzheimer’s disease progresses. This information can provide a window of intervention to reduce brain injury induced neurodegeneration and other inflammatory conditions such as Alzheimer’s disease.
 
I joined the Translational Neurotrauma Research program at the University of Arizona College of Medicine- Phoenix under the director, Dr. Jonathan Lifshitz, after I received my PhD from the Cleveland Clinic’s Molecular medicine program. In my time in the lab, I have shown that TBI is not only a central injury; there is a large peripheral component to brain injury that can exasperate chronic conditions. This peripheral component is largely overlooked, specifically the effects of peripheral inflammation on the injured brain. I plan on continuing my work in peripheral inflammation after brain injury throughout my fellowship.
 
Though my fellowship is through the Evelyn F. McKnight Brain Institute for Aging in Tuscan, I live and work in Phoenix. My time in Arizona so far has been a great experience, and I am excited to see what the next year of my fellowship brings.

​I am absolutely fascinated by viruses and how they interact with their hosts via elegant molecular processes. To continue my scientific journey, last month I moved to Tucson from Canada to join as a postdoc in Dr. Koenraad Van Doorslaer’s lab at the BIO5 Institute. Here we explore the importance of papillomavirus evolution and seek to understand how infection with some of these viruses leads to cancer. Papillomaviruses are an ancient family of pathogens that infect cells of the skin and mucosa, with some types of human papillomaviruses (HPVs, such as type 16 and 18) that are transmissible via sexual contact and able to cause genital cancers (e.g., cervical cancer) as well as cancers of the head and neck (e.g., throat cancer). It is poorly understood why and how only a small proportion of infections will ultimately lead to cancer.
                           
Prior to coming to Arizona, I completed my doctoral training in "the land of ice and snow": Northwestern Ontario, Canada, in the city of Thunder Bay. There I become hooked on studying human papillomaviruses and cervical cancer, using “life-like” 3D human tissue culture, with Dr. Ingeborg Zehbe at the Thunder Bay Regional Health Research Institute and Lakehead University. This method of growing cells in the lab enables experimentalists to create “life-like” human skin or mucosa, supporting an active viral life cycle needed to study the virus and its carcinogenic abilities in its natural environment. This level of realism is not possible with standard and traditional 2D or monolayer cell culture.
                           
In the Van Doorslaer lab, I am incredibly excited to study the early infection process of papillomaviruses using 3D human tissue culture along with novel techniques such as single-cell sequencing and bioinformatics. This will allow us to uniquely pinpoint the molecular and cellular changes that are occurring in the specific cells that give rise to cancer. By teasing apart the specific factors and processes that influence persistent infection of the virus in host cells we aim to gain insight into the earliest stages of cancer development. We predict that with a realistic methodology (3D tissue culture), the right set of analytical tools (single-cell sequencing), and a great team here at UA, that we can help uncover the molecular basis of why only certain HPV infections lead to cancer.
                           
While I have only been in Tucson for a short time, I am enjoying it! The desert landscape and wildlife has been enchanting, the sky has been striking, the people friendly and fun, and the food... delicious.

​The planets, moons, and asteroids in our solar system offer a host of mysteries that if (when!) solved will enlighten us about processes occurring on Earth and throughout the universe.  As a planetary scientist, I study the geology and physics of the solid worlds orbiting the Sun in an effort to explore Earth’s neighborhood and shed light on how planets evolve.
 
NASA robotic spacecraft provide the data I use in my research.  During my Ph.D. at MIT and postdoctoral work at the University of Arizona, I’ve been involved with four of these NASA missions: the Lunar Reconnaissance Orbiter and GRAIL missions studying the Moon, the Mars Reconnaissance Orbiter studying Mars, and the Dawn mission that orbited Ceres, the largest object in the asteroid belt.  These missions used a variety of scientific instruments to study the surfaces and interiors of these worlds, including cameras, spectrometers, and tools to precisely measure gravity.  One of these instruments that has special importance to the University of Arizona is the HiRISE camera, an imager that is the most powerful of its kind ever sent to another planet and operated from our own campus. 
 
I enjoy keeping a diverse set of scientific interests – there are far too many fascinating worlds in our solar system to pick just one! – but my research all falls under the theme of “planetary geophysics.”  I’ve studied ice volcanoes on Ceres, regular volcanoes on the Moon, glaciers on Mars, the interior of Mercury, and mysterious bright patches on the distant moons of Uranus.  Planetary science is a data-rich field with guarantees of major discovery that come with each successful NASA mission, and I can’t wait to see where our journey of exploration takes us next. 

Behavioral genetics is a growing field that seeks to explain how genes and neurons influence the behavior of an organism. Through a multi-disciplinary approach using genetic and neurobiological techniques, my ultimate research goal is to understand how organisms use their behavioral repertoire to enhance their survival, and to learn how these innate behaviors evolved.
 
For my graduate work, I focused on intraspecific aggressive behavior. Males of the same species will fight one another to compete over territory, food, and mates. This trait is found broadly across the animal kingdom, suggesting that it originated very early in the animal lineage and has been maintained and modified throughout evolution, but the underlying genetic factors remains unknown. We used the fruit fly, Drosophila melanogaster, as a model organism due to the numerous genetic tools to alter genes or neuronal function. I found that co-housing aggressive males lead to an accumulation of physical damage to their wings and used this phenotype to perform the first mutagenesis screen for altered aggressive behavior, in which I identified two genes that were previously not associated with aggression. 
 
In my postdoctoral position here at the University of Arizona, I am branching out into the behavioral defenses of interspecific host-parasite interactions. Flies encounters numerous threats to its survival in the wild. One common threat is that from parasitoid wasps. These small insects inject a single egg into a fly larvae which, once hatched, develops within and ultimately consumes the host. However, flies have behavioral defenses to avoid infection from these wasps, and to cure themselves once infected. While adult female flies are not directly attacked by wasps, they do reduce the number of eggs they lay in the presence of wasps, which is thought to limit their offspring to wasp exposure. I am currently investigating the visual and olfactory systems to understand mechanistically how the fly senses the presence of these wasps. The ultimate goal is to identify the neuronal circuits from sensory inputs to behavioral outputs and understand how these circuits interact to regulate egg laying behavior in a complex environment.
 
In my time at the University of Arizona, I have been encouraged to pursue interdisciplinary research questions, not just from my advisor but across the entire campus. This is exemplified when my work on the olfactory system showed that flies not only respond to the presence of parasitoid wasps but also to other Hymenoptera insects such as ants. This lead to an unanticipated collaboration with Greg Chism from the Dornhaus lab to examine the evolutionary response to olfactory signals from the threats of other insects. Furthermore, I have worked closely with Dr. Diana Ferro of the Zarnescu lab to study altered innate behaviors in a fly model of frontotemporal dementia, resulting in a Center for Insect Science seed grant to advance our work. Finally, I have been awarded the BIO5 Postdoctoral Fellowship on my work of behavioral defenses against parasitoid wasps. These opportunities will allow me to broaden the scope of my research and mentor undergraduate students in the pursuit of obtaining a faculty position at a primarily undergraduate institution or a small liberal arts college where teaching and research experiences are passed down directly from professors to students.
 

As an animal behavior researcher, I am fascinated by the decision-making and problem-solving processes of other organisms and enjoy investigating what contributes to individual differences in these abilities. During my dissertation work, I became particularly interested in the early developmental factors that influence later temperament, cognition, and outcomes. Studying a population of guide dogs, I quantified the amount of maternal care that puppies received over the first few weeks of life and then tracked the puppies for two years. I found strong associations between the amount of mothering a puppy received and reactivity and problem-solving skills around 18 months of age. Moreover, mothering style was also associated with whether a puppy successfully graduated as a guide dog. Surprisingly, the dogs whose mothers were the most involved over those first few weeks of life were the least likely to graduate. While more research is needed, as is so often the case, one hypothesis is that a little bit of stress in early life is actually beneficial, and can build future resilience.

Since starting my postdoc position at the University of Arizona, I’ve been living at our lab’s “field site” in Northern California – Canine Companions for Independence (CCI). CCI is the largest non-profit provider of assistance dogs for people with disabilities in the United States. These dogs are expertly trained to offer physical and emotional support, providing their handlers with the freedom and self-confidence to navigate the world more independently. While being so far from campus can be challenging, living year-round at CCI has allowed for large amounts of data collection across many projects. In addition to banking biological samples for hormone analysis and recording observational videos of behavior, most of the data collection involves building a cognitive and behavioral phenotype of individual dogs through highly standardized experiments. In practice, this means that dogs spend a few fun and interactive hours with us, participating in voluntary food-finding games that allow us to quantify skills like memory, impulse control, problem solving, social acuity, and sensory discrimination.

Over the past year and a half, I have overseen the temperament and cognition testing of over 300 8-week old puppies, half of which have been re-tested as adults, as well as over 150 of their dams and sires. We plan to use these data to answer a variety of questions, ranging from how stable these behaviors are over time to how heritable these behaviors are across generations to how predictive they are of eventual outcome. One thing I love about this research is the potential for practical application of our findings. By investigating how the emergence of cognitive traits and early experiences with maternal style contribute to the best working dog phenotypes, one of the applied goals of my research is to help inform the allocation of resources and selection of breeding stock. Furthermore, by exploring questions like how dogs navigate space, control impulses, or categorize objects, I hope to help trainers develop techniques that take advantage of a dog’s natural abilities in applied settings. In these ways, I aim to finetune the efficiency of the process by which organizations breed, raise, and train future service dogs, thereby maximizing the impact for people with disabilities who receive these life-changing animals.

​The sky has always been a source of curiosity, astonishment, and mystery for the human being. From the very early ages, humans were mesmerized by its vastness and presence; the sky was everywhere, yet completely unreachable. Some put their mythological heroes and gods up in there, some got more curious and started to look for patterns, observe closely, and record the movements of the celestial objects to analyze what is this azure dome above us. Centuries later, now not only we have 10-meter-wide eyes (mirrors) monitoring the sky on every single clear night, but also we have sent telescopes into space looking for the furthest and earliest galaxies in the history of the universe!
 
As an astronomy postdoc at Steward Observatory and a NASA Hubble Fellow, I study early galaxies that were formed 10 billion years ago – only about 3 billion years after the Big Bang. The main questions that I try to address in my research are:  How do galaxies form and evolve throughout cosmic time? How does the stellar, gas, and dust content of galaxies evolve? How do early galaxies synthesis heavy elements and enrich their inter-stellar medium?
 
I use ground- and space-based telescopes to gather the light emitted from these galaxies, either in the form of taking images (photometry) or taking their spectra (spectrometry) in different filters. To fully understand the characteristics of a galaxy, one has to observe it in multiple wavelengths, as each component of a galaxy emits light in different wavelengths. For example, very hot, massive, young stars emit mostly in shorter wavelengths, i.e. ultraviolet, while older stars emit light mostly in the optical and near-infrared. My Ph.D. thesis and current research is mostly focused on combining the ultraviolet, optical, and infrared light of galaxies during the era of highest star formation activity in the universe, to study the galaxies’ physical characteristics, such as the rate of star formation, stellar mass, and chemical abundances. More specifically, I have recently focused on characterizing the properties of dust in early galaxies. Cosmic dust grains are solid particles with sizes of < 1 micron that exist in the inter-stellar medium inside galaxies. Dust grains absorb the optical and ultraviolet light emitted from stars and re-radiate the absorbed light at longer infrared wavelengths. Therefore, infrared emission from dust particles points to obscured stellar regions that we would otherwise miss. I use a wealth of data from various telescopes to measure the dust emission and absorption in distant galaxies and incorporate it with the unobscured ultraviolet and optical light to measure the total rate of star formation in galaxies.
 
I am also part of the science team of the NASA’s next decade space telescope, the James Webb Space Telescope (JWST). JWST is a successor of the Hubble Space Telescope, which has a larger mirror, longer wavelength coverage, and greatly improved sensitivity compared to Hubble. With JWST we will be able to observe the first galaxies in the universe and look deep into the nearby dust clouds where stars and planets form. We expect JWST to launch in 2021.
 
Besides research and fulfilling our curiosity to know where we are from and where we are going, an exciting aspect of my job is to share the beauties of the sky with people and show them how amazing science is. Since undergraduate years, I have been an active science promoter. Currently, I am mostly involved in two outreach programs: the Staryab website as the co-founder, and the MESCIT mentorship program as the PI. Staryab (www.staryab.com) is a bi-weekly astrophysical literature journal in Persian, my native language, written by Iranian astronomers across the world since 2014. Our goal is to present interesting research papers in a brief and simple format that is understandable to Persian-speaking undergraduate students in the physical sciences and amateur astronomers who are interested in research. The Mentorship and Education for SCIence in Tucson (MESCIT; www.ireneshivaei.com/mescit), started in February 2018, is a mentorship and math tutoring program for the Native American students, focusing on the Ha:san Preparatory and Leadership school -- a bicultural public high school in Tucson, serving the Tohono O'odham youth and Native students. Our tutors, who are selected from the University of Arizona undergraduate students, visit the school on a weekly basis to tutor math in small classes of 2-3 students. We hope this connection serves to give the high school students someone they can contact for homework help, advice, and accountability.