Acknowledgements

For those who know me, it will be no surprise to hear that I’ve finished up my PhD out of order—somehow letting the next most pressing thing capture my attention and focus before tying a bow on all of the previous items. I find myself writing the “glue” of my dissertation several thousand miles away from Caltech and the physical Clemons Lab space while my attention is completely and wholeheartedly focused on how my own laboratory and team at Neelyx Labs. With this in mind, I’m pausing to consider all the people in my life who have helped me get to where I am now via my journey over now a decade associated with the Clemons Lab. Given my current headspace, the fact that there are both too many to actually be listed, and too little space to properly thank each of you, I must consider the following an incomplete list:

After all these years, I come to realize that I’ll never really quite understand Bil Clemons and the way his mind works. Several years in during a term Bil was teaching undergraduate biochemistry while writing a manuscript in his office, Bil picks up the ball-and-stick model on his desk he’d prepared for teaching earlier that day and asks myself and Michelle, “What molecule is this?” I thought he was joking (e.g. he usually asks me things like “What song is playing?” and I never do). It might have been Leucine, something obvious to him and probably any other crystallographer. To me, I know this residue as “Leu”, “L”, and conceptually in lots of ways, e.g. the only residue with 6 codons, a residue prevalent in transmembrane domains of low/mid GC bacteria, but never as the composition/connectivity of its atoms (Indeed, I failed a high school biochemistry course which included quizzes that required me to draw out prescribed tripeptides by simply turning in blank sheets, angry at the premise. Some years later, I had studied for days for a undergraduate exam faced with significant anxiety). Bil insisted that it was critical to have these committed to memory, especially doing a PhD in a “biochemistry lab”. I think Michelle took his advice, but I disagreed it was critical although I can draw each now having picking it up by osmosis. All this goes to say that it’s incredible that Bil took me on and has supported, believed in, and even “put up” with me all these years. I am so grateful that we have had this opportunity to grow and attack questions together—a student and mentor with different scientific spectacles. Thank you, Bil.

My proudest achievement out of my years at Caltech, maturing into an able computationalist with a framework to attack nearly anything on the computer, is due in major part to Justin Bois. Ever from my first graduate course (coincidentally his first course at Caltech as a new Lecturer), Be/Bi 103: Data Analysis in the Biological Sciences, where he first revealed his “Orange & Blue” pride, Justin has been an instrumental part of my growth. Among the 8 courses, I’ve had the privilage to teach with you, I’ll never forget our Programming Bootcamp at EPFL in Lausanne where I watched my first “football” game (Swiss vs French) on a public screen on the shores of the Lake Geneva. Over these years, Justin has shaped my approach to programming, data, visualization, and everything computational while being a friend and colleague to share my bottomless love of everything having to do with computers. Thank you, Justin.

Axel Muller, my initial mentor at Caltech, gave me my first taste of doing computation surrounded by experimentalists, and, now close friend, has written me on all my travels and adventures over my PhD time to share his own experiences in those places—the best things to visit and just share my excitement of travelling. It’s been such a pleasure to explore with computational & theory extraordinaires: Griffin Chure (master of data), Davi Ortega (crazy hacker), Andrew Jewett (emacs user), and Andy Zhou (infinite laughter). I’m grateful to my yet-unmentioned co-authors and buddies Stephen Marshall, Michelle Fry, Ku-Feng (Geoffrey) Lin, Ailiena Maggiolo, Kate Radford, Alexandra Barlow, and other current and past members of the Clemons and Rees Lab, like Hyun Gi Yun, Lada Kacic, Nadia Riera, Allen Lee, Jeff Li, Jens Kaiser, Welison Floriano, Victor Garcia, and Karen Orta, who have all willingly shared all of their wet-lab experience without limit by answering my endless questions, sharing their experience by osmosis, and above all never discouraging me from being at the bench myself.

To the undergraduate students who choose to work with me, thanks for your ever patience and willingness to follow my lead and explore those questions I posed, no matter how preliminary or far from a real publication that might have concretely served you: Nauman Javed, Mathilda Li, Sam Schulte, Alex Chu, Nadine Bradbury, Tatiana Brailovskaya, Charles Nelson, Alex Guerra, Kate Zator, and Tina Wang. It’s been a pleasure. Thank you to my colleagues from afar who have given an academic & scientific excuse to spend time abroad: Suresh Ramasamy (hosting me in at the National Chemical Laboratory, Pune, India even before the start of my PhD), Vladimira Najdrova (hosting me in Prague, Czech Republic), and Nir Fluman & Gunnar von Heijne (who hosted me at Stockholm University and an incredible source of scientific camaraderie throughout my PhD). To my colleagues at eLife and the Early Career Advisory Group (ECAG), it has been such a joy to try to push and improve practice in science and scientific publication: Tracey Weissgerber, Devang Mehta, Benjamin Schwessinger, Vinodh Ilangovan, Hedyeh Ebrahimi, Kora Korzec, Andy Tay, and Naomi Penfold with others too numerous to list.

To my undergraduate mentors, I am forever grateful to Claudio Grosman, Giselle Cymes, and Eric Jakobsson. Claudio took me in and allowed me to converse, explore unhindered, and maybe even help a little bit in the lab to experience the exhilaration of scientific problem solving while showing me what it meant to be work in a purely scientific and completely egalitarian environment (Grosman lab trainees frequently see Claudio doing the dishes, passaging cells, and other “minutiae”). Eric gave me my first taste of the joy that using the computer to ask questions about biology and humored my held-over-from-high-school yearning to be at a “selective” institution. Both he and Claudio encouraged me to spend a summer at Caltech and continuing on there even through our work was left not-quite-finished. Claudio and Giselle have become like family to me, always writing how I am doing (no matter my lack of reply), and reminding me to be happy and to see all the goodness in my life, no matter my yearning to have chosen my path differently. To you both, I am ever grateful.

To my Pasadena buddies from 2012 onwards, Jake Wellens, Udaya Ghai, Michael Teng, Seohyun (Chris) Kim, Connie Hseuh, Caroline Werlang, Meaghan Sullivan, Anupama Lakshmannan, Pradeep Ramesh, Shane Flynn, Heidi Klumpe, Stephen Wang, and others; to my IMSA-to-UIUC-to-Caltech friends, James Parkin, Dawna Bagherian, Eric Kwan, Noreen Wu, Stefan Petrovic, and Jessica Slagle; and to others who I have missed, thanks for your ideas, conversation, and friendship. To mom, dad, Niki, Shylee, tatha, ammamma, tathayya, and nainamma, thanks for your ever-present support, encouragement, and love. And to Janani, thank you for I am only making it across this finish line because of you.

Land Acknowledgement

The California Institute of Technology sits in the traditional territory and homeland of the Gabrielino Tongva people. The Gabrielino Tongva people are a state-recognized tribe and are working toward federal recognition. Tongva people still live in the Los Angeles area but are now a minority group on their own land. We are settlers and guests on this land, a land which had and continues to have significant connection to the Gabrielino Tongva tribe. The indigenous people of Los Angeles are still here despite ethnic cleansing, forcible removal, unrecognized sovereignty, and outright denial of their existence. My use of land is not limited to Caltech’s Pasadena campus, and I have conducted research or collaborated with others around the world in facilities situated in traditional territories of indigenous people.

Adapted from the Caltech Library.