Dan is a veteran in the biotech industry and has worked for companies ranging in size from tiny startup to big pharma.  Prior to joining Octant, he was CFO at Kriya Therapeutics where he started and built the finance and HR organizations.  Before that, Dan served as VP Finance at Portola Pharmaceuticals and was an instrumental member of the leadership team that transformed the company from a private, development stage, US company to a public, commercial stage company which launched two products in the US and expanded into Europe.  He has also worked at Johnson & Johnson and Gilead Sciences, holding positions of increasing responsibility.  Dan started his career as a Research Associate at SyStemix, Inc. where he realized that though he loved science, he was not a scientist, and so transitioned to a career in Finance.

Dan received a B.A. in Molecular Cell Biology from the University of California, Berkeley and an MBA from the University of Southern California.  

When not at Octant, Dan enjoys spending time with family, traveling the world, and exploring museums floor by floor and exhibit by exhibit.

Josh is an engineer passionate about working at the intersection of biology, statistics, and computation. He was previously the Head of Bioinformatics at Invitae, where he built and supported a team responsible for delivering methods and software for the genomic analysis of millions of patients per year. He has led technical efforts ranging from the design and validation of novel statistical techniques to architecting enterprise software systems.

Josh received his PhD in Computer Science at UC Berkeley in Yun Song's group, where he worked on computationally tractable approaches to incorporating recombination in population genetic models. He received a BS in Physics and Computer Science at the University of Illinois.

Outside of work, Josh enjoys riding vintage bicycles, minimalist running, rock climbing, and cooking for his wife and two sons.

Papers

Truty, R., Paul, J.S., Kennemer, M., Lincoln, S.E., Olivares, E., Nussbaum, R.L., Aradhya, S. Prevalence and properties of intragenic copy-number variation in Mendelian disease genes. Genetics in Medicine, 21 (2019) 114-123.

Lincoln, S.E., Truty, R., Lin, C, Zook, J.M., Paul, J.S., Ramey, V.H., Salit, M., Rehm, H.L., Nussbaum, R.L.,Lebo, M.S. A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing. The Journal of Molecular Diagnostics, 21 (2019) 318-329.

Westbrook, M., Kvitek, D., Gafni, E., Paul, J.S., Kennemer, M., Winder, T., Shieh, P. Prevalence and properties of intragenic copy-number variation in Mendelian disease genes. Neurology, 90 (2018)

Steinrücken, M., Paul, J.S., and Song, Y.S. A sequentially Markov conditional sampling distribution for structured populations with migration and recombination. Theoretical Population Biology 87 (2013) 51-61.

Paul, J.S. and Song, Y.S. Blockwise HMM computation for large-scale population genomic inference. Bioinformatics, 28 (2012) 2008-2015.

Nielsen, R., Paul, J.S., Albrechtsen, A., and Song, Y.S. Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics 12 (2011) 443-451.

Paul, J.S., Steinrücken, M., and Song, Y.S. An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics 187 (2011) 1115-1128

Paul, J.S. and Song, Y.S. A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination. Genetics 186 (2010) 321-338.

Mark Murcko was an early leader in structure-based drug design and has directly contributed to nine marketed drugs spanning HIV, HCV, cystic fibrosis, and glaucoma. He is a Founder, Board member, and was the interim CSO at Relay Therapeutics. More recently he was the founding CSO and remains a board member and advisor to Dewpoint Therapeutics.  In addition, Mark is a senior lecturer in the Department of Biological Engineering at MIT, and has served on numerous scientific advisory boards and corporate boards of directors for a diverse range of organizations.  Mark was chief technology officer and chair of the SAB of Vertex Pharmaceuticals and was responsible for the identification, validation and implementation of disruptive technologies across R&D. Mark is a co-inventor of the HCV protease inhibitor Incivek (telaprevir), as well as Agenerase (amprenavir) and Lexiva (fosamprenavir), Vertex’s two marketed drugs for the treatment of HIV. In addition, he guided the early efforts of Vertex’s cystic fibrosis program that has produced four marketed drugs.

Prior to Vertex, Mark worked at Merck Sharpe & Dohme, where he helped discover multiple clinical candidates, including Dorzolamide, a carbonic anhydrase inhibitor for the treatment of glaucoma which was commercialized in two approved drugs, Trusopt and Cosopt.  Trusopt was the first medicine in history to come from a structure-based drug design program.  He is a member of the Board of Trustees of the GRC and the Board of Advisors of the Boston Museum of Science.  He is a co-inventor on more than 50 issued patents and has co-authored more than 85 scientific articles. Mark holds a Ph.D. in organic chemistry from Yale University.

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Matthew brings over two decades of experience in discovery research, pharma and biotechnology to Octant. His expertise includes immuno-oncology, autoimmunity, metabolic diseases and neuro-degeneration. Prior to joining Octant, he was Chief Translational Officer at Human Immunology Biosciences, served as SVP at insitro where he directed the Department of Translational Genetics and Biology, and was founder and Head of the Reverse Translation Organization at Genentech in the Cancer Immunology Department. His academic positions included Director of the Immunology Department at Institut Pasteur, Paris and co-founder of the Milieu Interieur Consortium, a global real-world data effort that has identified actionable insights into the genetic, microbiome and environmental determinants of health and disease. 

Matthew's contributions have led to the discovery of new drug targets and he has helped to advance multiple drug candidates in first-in-human Ph1 studies and through post-marketing / indication expansion trials. His seminal work offered definitive evidence that naturally occurring tumor immunity in humans is established by the cross-priming of antigen-specific cytotoxic (CD8+) T cells, establishing the foundation for current approaches in immuno-oncology. He holds a Ph.D. in Immunology, an M.D. and residency training in Clinical Pathology, from Rockefeller University, Weill Cornell Medical School and New York Presbyterian Hospital, respectively. 

Matthew enjoys spending quality time with his wife and daughter, as well as cycling, backcountry skiing and cooking.

Before joining Octant, Michelle advised the asset management industry as an attorney at a large global law firm and worked in sales, training and marketing at Johnson & Johnson.  She was shortlisted by Chambers in 2019 as a “Future Leader” for her commitment to promoting diversity and inclusion in the legal profession.

In addition to her law degree from Northwestern, Michelle received her MBA from Drexel University and a B.S. in health studies from Georgetown University. She volunteers for the regional alumni chapters of Georgetown University and Northwestern Pritzker School of Law.

Michelle enjoys food and sailing in the San Francisco Bay and further afield.

Naomi is a quantitative cell biologist by training. At Octant she's worn a few different hats including recruiting, establishing the OA program, building Octant HQ, demonstrating Octant's multiplexed platform technology, building cell engineering, and more.

Naomi received her PhD from the University of California, San Diego under Roy Wollman quantifying how cells communicate with one another to determine their position in relation to a wound. She's passionate about bringing science to the public through effective scientific communication and meaningful technological advances.

Outside of work you'll find Naomi spending time with her family and two dogs, hiking, running, and playing the piano.

Papers

Wound induced Ca2+ wave propagates through a simple Release and Diffusion mechanism. Mol. Biol. Cell. Handly LN, Wollman R. 2017. 28:1457-66.

Signal Transduction at the Single-Cell Level: Approaches to Study the Dynamic Nature of Signaling Networks. Handly LN, Yao J, Wollman R, J. Mol. Biol. 2016, 428: 3669-82.  

Paracrine communication maximizes cellular response fidelity in wound signaling. Handly LN; Pilko, A, Wollman R. eLife. 2015, 4:e09652.

Ramsey has spent his career building high-performance teams and technology companies. Before Octant, he was an executive at Dropbox, where he had roles leading Dropbox's communications, public policy & government affairs, human resources, legal, and trust & security teams. During that time Dropbox raised $1+ billion in capital, grew to more than 500 million users, and was the fastest SAAS company in history to reach $1 billion in revenue run rate. Prior to Dropbox, Ramsey was a Vice President at Google, where he managed Google's commercial legal groups and negotiated some of the internet industry's largest partnerships.    

Before that, Ramsey was a technology attorney at Wilson Sonsini Goodrich & Rosati and a Lecturer at the University of Pennsylvania Law School. He has also done pro bono work representing indigent clients seeking political asylum. Ramsey received a B.S. in Chemical & Biochemical Engineering from Rutgers University and a J.D. from NYU.

Ramsey is a Board member at the Rutgers College of Engineering, and Represent.us, a grassroots political reform organization.

Ramsey grew up in Athens, Greece and Sparta, NJ. He enjoys hiking, camping, cooking over fire, punk music, and wandering through neighborhood art galleries.

Sri is a biologist that has helped build technologies, labs, and companies in synthetic biology, functional genomics, and bioinformatics over the last 20 years. He is passionate about developing more rational ways to understand and engineer biology.

Sri is a co-founder at Octant and an Associate Professor at UCLA in the Chemistry and Biochemistry Department, where his lab has worked on building large-scale ways of empirically exploring questions in protein biochemistry, human genetic variation, gene regulation, chemical biology, synthetic biology, and functional genomics.

Sri previously worked at the Wyss Institute and Harvard, where he built numerous technologies in gene synthesis, DNA information storage, gene editing, and large-scale multiplexed assays. He helped build Gen9, a gene synthesis company, as a member of the SAB and was the first employee of Joule Unlimited, an engineered algal biofuel company. He is a Searle Scholar (2015), NIH New Innovator (2014), and received his ScD in Biological Engineering at MIT and BS in Bioengineering at UC Berkeley.

Sri is originally from New Jersey, by way of Philadelphia and Kansas, and was born in North Carolina. He enjoys eating, getting outdoors, and traveling with his wife and two children.

More papers…

Sri is a biologist that has helped build technologies, labs, and companies in synthetic biology, functional genomics, and bioinformatics over the last 20 years. He is passionate about developing more rational ways to understand and engineer biology.

Sri is a co-founder at Octant and an Associate Professor at UCLA in the Chemistry and Biochemistry Department, where his lab has worked on building large-scale ways of empirically exploring questions in protein biochemistry, human genetic variation, gene regulation, chemical biology, synthetic biology, and functional genomics.

Sri previously worked at the Wyss Institute and Harvard, where he built numerous technologies in gene synthesis, DNA information storage, gene editing, and large-scale multiplexed assays. He helped build Gen9, a gene synthesis company, as a member of the SAB and was the first employee of Joule Unlimited, an engineered algal biofuel company. He is a Searle Scholar (2015), NIH New Innovator (2014), and received his ScD in Biological Engineering at MIT and BS in Bioengineering at UC Berkeley.

Sri is originally from New Jersey, by way of Philadelphia and Kansas, and was born in North Carolina. He enjoys eating, getting outdoors, and traveling with his wife and two children.

More papers…

Ramsey has spent his career building high-performance teams and technology companies. Before Octant, he was an executive at Dropbox, where he had roles leading Dropbox's communications, public policy & government affairs, human resources, legal, and trust & security teams. During that time Dropbox raised $1+ billion in capital, grew to more than 500 million users, and was the fastest SAAS company in history to reach $1 billion in revenue run rate. Prior to Dropbox, Ramsey was a Vice President at Google, where he managed Google's commercial legal groups and negotiated some of the internet industry's largest partnerships.    

Before that, Ramsey was a technology attorney at Wilson Sonsini Goodrich & Rosati and a Lecturer at the University of Pennsylvania Law School. He has also done pro bono work representing indigent clients seeking political asylum. Ramsey received a B.S. in Chemical & Biochemical Engineering from Rutgers University and a J.D. from NYU.

Ramsey is a Board member at the Rutgers College of Engineering, and Represent.us, a grassroots political reform organization.

Ramsey grew up in Athens, Greece and Sparta, NJ. He enjoys hiking, camping, cooking over fire, punk music, and wandering through neighborhood art galleries.

Dr. Jason Kelly is the co-founder and CEO of Ginkgo Bioworks, the leading horizontal platform for cell programming. Headquartered in Boston, Ginkgo is a synthetic biology company that enables customers across industries to program cells as easily as we can program computers. Ginkgo supports the development of applications ranging from vaccine manufacturing and new pharmaceutical modalities to fragrances, sustainable dyes, and biosynthetic cannabinoids, as well as pandemic response and biosecurity tools including K12 pooled testing for COVID-19. Ginkgo is listed on the New York Stock Exchange under the ticker $DNA. Prior to Ginkgo, Jason received B.S. degrees in Chemical Engineering and Biology and a PhD in Biological Engineering all from MIT.

Jorge Conde is a General Partner at Andreessen Horowitz where he leads investments at the cross section of biology, computer science and engineering.

Prior to joining a16z, Jorge served as Chief Strategy Officer for Syros (NASDAQ: SYRS), which is advancing a new wave of medicines that control expression of disease-driving genes to treat cancer and other diseases. He previously served as the company's Chief Financial Officer and Chief Product Officer, leading the platform strategy for Syros' novel gene regulation technology. Jorge also cofounded Knome, a human genome interpretation company acquired by Tute Genomics in 2015. Earlier in his career, Jorge worked in marketing and operations at MedImmune and as a biotechnology investment banker at Morgan Stanley.

Jorge holds an MBA from Harvard Business School, an MS from the Harvard-MIT Division of Health Sciences and Technology, and a BA in Biology from Johns Hopkins University.

Jorge was named one of the top 35 young innovators in the world by the MIT Technology Review and is a Henry Crown Fellow of the Aspen Institute and a member of the Aspen Global Leadership Network. He previously served on the board of the Museum of Science, Boston.

Jorge serves on the board of the following Andreessen Horowitz portfolio companies: Asimov, Camp4, EQRx, Komodo Health, Octant Bio, Tmunity, and twoXAR.

Mark Murcko was an early leader in structure-based drug design and has directly contributed to nine marketed drugs spanning HIV, HCV, cystic fibrosis, and glaucoma. He is a Founder, Board member, and was the interim CSO at Relay Therapeutics. More recently he was the founding CSO and remains a board member and advisor to Dewpoint Therapeutics.  In addition, Mark is a senior lecturer in the Department of Biological Engineering at MIT, and has served on numerous scientific advisory boards and corporate boards of directors for a diverse range of organizations.  Mark was chief technology officer and chair of the SAB of Vertex Pharmaceuticals and was responsible for the identification, validation and implementation of disruptive technologies across R&D. Mark is a co-inventor of the HCV protease inhibitor Incivek (telaprevir), as well as Agenerase (amprenavir) and Lexiva (fosamprenavir), Vertex’s two marketed drugs for the treatment of HIV. In addition, he guided the early efforts of Vertex’s cystic fibrosis program that has produced four marketed drugs.

Prior to Vertex, Mark worked at Merck Sharpe & Dohme, where he helped discover multiple clinical candidates, including Dorzolamide, a carbonic anhydrase inhibitor for the treatment of glaucoma which was commercialized in two approved drugs, Trusopt and Cosopt.  Trusopt was the first medicine in history to come from a structure-based drug design program.  He is a member of the Board of Trustees of the GRC and the Board of Advisors of the Boston Museum of Science.  He is a co-inventor on more than 50 issued patents and has co-authored more than 85 scientific articles. Mark holds a Ph.D. in organic chemistry from Yale University.

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George Petrocheilos is a Co-Founder & Managing Partner of Catalio Capital Management, LP. He is primarily responsible for managing the firm and for making investments in breakthrough biomedical technology companies founded by world renowned scientist-entrepreneurs. He also serves on the Nexus Investment Committee and the firmwide Management Committee.

In addition to Octant, George currently serves on the Boards of Haystack Oncology, Spiral Therapeutics, MindX, DNA Script, Sisu Global Health, Inc., WindMIL Therapeutics, and LifeSprout. He also serves as President of the HealthCor Catalio Special Purpose Acquisition Corp. (NASDAQ: HCAQ) and on the Board of Directors of the family-owned PETKA S.A., a construction & development company headquartered in Athens, Greece.

Prior to founding Catalio, he was a General Partner at Camden Partners Holdings, LLC, a private equity firm, where he focused on making biomedical technology investments.

George serves on the Board of Trustees of the Kennedy Krieger Institute, the Baltimore School for the Arts and the Johns Hopkins Center for Financial Economics. He also serves on the Investment Advisory Committee of the Halcyon Incubator in Washington D.C. and the MIT Enterprise Forum. George’s honors include Baltimore Business Journal’s 2019 ‘Tech 10’ leaders in Maryland, BBJ’s 2013 “40 Under 40 Business Leaders” and The Hill’s 2013 “Washington D.C. Rising Stars”, among others.

George earned his B.A. degree in Financial Economics from the Johns Hopkins University.

Rebecca is a versatile CEO and board director with twenty-five years of experience in drug development, manufacturing and leadership. Her experience spans a wide range of therapeutic areas and platforms in large pharma and small biotech. She has served as President and CEO of Siduma Therapeutics since 2021. In addition to Octant, she also serves on the board of Halda Therapeutics. She has previously held key operational leadership roles in emerging biotech companies including EvolveImmune Therapeutics, Cardurion Pharmaceuticals and Prevail Therapeutics. Prior to these roles, she spent eleven years working in medical affairs, development, corporate affairs and manufacturing at Alexion Pharmaceuticals where she led successful development programs, integrations and global enterprise projects. Earlier in her career she worked in development and medical affairs at Novartis Pharmaceuticals. 

Rebecca is passionate about building a strong and inclusive bioscience ecosystem. She serves as venture partner with Elm Street Ventures and volunteers with BioLaunch, a biotech job training program based in New Haven, Connecticut. In 2020 she co-founded Executive Women in Bio of Connecticut. She is a member of the Dean’s Advisory Board of the Bouvé College of Health Sciences at Northeastern University and is an active member of Latinos in Bio.

Rebecca earned a Doctorate in Pharmacy from Northeastern University and completed a clinical fellowship at Tufts Medical Center. She additionally holds an Executive Certificate in Management and Leadership from the MIT Sloan School of Management.

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Alexa joined Octant as an Apprentice in 2024. She is a part of the Platform Biology team, contributing to the dissection of sequence-function relationships observed in rare diseases to advance optimized and novel drug discovery.

Motivated by her little brother who lives with a rare genetic disorder of his own, Alexa received her Honors BS in Biology with emphasis in Genetics and Genomics and a Chemistry minor from the University of Utah before coming to Octant. During her undergraduate years, Alexa was involved in a slew of projects in the English Lab. She worked on quantifying transcriptional output of synthetic mammalian reporters as a part of an massively parallel reporter assay, investigating the precision in rare mutation profiling for the creation of a high-throughput sequencing pipeline, and expanding the tetracycline-inducible toolbox by saturation mutagenesis of the operator and analysis of resulting transcription factor function. She also enjoyed spending three years assistant teaching genetics labs and mentoring other biology students.

When not in the lab, Alexa loves to snowboard, powerlift, play tennis, and jam out to pop punk.

Alexia joined Octant in 2024 as an apprentice on the Discovery Biology team. She is currently focused on assay development to further understand p53 biology and characterize compounds that correct p53-variant activity.

Before coming to Octant, Alexia earned an honors bachelor’s degree in Molecular and Cellular Biology from Harvard College. She developed a strong interest in protein biochemistry after three years of structural biology research in the Léger-Abraham lab located at Harvard Medical School. In the Léger-Abraham lab, Alexia studied protein-protein interactions involved in translation regulation in Leishmania and Plasmodium parasites. In addition to her research, she worked as a campus research ambassador and a course facilitator for introductory molecular biology, genetics, and physics.

Outside the lab, Alexia enjoys playing volleyball, drinking matcha, and exploring new restaurants in the Bay Area.

Angela is currently the Assistant Controller at Octant. Prior to joining Octant, Angela was Senior Manager, SEC Reporting at Global Blood Therapeutics (acquired by Pfizer). She worked on SEC reporting, technical accounting and SOX. Before that, Angela was Assurance Manager at Ernst and Young, serving mainly public biotech clients. Angela is an active CPA in the state of California.

Angela received her B.S. in Business Administration and Accounting, with a minor in Psychology from the University of Southern California.

Outside of Octant, Angela enjoys taking workout classes, traveling and attempting to learn French.

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Bryan joined Octant as a Research Associate and will assist in running and optimizing Octant's technology. He recently received his B.S. in Microbiology, Immunology, and Molecular Genetics with a minor in Bioinformatics from UCLA. There, he took part in a virology lab where he focused on characterizing genetic and genomic relationships between bacteriophages infecting separate host genera.

In his free time Bryan enjoys trying new foods, learning about languages, hiking, and programming.

Calvin is a chemistry apprentice at Octant on the high-throughput synthesis team. He graduated from Notre Dame with a B.S. in biochemistry, concentrating in neuroscience and minoring in patient advocacy. In the Serianni Lab at Notre Dame, he synthesized carbohydrates and glycoconjugates to study the three-dimensional structure and conformation of these biomolecules using NMR.

Calvin has prior experience in the biopharmaceutical industry developing large-molecule analytical methods at AstraZeneca and Merck. At AstraZeneca/MedImmune, he developed a two-dimensional HPLC method that accurately characterizes mAbs and ADCs in high concentrations of a micelle-forming surfactant excipient. At Merck Research Laboratories, he developed high-throughput CE-SDS methods for a wide range of next-generation therapeutic proteins, including fusion proteins, bispecific engagers, Fc-peptide conjugates, and trispecific antibodies (in addition to traditional mAbs and ADCs).

Outside of the lab, you can find him sewing for fun or mountain biking around the Bay.

PAPERS
Hawe, C.; Tunink, K.; Wenger, D. “Krabbe Disease.” National Organization for Rare Disorders 2024, https://rarediseases.org/rare-diseases/leukodystrophy-krabbes/

Arruebarrena, M.A.; Hawe, C.T.; Lee, Y.M.; Branco, R.C. “Mechanisms of Cadmium Neurotoxicity.” International Journal of Molecular Sciences 2023, 24, 16558. https://doi.org/10.3390/ijms242316558

Carmen joined Octant in the 2023 class of Octant Apprentices. She is currently working with the Deep Mutational Scanning team to drive deeper understandings of how sequence-function relationships can give greater insights into disease and be further applied towards our drug discovery platform.

Prior to arriving at Octant, Carmen obtained her BS in Biochemistry at the University of Oregon (along with a minor in Theater Arts and Production!). During her undergraduate career, Carmen spent three years in the Plesa Lab at the Knight Campus for Advancing Scientific Impact developing a system to perform Broad Mutational Scans using a massive and diverse library of genes to observe antibiotic resistance in Dihydrofolate Reductase homologs and mutants. In addition to her work in the lab, she also led the inaugural iGEM team at the university to present in the Grand Jamboree in Paris on their work developing a genetic-circuit-fueled, field-side concussion diagnostic tool.

Outside of her research, Carmen plays Ultimate Frisbee with a mixed team in the bay, climbs, hikes, runs, plays piano, and enjoys spending any free time with her cat, Juniper.

Carter is a molecular biologist with a background in molecular diagnostics, assay development, and genetic engineering of mammalian cells. 

He received his M.S. in Clinical Laboratory Sciences from Rush University Medical Center and completed his clinical training at Northwestern Memorial Hospital. He is an ASCP certified molecular biologist and worked as a clinical laboratory scientist in molecular diagnostics at the University of Illinois Medical Center and the Denver VA Medical Center. He received his Ph.D. in Cancer Biology from the University of Nebraska Medical Center then completed his postdoctoral training at UCSF. He worked as a scientist at Guardant Health before joining Octant in 2021.

Outside of the lab, Carter enjoys spending time outdoors with his family and dog.  ‍

Papers‍

FOXM1: A Multifunctional Oncoprotein and Emerging Therapeutic Target in Ovarian Cancer.

Liu C, Barger CJ, Karpf AR. Cancers (Basel). 2021 Jun 19;13(12):3065. 

Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer. Barger CJ, Chee L, Albahrani M, Munoz-Trujillo C, Boghean L, Branick C, Odunsi K, Drapkin R, Zou L, Karpf AR. Elife. 2021 Apr 23;10:e55070. 

Pan-Cancer Analyses Reveal Genomic Features of FOXM1 Overexpression in Cancer. Barger CJ, Branick C, Chee L, Karpf AR. Cancers (Basel). 2019 Feb 21;11(2):251.

Genetic determinants of FOXM1 overexpression in epithelial ovarian cancer and functional contribution to cell cycle progression. Barger CJ, Zhang W, Hillman J, Stablewski AB, Higgins MJ, Vanderhyden BC, Odunsi K, Karpf AR. Oncotarget. 2015 Sep 29;6(29):27613-27. 

Extended list of papers‍

https://scholar.google.com/citations?user=gHskM6sAAAAJ&hl=en

Connor is a synthetic and systems biologist with a background in mammalian gene regulation and functional genomics. He is currently developing new screening approaches to expand Octant's drug discovery capabilities.

Before joining Octant, Connor completed his PhD in Bioengineering at Stanford University in the lab of Dr. Lacramioara Bintu. The bulk of his thesis work focused on the large-scale discovery and characterization of viral proteins that can affect transcription in human cells.

Outside of Octant, Connor enjoys making music, drawing, painting, playing board games, and playing pickleball.

Papers

Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells. Lensch S, Herschl MH, Ludwig CH, Hinks MM, Mukund A, Fujimori T, Bintu L (2022). eLife.

High-throughput functional characterization of combinations of transcriptional activators and repressors. Mukund AX, Tycko J, Allen SJ, Robinson SA, Andrews C, Ludwig CH, Spees K, Bassik MC, Bintu L (2022). bioRxiv.

High-Throughput Discovery and Characterization of Viral Transcriptional Effectors in Human Cells. Ludwig CH, Thurum AR, Yang KJ, Tycko J, Bassik MC, Glaunsinger BA, Bintu L (2022). bioRxiv.

Large-scale mapping and systematic mutagenesis of human transcriptional effector domains. DelRosso N, Tycko J, Suzuki P, Andrews C, Aradhana FNU, Mukund A, Liongson I, Ludwig CH, Spees K, Fordyce P, Bassik MC, Bintu L (2022). bioRxiv.

More papers

Conor is a protein biochemist and molecular biologist by training. He is currently employing Octant's multiplex capabilities toward the optimizing and scaling of our Deep Mutational Scanning (DMS) approach, with the goal of harnessing this technology as a tool for rational genetics- and structure-driven drug design.

Conor received his PhD from the University of California, San Francisco in the lab of Adam Frost. There he worked on the biochemical and structural determinants of Ribosome-associated Quality Control (RQC). Prior to this he did his undergraduate work at UC Berkeley, where he worked under Liam Holt studying the evolutionary plasticity of kinase specificity and poly-glutamine repeat expansions in yeast. Before graduate school Conor also spent some time at the University of Copenhagen in Rune Linding's lab studying the proteomic effects of cancer therapies. Conor thrives working at the intersection of many disciplines and is fascinated with how biology emerged in the universe. He believes mechanistic dissection of molecules in the context of mutational plasticity can help tackle some of the most complex problems in biology and disease.

Outside of work you'll find Conor traveling, skiing, scouting new breweries, playing tennis, experimenting with hot sauce recipes, and exploring unusual agave spirits.‍

Papers

Ribosome-associated quality control and CAT tailing. Howard CJ, Frost A (2021). Critical Reviews in Biochemistry and Molecular Biology.

Phosphoregulation of phase separation by the SARS-CoV-2 N Protein suggests a biophysical basis for its dual functions. Carlson CR*, Asfaha JB*, Ghent CM*, Howard CJ, Hartooni N, Safari M, Frankel AD, Morgan DO (2020). Molecular Cell.

Rapid deployment of SARS-CoV-2 testing: The CLIAHUB. Crawford ED, et al. (2020). PLoS Pathogens.

Probability-based detection of phosphoproteomic uncertainty reveals rare signaling events driven by oncogenic kinase gene fusion. Robin X, Voellmy F, Ferkinghoff-Borg J, Howard CJ, Altenburg T, Engel M, Simpson CD, Saginc G, Koplev S, Klipp E, Longden J, Linding R (2019). bioRxiv.

Vms1p is a release factor for the Ribosome-associated Quality control Complex. Rendon OZ*, Fredrickson EK*, Howard CJ*, Vranken JV, Fogarty S, Tolley ND, Kalia R, Osuna BA, Shen PS, Hill CP, Frost A, Rutter J (2018). Nature Communications.

Intrinsic cooperativity potentiates parallel cis-regulatory evolution. Sorrells TR, Johnson AN, Howard CJ, Britton CS, Fowler KR, Feigerle, JT, Weil PA, Johnson AD (2018). eLife.

CDKL family kinases have evolved distinct structural features and ciliary function. Canning P, Park K, Goncalves J, Li C, Howard CJ, Sharpe TD, Holt LJ, Pelletier L, Bullock AN, Leroux MR (2018). Cell Reports.

In vitro analysis of RQC activities provides insights into the mechanism and function of CAT tailing. Osuna BA, Howard CJ, Subheksha KC, Frost AS, Weinberg DE (2017). eLife.

Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity. Howard CJ*, Hanson-Smith V*, Kennedy KJ, Miller CJ, Lou HJ, Johnson AD, Turk BE, Holt LJ (2014). eLife.

Dan is a veteran in the biotech industry and has worked for companies ranging in size from tiny startup to big pharma.  Prior to joining Octant, he was CFO at Kriya Therapeutics where he started and built the finance and HR organizations.  Before that, Dan served as VP Finance at Portola Pharmaceuticals and was an instrumental member of the leadership team that transformed the company from a private, development stage, US company to a public, commercial stage company which launched two products in the US and expanded into Europe.  He has also worked at Johnson & Johnson and Gilead Sciences, holding positions of increasing responsibility.  Dan started his career as a Research Associate at SyStemix, Inc. where he realized that though he loved science, he was not a scientist, and so transitioned to a career in Finance.

Dan received a B.A. in Molecular Cell Biology from the University of California, Berkeley and an MBA from the University of Southern California.  

When not at Octant, Dan enjoys spending time with family, traveling the world, and exploring museums floor by floor and exhibit by exhibit.

Daniel is an organic chemist with a background in synthetic methodology, high-throughput experimentation, and phenotypic screening. He earned his Ph.D. in Organic Chemistry at the University of Illinois at Urbana-Champaign (UIUC), co-advised under the synthetic chemist Prof. David Sarlah, and the chemical biologist Prof. Angad Mehta.

Within Prof. Sarlah’s lab, Daniel worked to develop the platform now dubbed “Reaction Mining”, where he and his coworkers utilized artificial mass is otopologue distributions to autonomously discern the occurrence of reactions by LC/MS. He then demonstrated the utility of this system in high-throughput screens to map the “reaction scope” of metal catalysts, towards the goal of creating an automated method to discover novel chemical reactivity.

In Prof. Mehta’s lab, Daniel applied the same principles of high-throughput methodology towards the development of a phenotypic screen targeting viral RNA-capping enzymes, specifically the SARS-CoV-2 Nsp14 and MPoxVD1/VD12 complex. His work entailed the miniaturization of the system to a robust 384-well plate format, and its evaluation against a wide variety of small molecule inhibitor candidates. He carried out de novo synthesis of hypothesis-driven and computationally designed analogues, and evaluated the activity of diversity-oriented compound collections in high throughput assays.

When he’s not at Octant, you can find Daniel in the woods identifying wildflowers and edible plants, tending to his garden, or in the kitchen cooking with friends.

Danny Tagaloa is in Laboratory Operations for Octant. For over a decade, he led the Facilities group for Plexxikon Inc. and contributed to the success of two market drugs, Zelboraf and Pexidartinib. Danny spent part of his childhood in American Samoa and enjoys the outdoors to garden, camping, or going fishing. In his spare time, he loves spending time with his family, including his grandchildren.

Deepali is a medicinal chemist with background in synthetic organic chemistry. She received her M.Sc. degree in organic chemistry from the University of Pune, India. After a stint at AMRI as a research scientist, she moved to KU Leuven where she received her PhD in organic chemistry under the guidance of Prof. Wim Dehaen, working on novel methods for the synthesis and resolution of helically chiral molecules with optoelectronic applications. She then moved to The Scripps Research Institute in La Jolla as a postdoctoral research associate and worked on structure-based drug design of small molecule ligands for SMO and P-glycoprotein an efflux transporter involved in cancer multidrug resistance.

Prior to joining Octant, she worked as a medicinal chemistry scientist at Bristol Myers Squibb in Redwood City, CA in the small molecule drug discovery group (SMDD) contributing to hit-to-lead and lead op programs in the immuno-oncology therapeutic area. She has co-authored 15 publications from her PhD and postdoctoral work.

In her free time, Deepali enjoys cooking/trying different cuisines and exploring new places for hiking. 

Diane is a genomicist who leads Octant’s Deep Mutational Scanning team.  She is passionate about elucidating the genetic contributors to human disease and harnessing this information to improve treatments.

Diane was previously a Staff Scientist (Principal Investigator) at Lawrence Berkeley National Lab, where she co-led a research group that used genomics technologies and in vivo genome engineering in mice to understand the functions of noncoding DNA sequences in development, disease, and evolution.  She received her PhD in Genome Sciences from the University of Washington, where she was the recipient of a National Institutes of Health Kirschstein Predoctoral Fellowship, and her BA in Biology from the University of Chicago.  She has co-authored 50+ publications/preprints to date on mammalian gene expression regulation, human genetics, genomics technologies, and plant biology.

Diane is an avid reader who enjoys hiking, bicycling, and playing board games with her family.

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Dom is a Research Associate leading high-throughput screening for Octant’s rare disease programs. He is passionate about enhancing Octant’s platform to accelerate and optimize early drug discovery efforts. His experience in the biotechnology industry stems from local companies including Bayer and Zymergen (now Ginkgo Bioworks).

Dom formerly worked as a college counselor at Y-Scholars, a nonprofit college-readiness program, where he supported hundreds of high school seniors with applying to and preparing for higher education. With fellow Octonauts, he established a partnership between Octant and the YMCA to foster opportunities geared towards underrepresented youth, with a vision of further diversifying the STEM world.

Outside the lab Dom enjoys long walks, catching the perfect sunset, and adventuring with his favorite humans and canines.

Eric is a molecular biologist with a background in synthetic biology and functional genomics. He completed his Ph.D. in Molecular Biology at UCLA in the lab of Sriram Kosuri. His graduate work focused on constructing a massively parallel reporter assay for mapping olfactory receptor-odorant interactions and performing a deep mutational scan of the Beta-2 Adrenergic Receptor. Outside of the lab you can find him playing basketball, sailing, or going to shows.

Papers

J. S. Bloom, L. Sathe, C. Munugala, E. M. Jones, M. Gasperini, N. B. Lubock, F. Yarza, E. M. Thompson, K. M. Kovary, J. Park, D. Marquette, S. Kay, M. Lucas, T. Love, A. Sina Booeshaghi, O. F. Brandenberg, L. Guo, J. Boocock, M. Hochman, S. W. Simpkins, I. Lin, N. LaPierre, D. Hong, Y. Zhang, G. Oland, B. J. Choe, S. Chandrasekaran, E. E. Hilt, M. J. Butte, R. Damoiseaux, C. Kravit, A. R. Cooper, Y. Yin, L. Pachter, O. B. Garner, J. Flint, E. Eskin, C. Luo, S. Kosuri, L. Kruglyak, V. A. Arboleda, Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. Nat Biomed Eng. 5, 657–665 (2021).

E. M. Jones*, R. Jajoo*, D. Cancilla, N. B. Lubock, J. Wang, M. Satyadi, R. Cheung, C. de March, J. S. Bloom, H. Matsunami, S. Kosuri, A Scalable, Multiplexed Assay for Decoding GPCR-Ligand Interactions with RNA Sequencing. Cell Syst. 8, 254-260.e6 (2019).

Jones EM*, Lubock NB*, Venkatakrishnan AJ, Wang J, Tseng AM, Paggi JM, Latorraca NR, Cancilla D, Satyadi M, Davis JE, Babu MM, Dror RO, Kosuri S. 2020. Structural and functional characterization of G protein–coupled receptors with deep mutational scanning. Elife 9:e54895.

Joshua S. Bloom, Eric M. Jones, Molly Gasperini, Nathan B. Lubock, Laila Sathe, Chetan Munugala, A. Sina Booeshaghi, et al. 2020. “Swab-Seq: A High-Throughput Platform for Massively Scaled up SARS-CoV-2 Testing.” medRxiv.

Jessica E. Davis, Kimberly D. Insigne, Eric M. Jones, Quinn A. Hastings, W. Clifford Boldridge, and Sriram Kosuri. 2020. “Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays.” Cell Systems 11 (1): 75–85.

R. Cheung, K. D. Insigne, D. Yao, C. P. Burghard, J. Wang, Y.-H. E. Hsiao, E. M. Jones, D. B. Goodman, X. Xiao, S. Kosuri, A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions. Mol. Cell. 73, 183-194.e8 (2019).

Structure-based design of functional amyloid materials. Li D, Jones EM, Sawaya MR, Furukawa H, Luo F, Ivanova M, Sievers SA, Wang W, Yaghi OM, Liu C, Eisenberg DS. J Am Chem Soc. 2014 Dec 31;136(52):18044-51. doi: 10.1021/ja509648u. Epub 2014 Dec 19.

Erin is a protein biochemist/biophysicist with a background in developing high-throughput screening platforms.

Before joining Octant, she completed her Ph.D. in Chemistry & Chemical Biology at UCSF in Jaime Fraser’s lab. Her thesis work broadly focused on the functional characterization of enzyme conformational states using deep mutational scanning, in vitro kinetics, and structural techniques.

Outside of the lab, Erin loves to get outside to bike, run, hike, and backpack.

Papers

Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing. Joshua S. Bloom Eric M. Jones, Molly Gasperini, Nathan B. Lubock, Fauna Yarza, Erin M. Thompson, Kyle M. Kovary, Jimin Park, Myles Hochman,. medrxiv. 2020.

Before joining Octant as Platform Runner on the High-Throughput Screening team, Heidi had a twenty-four year career as a professional baker in the Bay Area. She did everything from wedding cake design and execution to making that perfect croissant for your breakfast. In 2020 she began an undergraduate degree in biological sciences while continuing to work full time as a baker. In 2023 she earned a spot in Genentech’s inaugural California Community College Internship Program. While working in their Pharmaceutical Technical Development lab she set her sights on drug discovery for rare disease and genetic disorders. As someone living with Diamond Blackfan Anemia Syndrome, she is uniquely aware of the urgency for acceleration of drug discovery for rare genetic disorders. This unique perspective inspired her career change and ultimately drives her dedication to small molecule drug discovery.

Outside of the lab Heidi enjoys pretty much anything to do with the great outdoors, tinkering with new recipes, and road trip adventures.

Henry is a structural and molecular biologist. As a scientist, Henry develops technologies to enable the rapid development of synthetic biology tools at Octant.

Henry received his PhD in Biochemistry from UCLA, where he studied the molecular architecture and structure of the telomerase enzyme. Prior to graduate school, he was the 2nd hire at Inhibrx, where he helped start the lab and develop antibodies and antibody generation techniques.

Henry received his B.S. and M.S. at UCSD in molecular biology where he did research in protein engineering and evolution, and bioinformatics. Outside of work his hobbies include Brazilian Jiu Jitsu, sailing, and rock climbing.

Papers

Structure of Tetrahymena telomerase reveals previously unknown subunits, functions, and interactions. Jiang J, Chan H, Cash DD, Miracco EJ, Loo RRO, ...Feigon J. Science. 2015. (6260).

Progress in Human and Tetrahymena Telomerase Structure Determination. Chan H, Wang Y, Feigon J, Ann Rev. of Biophysics. 2017. 46, 199-225.

The p-type ATPase superfamily. Chan H, Babayan V, Blyumin E, Gandhi C, ...Saier M.H., Jou. Mol. Micro. Bio. 2010 19(1-2), 5-104.

More papers…

Hugh has 20 years of experience in biotech and another 5 years in healthcare. He joined Octant as Compound Manager in 2023. Prior to Octant, he was Compound Manager at Vir Biotechnology in San Francisco, registering, inventorying and distributing small molecules and reagents for drug discovery while bringing database applications and automation online. He supported Vir and GSK’s collaborative success, bringing the monoclonal antibody drug Sotrovimab to patients all around the world via emergency use authorization at the height of the Covid-19 pandemic.

Before pharma, he specialized in tech transfer, development and preparation of molecular biology, assay and culture media in industrial biotech settings, such as Zymergen in Emeryville and Genencor (now International Flavors and Fragrances) in Palo Alto. During his long tenure at Genencor, he mentored over two dozen community college and high school interns in his media lab, and received a certificate of appreciation for his support of the San Mateo High School Biotechnology Program. During his first several years at Genencor he was a bioreactor operator in the small-scale fermentation lab and helped program the SCADA (factory control and monitoring applications).

Hugh had a non-traditional route to science, including acting school at the University of Colorado in Boulder and a stint in the Army as a medic. He studied biology, chemistry and mathematics at San Francisco State University and Foothill College, but learned most of what he knows on the job or by reading.

Helping bring new drugs to patients is his passion, but when not busy at that he enjoys traveling with his wife, or sampling the great television programming available these days, on the couch with their orange tabby. He is an avid swimmer, especially outdoor/wild swimming when possible.

Idriss is a seeker of truth, solutions, joy, peace, and forever happiness on the ops team. Born and raised in Douala, Cameroon, he transitioned to the U.S to pursue his education. From the year round tropical sun of Cameroon, he first landed in the frigid arctic temperatures of Minnesota where he graduated from Southwest Minnesota State University with a Bachelor's in Business Administration and Marketing. Longing for more gelid temperatures, he moved to Syracuse University where he completed a Master of Science in Finance. His hobbies are working out, adventurous road trips and he hates long walks on the beach.

Jeff has a background in biophysics and cell biology and has worked in areas related to microscopy and sequencing. At Octant he’s helping to further push the performance and scale of the company’s core platform technology. Jeff received his PhD from the University of California, Berkeley where he studied nucleocytoplasmic transport and then investigated how yeast respond to nutrient deprivation during a postdoc at the ETH Zurich in Switzerland.

Prior to joining Octant, he was a scientist at Zymergen.

Besides tackling exciting problems in biology, Jeff enjoys hiking and playing ultimate frisbee, and he’s also an instructor at the Berkeley Kendo Club.

Papers

β-Oxidation and autophagy are critical energy providers during acute glucose depletion in Saccharomyces cerevisiae. Weber CA, Sekar K, Tang JH, Warmer P, Sauer U, Weis K. Proc Natl Acad Sci U S A. 2020 Jun 2;117(22):12239-12248.

A glucose-starvation response regulates the diffusion of macromolecules. Joyner RP, Tang JH, Helenius J, Dultz E, Brune C, Holt LJ, Huet S, Müller DJ, Weis K. Elife. 2016 Mar 22;5:e09376.

Natively unfolded FG repeats stabilize the structure of the nuclear pore complex. Onischenko E, Tang JH, Andersen KR, Knockenhauer KE, Vallotton P, Derrer CP, Kralt A, Mugler CF, Chan LY, Schwartz TU, Weis K. Cell. 2017 Nov 2;171(4):904-917.

Importin-β modulates the permeability of the nuclear pore complex in a Ran-dependent manner. Lowe AR, Tang JH, Yassif J, Graf M, Huang WY, Groves JT, Weis K, Liphardt JT. Elife. 2015 Mar 6;4:e04052.

Scaffold nucleoporins Nup188 and Nup192 share structural and functional properties with nuclear transport receptors. Andersen KR, Onischenko E, Tang JH, Kumar P, Chen JZ, Ulrich A, Liphardt JT, Weis K, Schwartz TU. Elife. 2013 Jun 11;2:e00745.

Jessica is a geneticist and molecular biologist with a background in platform development and rare disease therapeutics. She earned her PhD in Genetics at UC Davis studying the molecular mechanism of DNA double-strand break repair in the lab of Neil Hunter. She then returned home to the Bay Area to undertake her postdoctoral study. At UCSF in David Toczyski’s lab, she studied how the DNA Damage Response surveillance machinery regulate cellular metabolism in response to DNA damage. Since then, she has worked on discovering and developing therapeutics for rare diseases across several drug modalities. From small molecule screening at Perlara to protein engineering for enzyme replacement therapies at Codexis and more recently developing nucleic acid therapeutics at Ultragenyx. She is excited to continue her passion for rare disease at Octant.

When she’s not in the lab, Jessica enjoys trying out new recipes, exploring new places, and spending time with her playful cat.

Jillian is a medicinal chemist with a background in synthetic organic chemistry. She received her B.A. from New York University in Chemistry. She went on to earn her Ph.D. in 2018 at New York University under the advisement of Professor K. A. Woerpel working on the development of new synthetic reactions involving strained cyclic alkenes. Prior to joining Octant, she served as a medicinal chemist at Merck Research Laboratories in South San Francisco, CA in both the internal and external discovery chemistry groups. She has co-authored over ten publications and patents.In her free time, Jillian enjoys riding her motorcycle or bicycles, hiking, and exploring dive bars in the Bay Area and beyond.

Johan has spent the last 7 years in biotech working with metabolic disease and weight loss. As an employee of Carmot Therapeutics Johan spearheaded the in vivo pharmacology effort, establishing all in vivo models necessary to push an in house project from inception to Phase 1 clinical trials.

Johan spent his early education getting an MSc in cell and molecular pharmacology at Lund University (1999), with a focus on intracellular movements of GPCRs. Johan followed up his MSc with a PhD from Lund University (2007) extending his studies from his undergraduate degree in GPCR pharmacology - exploring several families of GPCRs. During his postdoctoral fellowship at UCSF (2007-2013) Johan applied his findings from his MSc and PhD to animal models of addiction and tolerance, learning crucial methodology in physiological and behavioral readouts in rodent models, drug delivery and survival surgery techniques.

Along the way Johan has taught medical and biomedical students (lecture series), trained research students, technical staff and scientists, and managed technical staff and scientists in cross functional research teams in both academia and biotech.

Jonathan is a biochemist and molecular biologist with a background in cell cycle regulation and biotherapeutic discovery. He is currently deploying Octant’s high-throughput and multiplex technologies to understand the pharmacology of the small molecules we discover. 

He received his BA from Berkeley in Molecular Biology & Biochemistry and a PhD in Biochemistry from UCSF with David O. Morgan. His thesis focused on understanding how Cyclin-dependent kinases regulate transcription through multisite phosphorylation mechanisms. 

Outside of the lab, Jonathan enjoys cooking for friends and hunting for new bottles at local wineries and importers. 

Selected Publications

Asfaha JB, Örd M, Carlson CR, Faustova I, Loog M, Morgan DO. Multisite phosphorylation by Cdk1 initiates delayed negative feedback to control mitotic transcription. Curr Biol. 2021. 

Carlson CR*, Asfaha JB*, Ghent CM*, Howard CJ, Hartooni N, Safari M, Frankel AD, Morgan DO. Phosphoregulation of Phase Separation by the SARS-CoV-2 N Protein Suggests a Biophysical Basis for its Dual Functions. Mol Cell. 2020. *Equal Contribution

Rosen LE, Klebba JE, Asfaha JB, Ghent CM, Campbell MG, Cheng Y, Morgan DO. Cohesin cleavage by separase is enhanced by a substrate motif distinct from the cleavage site. Nat Commun. 2019

De La Rosa VY, Asfaha J, Fasullo M, Loguinov A, Li P, Moore LE, Rothman N, Nakamura J, Swenberg JA, Scelo G, Zhang L, Smith MT, Vulpe CD. High-Throughput Functional Genomics Identifies Modulators of TCE Metabolite Genotoxicity and Candidate Susceptibility Genes. Toxicol Sci. 2017 

Josh is an engineer passionate about working at the intersection of biology, statistics, and computation. He was previously the Head of Bioinformatics at Invitae, where he built and supported a team responsible for delivering methods and software for the genomic analysis of millions of patients per year. He has led technical efforts ranging from the design and validation of novel statistical techniques to architecting enterprise software systems.

Josh received his PhD in Computer Science at UC Berkeley in Yun Song's group, where he worked on computationally tractable approaches to incorporating recombination in population genetic models. He received a BS in Physics and Computer Science at the University of Illinois.

Outside of work, Josh enjoys riding vintage bicycles, minimalist running, rock climbing, and cooking for his wife and two sons.

Papers

Truty, R., Paul, J.S., Kennemer, M., Lincoln, S.E., Olivares, E., Nussbaum, R.L., Aradhya, S. Prevalence and properties of intragenic copy-number variation in Mendelian disease genes. Genetics in Medicine, 21 (2019) 114-123.

Lincoln, S.E., Truty, R., Lin, C, Zook, J.M., Paul, J.S., Ramey, V.H., Salit, M., Rehm, H.L., Nussbaum, R.L.,Lebo, M.S. A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing. The Journal of Molecular Diagnostics, 21 (2019) 318-329.

Westbrook, M., Kvitek, D., Gafni, E., Paul, J.S., Kennemer, M., Winder, T., Shieh, P. Prevalence and properties of intragenic copy-number variation in Mendelian disease genes. Neurology, 90 (2018)

Steinrücken, M., Paul, J.S., and Song, Y.S. A sequentially Markov conditional sampling distribution for structured populations with migration and recombination. Theoretical Population Biology 87 (2013) 51-61.

Paul, J.S. and Song, Y.S. Blockwise HMM computation for large-scale population genomic inference. Bioinformatics, 28 (2012) 2008-2015.

Nielsen, R., Paul, J.S., Albrechtsen, A., and Song, Y.S. Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics 12 (2011) 443-451.

Paul, J.S., Steinrücken, M., and Song, Y.S. An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics 187 (2011) 1115-1128

Paul, J.S. and Song, Y.S. A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination. Genetics 186 (2010) 321-338.

Before joining Octant, Kaela worked as an Office Manager at Keegan & Coppin. There, they oversaw the office, assisted the agents with leases, graphic design and marketing. Before that, Kaela was a Senior Administrative Assistant at Verisk Analytics in the Finance department where, along with administrative duties, they assisted in accounting through billing, invoicing, and office expenses and budgeting.

Outside of work, Kaela enjoys boardgames, dungeons and dragons, and digital art.

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Kiran is a software engineer at Octant on the compute team. Prior to starting his career as a software engineer, Kiran studied Computer science and Economics as an undergrad at UC Berkeley. Outside of work, Kiran is avid sports fan and supports the Las Vegas Raiders and Golden State Warriors.

Kyle is a quantitative cell biologist with a background in proteomics, next-generation sequencing, and CRISPR screening.

He finished his Ph.D in Chemical and Systems Biology at Stanford University with Mary Teruel where he studied the impacts of gene expression noise on signaling and metabolic pathways, and cellular decisions.

Outside of work, Kyle enjoys travel, the outdoors, and playing with his dog.

Papers

Expression variation and covariation impair analog and enable binary signaling control. KM Kovary, B Taylor, ML Zhao, MN Teruel, Molecular systems biology 14 (5), e7997.

Molecular Competition in G1 Controls When Cells Simultaneously Commit to Terminally Differentiate and Exit the Cell Cycle. ML Zhao, A Rabiee, KM Kovary, Z Bahrami-Nejad, B Taylor, MN Teruel, Cell Reports 2020.

Heterogeneous ribosomes preferentially translate distinct subpools of mRNAs genome-wide. Z Shi, K Fujii, KM Kovary, NR Genuth, HL Röst, MN Teruel, M Barna, Molecular cell 67 (1), 71-83. e7.

Controlling low rates of cell differentiation through noise and ultrahigh feedback. R Ahrends, A Ota, KM Kovary, T Kudo, BO Park, MN Teruel, Science 344 (6190), 1384-1389.

Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing. Joshua S. Bloom Eric M. Jones, Molly Gasperini, Nathan B. Lubock, Fauna Yarza, Erin M. Thompson, Kyle M. Kovary, Jimin Park, Myles Hochman,. medrxiv. 2020.

More papers…

Leon is a molecular geneticist. He builds platforms to engineer biology and designs the sensors that read out the cellular response to the chemical world.

Leon did his post doctoral work in Karsten Weis's lab at UC Berkeley where he developed tools to measure the dynamics of the transcriptome and applied these tools to uncover the relationship between how proteins are made and how long the transcriptome persists in the cell. Prior to this, he did his doctoral work in Angelika Amon's lab at MIT where he elucidated how cells translate spatial information into chemical signals in the context of mitotic checkpoints. It was also at MIT where in Drew Endy's lab Leon helped to construct the first designed synthetic genome and organism.

Leon rock climbs, enjoys mixing up cocktails and wrangling his cats.

Papers

Non-invasive measurement of mRNA decay reveals translation initiation as the major determinant of mRNA stability. Chan LY, Mugler CF, Heinrich S, Vallotton P, Weis K. elife. 2018. 7;7.

Spindle position is coordinated with cell-cycle progression through establishment of mitotic exit-activating and -inhibitory zones. Chan LY, Amon A. Mol Cell. 2010, 13;39(3):444-54.

Refactoring bacteriophage T7. Chan LY, Kosuri S, Endy D. Mol Syst Biol. 2005. 1:2005.0018.

More papers…

Liam Landon is currently an Octant Apprentice on the HTChem team. Before joining Octant, Liam honed his skills at UC Berkeley, working under the mentorship of Richmond Sarpong where his research focused on the total synthesis of immunosuppressive natural products through innovative modifications to the Hopf electrocyclization reaction.

In addition to his academic achievements, Liam brings a unique perspective to the team from his three years of experience as an EMT while studying at Berkeley—a role that provided him with creative problem-solving skills and a deep appreciation for the human side of science. When he's not in the lab, Liam enjoys surfing, camping, and other outdoor activities. He’s also on a quest to find the best sandwiches in San Francisco—an endeavor that keeps his taste buds as sharp as his research skills.

Lizvette joined Octant as a Research Associate. She currently helps operate Octant’s sequencing pipeline. Lizvette received her B.S. in Biology with a concentration in Biomedical Sciences from CSU Sacramento. There, she was part of a molecular ecology lab where she focused on looking at how changes in gene expression affect individual and population differentiation in marine organisms.

Prior to Octant, Lizvette worked as a Molecular Biology RA where she screened for genetic mutations in multiple cell lines using Next Generation Sequencing.

Outside of the lab, you can find Lizvette chilling with her 2 cats & 1 dog, traveling, or just taking a nap.

Luke is biotech generalist with a diverse career spanning science and operations.

Luke began his career as a scientist, spending nearly ten years at two biotech startups—Native Microbials and Zymergen—where he played pivotal roles in developing and commercializing innovative products. As the first employee at Native Microbials, Luke developed and commercialized the company’s flagship product. For five years at Zymergen, Luke led his team to develop the company’s first successful product in the Ag sector.

Before joining Octant, Luke led operations at Synthace, a biotech SaaS company.Luke holds a B.S. in Microbiology and Molecular Biology from the University of Washington.

Marco is a software engineer with over two decades of experience in cheminformatics, bioinformatics and enterprise software development.He earned his PhD in physics at Syracuse University and completed postdoctoral studies at UCLA.  He started his career at Symyx Technologies (now Biovia) working on cheminformatics, LIMS and ELN. In the past decade Marco worked in early startups and larger companies, ranging from clinical human genetics to synthetic biology. Marco joined the Compute team at Octant in early 2023. In his spare time Marco enjoys sailing, cooking, singing and spending time with his wife and two teenage children.

Matthew brings over two decades of experience in discovery research, pharma and biotechnology to Octant. His expertise includes immuno-oncology, autoimmunity, metabolic diseases and neuro-degeneration. Prior to joining Octant, he was Chief Translational Officer at Human Immunology Biosciences, served as SVP at insitro where he directed the Department of Translational Genetics and Biology, and was founder and Head of the Reverse Translation Organization at Genentech in the Cancer Immunology Department. His academic positions included Director of the Immunology Department at Institut Pasteur, Paris and co-founder of the Milieu Interieur Consortium, a global real-world data effort that has identified actionable insights into the genetic, microbiome and environmental determinants of health and disease. 

Matthew's contributions have led to the discovery of new drug targets and he has helped to advance multiple drug candidates in first-in-human Ph1 studies and through post-marketing / indication expansion trials. His seminal work offered definitive evidence that naturally occurring tumor immunity in humans is established by the cross-priming of antigen-specific cytotoxic (CD8+) T cells, establishing the foundation for current approaches in immuno-oncology. He holds a Ph.D. in Immunology, an M.D. and residency training in Clinical Pathology, from Rockefeller University, Weill Cornell Medical School and New York Presbyterian Hospital, respectively. 

Matthew enjoys spending quality time with his wife and daughter, as well as cycling, backcountry skiing and cooking.

Michael previously worked as a microbiologist in R&D for Roche Molecular Systems for 12 years. He worked on various assays, including the Cobas MPX & DPX system, as well as the HPV genotype test for women. He received a B.A. in Microbiology, with a minor in chemistry, at the University of Florida. Michael took a break from science to start his own food truck/catering business known as the GrilledCheezGuy in the Bay Area. His business lasted for 10 years and had two store locations & a brand that even made it on television! Now Michael has become a member of the Octant Operations team. Outside of the lab, Michael enjoys camping, fishing, being a foodie, and traveling the world.

Michael recently was on Wheel of Fortune and WON!

Before joining Octant, Michelle advised the asset management industry as an attorney at a large global law firm and worked in sales, training and marketing at Johnson & Johnson.  She was shortlisted by Chambers in 2019 as a “Future Leader” for her commitment to promoting diversity and inclusion in the legal profession.

In addition to her law degree from Northwestern, Michelle received her MBA from Drexel University and a B.S. in health studies from Georgetown University. She volunteers for the regional alumni chapters of Georgetown University and Northwestern Pritzker School of Law.

Michelle enjoys food and sailing in the San Francisco Bay and further afield.

Naomi is a quantitative cell biologist by training. At Octant she's worn a few different hats including recruiting, establishing the OA program, building Octant HQ, demonstrating Octant's multiplexed platform technology, building cell engineering, and more.

Naomi received her PhD from the University of California, San Diego under Roy Wollman quantifying how cells communicate with one another to determine their position in relation to a wound. She's passionate about bringing science to the public through effective scientific communication and meaningful technological advances.

Outside of work you'll find Naomi spending time with her family and two dogs, hiking, running, and playing the piano.

Papers

Wound induced Ca2+ wave propagates through a simple Release and Diffusion mechanism. Mol. Biol. Cell. Handly LN, Wollman R. 2017. 28:1457-66.

Signal Transduction at the Single-Cell Level: Approaches to Study the Dynamic Nature of Signaling Networks. Handly LN, Yao J, Wollman R, J. Mol. Biol. 2016, 428: 3669-82.  

Paracrine communication maximizes cellular response fidelity in wound signaling. Handly LN; Pilko, A, Wollman R. eLife. 2015, 4:e09652.

Nathan Lubock is a computational biologist interested in deriving insights from large-scale experiments. Before joining Octant, he completed his Ph.D. in Biochemistry at UCLA under Sriram Kosuri. There he developed computational tools to understand and improve methods for multiplexed gene synthesis and GPCR-ligand interaction screens. In his free time, Nathan spends too much money on wine.

Papers

A systematic comparison of error correction enzymes by next-generation sequencing. Lubock NB, Zhang D, Sidore AM, Church GM, KosuriS . Nucleic acids research 45 (15), 9206-17.

Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. Plesa C, Sidore AM, Lubock NB, Zhang D, Kosuri S. Science 359 (6373), 343-47.  

A Scalable, Multiplexed Assay for Decoding Receptor-Ligand Interactions. Jones EM, Jajoo R, Cancilla D, Lubock NB, Wang J, Satyadi M, Cheung R, March CD, Matsunami J, Kosuri S. bioRxiv, 358739.

Structural and functional characterization of G protein–coupled receptors with deep mutational scanning, EM Jones*, NB Lubock*, …, S Kosuri. eLife, 2020

A scalable, multiplexed assay for decoding GPCR-ligand interactions with RNA sequencing, EM Jones, R Jajoo, D Cancilla, NB Lubock, …, S Kosuri. Cell systems, 2020

Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples, JS Bloom, L Sathe, C Munugala, EM Jones, M Gasperini, NB Lubock, …, VA Arboleda. Nature Biomedical Engineering, 2021

More papers...

Nathan is a computational geneticist and a member of the Octant Compute team. He works on the design and statistical interpretation of multiplexed, high-throughput functional assays of human genetic variation. His other research interests include statistical human genetics, RNA-mediated post-transcriptional gene regulation and applied machine learning in molecular biology. He obtained his PhD in Genetics and MS in Statistics from Stanford University, and his BS in Molecular Biology and BA in Political Science from the University of Texas at Austin. In a past life, he contributed to empirical studies in comparative constitutional design and participated in/coached high school debate for many years.

Nathaniel is currently an Octant Apprentice on the HT Chem team. Before Octant, he studied The Dark Arts (Chemistry) at Harvey Mudd College with an emphasis in Environmental Analysis. While at Mudd, Nathaniel did research in a variety of fields, including computational chemistry, materials synthesis/characterization, and synthetic organic chemistry. For his undergraduate thesis, he worked in the Vosburg Lab on a collaboration with BMS, determining the effectiveness of TCFH as a coupling reagent for esterifications. Outside of the lab, Nathaniel enjoys fermenting various foods and beverages, experimenting with new recipes, and getting lost in sci-fi and fantasy worlds. If there’s one thing he’s learned in life so far, whether you let him cook in the lab or the kitchen, the results will certainly be interesting.

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Nithish is an intern-turned-apprentice on the Compute team. He has worked on projects to improve tools for chemists, and is currently working with Software to develop new tools and workflows to help biologists, chemists, and data scientists do their job better. His interests lie at the intersection of data science, computer science, and biology.

Prior to Octant, Nithish graduated with a BS in Bioengineering: Bioinformatics from UC San Diego with a minor in Computer Music! Through his undergraduate years, Nithish worked in the Alexandrov Lab at the Moores Cancer Center on developing SigProfilerExtractor and SigProfilerAssignment: two utilities to better understand and deduce the impact of mutational processes on the cancer genome through the use of mutational signatures— patterned genomic scars found in cancer cells due processes like radiation and smoking. Nithish also worked at Zentalis, a publicly traded drug discovery company, where he applied the tools he developed in the Alexandrov Lab on real patient data.

Nithish loves programming (in Rust!), coffee, biking, playing video games, and playing a slew of instruments including the guitar, violin, and singing (although he is shy sometimes).

Ramsey has spent his career building high-performance teams and technology companies. Before Octant, he was an executive at Dropbox, where he had roles leading Dropbox's communications, public policy & government affairs, human resources, legal, and trust & security teams. During that time Dropbox raised $1+ billion in capital, grew to more than 500 million users, and was the fastest SAAS company in history to reach $1 billion in revenue run rate. Prior to Dropbox, Ramsey was a Vice President at Google, where he managed Google's commercial legal groups and negotiated some of the internet industry's largest partnerships.    

Before that, Ramsey was a technology attorney at Wilson Sonsini Goodrich & Rosati and a Lecturer at the University of Pennsylvania Law School. He has also done pro bono work representing indigent clients seeking political asylum. Ramsey received a B.S. in Chemical & Biochemical Engineering from Rutgers University and a J.D. from NYU.

Ramsey is a Board member at the Rutgers College of Engineering, and Represent.us, a grassroots political reform organization.

Ramsey grew up in Athens, Greece and Sparta, NJ. He enjoys hiking, camping, cooking over fire, punk music, and wandering through neighborhood art galleries.

Robert trained as a biochemist and molecular biologist, and has joined Octant to work ondeveloping Deep Mutational Scanning (DMS) approaches to understand the biology of naturallyoccurring variants and unlock its potential to drive drug discovery.

Robert obtained his PhD at the University of Pennsylvania in Roberto Bonasio’s lab, where heworked on developing mass spectrometry-based technologies to identify and characterize RNA-binding proteins and applying these methods to understand the function of the chromatin regulator Polycomb Repressive Complex (PRC2). During the pandemic he also developed a high-throughput sequencing method using Loop Mediated Isothermal Amplification  (LAMP) to detect COVID-19 and Influenza from human saliva. Robert was drawn to Octant by its emphasis on ‘rapid empiricism’, underpinned by the converging technologies of inexpensive DNA synthesis and sequencing, and believes these trends will greatly increase our understanding of disease biology in the coming years.

Outside work Robert likes to go hiking, cook for family and friends, and boring himself to sleepwith newspaper articles about central bank policy.

Papers

Oksuz, O., Henninger, J.E., Warneford-Thomson, R., Zheng, M.M., Erb, H., Overholt, K.J.,Hawken, S.W., Banani, S.F., Lauman, R., Vancura, A., Robertson, A.L., Hannett, N.M., Lee, T.,Zon, L.I., Bonasio, R. & Young, R.A. Transcription factors interact with RNA to regulate genes. bioRxiv, 2022.

Warneford-Thomson, R., Shah, P.P., Lundgren, P., Lerner, J., Morgan, J., Davila, A., Abella,B.S., Zaret, K., Schug, J., Jain, R., Thaiss, C.A. & Bonasio, R. A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva. eLife, 2022.

Ren, W., Medeiros, N., Warneford-Thomson, R., Wulfridge, P., Yan, Q., Bian, J., Sidoli, S.,Garcia, B.A., Skordalakes, E., Joyce, E., Bonasio, R. & Sarma, K. Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function. Nature Communications, 2020.

Zhang, Q.§, McKenzie, N.J.§, Warneford-Thomson, R.§, Gail, E.H., Flanigan, S.F., Owen, B.M.,Lauman, R., Levina, V., Garcia, B.A., Schittenhelm, R.B., Bonasio, R. & Davidovich, C. RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2. Nature Structural & Molecular Biology, 2019.

He, C., Sidoli, S., Warneford-Thomson, R., Tatomer, D.C., Wilusz, J.E., Garcia, B.A. & Bonasio, R. High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. Molecular Cell, 2016.

Roy is a software engineer at Octant, working on building tools and infrastructure to empower scientists.

Roy received a Masters in Computer Science from the University of Toronto, and worked in the Tech industry for a number of years. Previous to Octant he discovered the Biotech world while working at Zymergen, and hasn’t looked back since.

In his spare time, Roy enjoys playing pool, making art, and doting on his pet lungfish.

Papers:

Luo, Roy; Valenzano, Richard; Li, Yi; Beck, J. Christopher; McIlraith, Sheila. "Using Metric
Temporal Logic to Specify Scheduling Problems." Proceedings, Fifteenth International Conference on Principles of Knowledge Representation and Reasoning (2016).

Sam joined Octant in 2024 as an apprentice on the Platform Biology team. They develop in-cell reporters for elucidating the behavior of downstream intermediates of GPCR signaling and apply that knowledge to interesting disease systems. His scientific interests include clinical & translational medicine and the intersection of computational and cellular biology.

Prior to Octant, Sam worked as a Research Tech & Data Analyst jointly for the Isacoff & Marqusee Labs at the UC Berkeley Helen Wills Neuroscience Institute and Department of Molecular and Cellular Biology. They studied the activation of metabotropic glutamate receptor 2 (mGluR2), a GPCR involved in learning and memory. Using molecular dynamics simulations that Sam designed, executed, and analyzed, his research group at UC Berkeley was able to identify a critical salt bridge which proved necessary for activation of mGluR2’s ligand binding domain.Sam also worked on a second project articulating a transmembrane transport pathway for cell wall synthesis by Gram-positive bacteria. Previously, he was a biology intern at Regel, a targeted therapeutics company, where he developed constructs for the rescue of haploinsufficiency disorders of the CNS.

Sam graduated from the University of California, Berkeley in 2023 with a major in Bioengineering and concentration in Synthetic and Computational Biology, and spent an exchange semester at Korea University in Seoul. They enjoy hot chocolate, road trips, reading sci-fi, practicing languages, and hanging out with cats and reptiles.

Sarah is a cell biologist with a background in high throughput screening.

She received her B.S. in Biological Sciences from University of Maryland Baltimore County. Sarah has worked in various industry labs over the years. She got her start at Precision Antibody, making custom monoclonal antibodies for customers. She then went to DNA Electronics, where she supported the development of a machine to rapidly diagnose sepsis. After that, Sarah returned to the Bay Area where she is originally from and worked at Marin Biologic Laboratories- a contract research organization- performing various cell-based assays for clients.

Before coming to Octant she worked at Carmot Therapeutics where she ran high throughput drug screening assays and developed cell-based assays to further characterize screening hits.

Outside of the lab, Sarah enjoys mountain biking, snowboarding, playing video games, and binge watching shows with her two cats.

Sathvik is a software engineer at Octant focused on building software tools and infrastructure to accelerate research. He obtained his B.S.E from the University of Michigan in Computer Science. At Michigan, he was a part of the Computer-Aided Diagnosis Lab in the Department of Radiology, where he applied machine learning methods towards breast cancer diagnosis.

Sathvik enjoys watching/playing basketball, taking long walks, reading the first three chapters of a book, and watching lots of Parks and Rec.

Saulo joined the data science team at Octant as a Cheminformatics/ML scientist. His background is multidisciplinary, but focused on the development and application of computational methods to address biology and chemistry problems in early discovery. He obtained his PhD from the University of Oxford and completed a joint postdoctoral training at Stanford and UCSF.  

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Prior to joining Octant, Saulo worked at two biotech startups, Frontier Medicines and Atomwise, where he helped develop methods for experimental automation, target selection, hit identification, and in silico hit-to-lead.

Outside of work, Saulo likes trying new foods, listening to live music, and tending to his coffee habit.

Scott is a computational biologist passionate about developing usable tools for analyzing new types of high-throughput, biological data. He completed his PhD in Bioinformatics and Computational Biology in the lab of Dr. Chad Myers at the University of Minnesota, where his thesis work focused on the design and analysis of high-throughput, chemical-genetic interaction screens in yeast.

Outside of the lab, Scott enjoys international travel, playing the bass, cooking, and drinking non-IPA craft beer.

Papers

Using BEAN-counter to quantify genetic interactions from multiplexed barcode sequencing experiments. Simpkins SW, Deshpande R, Nelson J, Li SC, Piotrowski JS, Ward HN, Yashiroda Y, Osada H, Yoshida M, Boone C, Myers CL. Nat. Protoc. 14, 415–440 (2019).

Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions. Simpkins SW, Nelson J, Deshpande R, Li SC, Piotrowski JS, Wilson EH, Gebre AA, Safizadeh H, Okamoto R, Yoshimura M, Costanzo M, Yashiroda Y, Ohya Y, Osada H, Yoshida M, Boone C, Myers CL. PLOS Comp. Biol. 14, e1006532 (2018).

Functional annotation of chemical libraries across diverse biological processes. *Piotrowski JS, *Li SC, *Deshpande R, *Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H, Gebre AA, Kubo K, Torres NP, LeBlanc MA, Andrusiak K, Okamoto R, Yoshimura M, DeRango-Adem E, van Leeuwen J, Shirahige K, Baryshnikova A, Brown GW, Hirano H, Costanzo M, Andrews B, Ohya Y, Osada H, Yoshida M, Myers CL, Boone C. Nat. Chem. Biol. 13, 982–993 (2017).

Sri is a biologist that has helped build technologies, labs, and companies in synthetic biology, functional genomics, and bioinformatics over the last 20 years. He is passionate about developing more rational ways to understand and engineer biology.

Sri is a co-founder at Octant and an Associate Professor at UCLA in the Chemistry and Biochemistry Department, where his lab has worked on building large-scale ways of empirically exploring questions in protein biochemistry, human genetic variation, gene regulation, chemical biology, synthetic biology, and functional genomics.

Sri previously worked at the Wyss Institute and Harvard, where he built numerous technologies in gene synthesis, DNA information storage, gene editing, and large-scale multiplexed assays. He helped build Gen9, a gene synthesis company, as a member of the SAB and was the first employee of Joule Unlimited, an engineered algal biofuel company. He is a Searle Scholar (2015), NIH New Innovator (2014), and received his ScD in Biological Engineering at MIT and BS in Bioengineering at UC Berkeley.

Sri is originally from New Jersey, by way of Philadelphia and Kansas, and was born in North Carolina. He enjoys eating, getting outdoors, and traveling with his wife and two children.

More papers…

Stacie is a Scientist in the Chemistry group with a background in chemical biology, metabolomics and (bio)synthesis.

She received her Ph.D. in Chemical Engineering from Stanford University under the supervision of Prof. Elizabeth Sattely. Her thesis work focused on medicinal plant natural product biosynthesis and engineering, accomplished with metabolite analysis of plant extracts and enzymatic assays by LC-qToF and metabolic engineering approaches for yield optimization.

Outside of the lab, Stacie enjoys traveling, cooking, and perhaps the combination of the two: trying out different cuisines.

Papers

Kim S. S. & Sattely E. S. Dirigent Proteins Guide Asymmetric Heterocoupling for the Synthesis of Complex Natural Product Analogues. (2021) J Am Chem Soc. 143 (13), pp 5011-5021. DOI: 10.1021/jacs.0c13164.

Schultz B. J., Kim S., Lau W., & Sattely E. S. Total Biosynthesis for Milligram-Scale Production of Etoposide Intermediates in a Plant Chassis. (2019) J Am Chem Soc. 141 (49), pp 19231-19235. DOI: 10.1021/jacs.9b10717.

Suzette is a biomedical scientist who is passionate about drug discovery and translational medicine. Prior to Octant, she worked for a decade in biotech/pharma. Most recently, she worked at Broadwing Bio leading preclinical biology efforts. She also worked in Discovery Biology at Merck and the Translational Genomics group at Ambry Genetics.

She received her BS and MS degrees at UCSD, where she engineered a high-throughput screen for molecules that drive insulin gene expression in the lab of Fred Levine. She completed her PhD in the lab of Seth Field at UCSD, where she discovered that DNA-damaging chemotherapeutic agents cause a dispersal of the Golgi apparatus.

Outside of work, Suzette enjoys spending time with her two very active kids. In her free time, she advocates for children with special needs and volunteers for a bird rescue.

Selected publications:

Farber-Katz Brown S, Nguyen H, Mzyk P, De Ieso ML, Unser AM, Brown I, Ramesh P, Afzaal H, Ahmed F, Torrejon KY, Nhan A, Markrush D, Daly T, Knecht E, McConaughy W, Halmos S, Liu ZL, Rennard R, Peterson A, Stamer WD*. “ANGPTL7 and its role In IOP and glaucoma.” Invest Ophthalmol Vis Sci, 2024. Mar 5;65(3):22. doi: 10.1167/iovs.65.3.22.

Lamy R, Farber-Katz S, Vives F, Ayanoglu G, Zhao T, Chen Y, Laotaweerungsawat S, Ma D, Phone A, Psaras C, Li X, Sutradhar S, Carrington P, Stewart JM. “Comparative analysis of multiplex platforms for detecting vitreous markers in diabetic retinopathy.” Transl Vis Sci Technol. 2020 Sep 2;9(10):3.

Farber-Katz S, Hsuan V, Wu S, Landrith T, Vuong H, Du X, Hoo J, Lam S, Nashed S, Li B, Lu H-M, Elliott A, Davis B, Karam R. “Quantitative Analysis of BRCA1 and BRCA2 Germline Splicing Variants Using a Novel RNA-Massively Parallel Sequencing Assay.” Frontiers Oncology, 2018. 8:286.

Farber-Katz SE, Dippold HC, Buschman MD, Peterman MC, Xing M, Noakes CJ, Tat J, Ng MM, Rajeng J, Cowan DM, Fuchs GJ, Zhou H, Field SJ. “DNA Damage Triggers Golgi Dispersal via DNA-PK and GOLPH3.” Cell, 2014. 156(3):413-427.

Kiselyuk A, Lee SH, Farber-Katz S, Zhang M, Athavankar S, Cohen T, Pinkerton AB, Ye M, Bushway P, Richardson AD, Hostetler HA, Rodriguez-Lee M, Huang L, Spangler B, Smith L, Higginbotham J, Cashman J, Freeze H, Itkin-Ansari P, Dawson MI, Schroeder F, Cang Y, Mercola M, Levine F. “HNF4a Antagonists Discovered by High-Throughput Screening for Modulators of the Human Insulin Promoter.” Chemistry and Biology, 2012. 19(7):806-18.

Swapnil is joining the clinical project management team at Octant. He will be working on getting the lead drug development program at Octant into the clinic. He has worked at several pharmaceutical and biotech companies in the project management roles in the past.

Taking a non-traditional route to the Drug Development Project Management, Swapnil has a bachelors degree in electrical engineering and an MBA from UMass Amherst.

Sylvia runs People Operations at Octant and is responsible for driving processes that make for a healthy and high-performing team. Prior to joining Octant, Sylvia was the first HR hire at Invitae and led the People team through the organization's rapid growth, developing areas like compensation, benefits, employee experience, people analytics, learning and development, talent acquisition, and M&A diligence and integration. She also ran HR at Carnegie Mellon University's Silicon Valley campus where she supported engineering faculty as well as researchers and engineers at NASA Ames. Sylvia has a B.S. in Business Administration from Carnegie Mellon University and an MBA from University of California, Davis with concentrations in Strategy and Organizational Behavior.

In her spare time, she cooks, listens to jazz, and plays ukulele for her twin toddler boys.

Tao Zheng is our medicinal chemist. She received her PhD in organic chemistry from Michigan State University in 2006 and spent two years at UC Davis as a postdoctoral fellow. She returned to China to begin her career in process chemistry and custom organic synthesis. In 2016, she brought her talents back to the United States, working for Nanosyn, Inc in Santa Clara CA for five years before finally becoming an Octanaut in September of 2021.

She enjoys watching movies, cooking, and spending quality time with her cat, Pinky.

Tarek does business operations at Octant and loves the multidisciplinary nature of being a generalist.

Prior to Octant, Tarek was an Operations Generalist at On Deck, both working internally on building operational processes, systems, and infrastructure as well as externally supporting founders and fellows in the community.

Tarek graduated from American University, spending most of his time learning and building as a member of the university’s startup incubator and Institute for IDEAS.

Terry is an organic chemist. He specialized in transition metal-catalysis and method development, with a background of flow chemistry and electrochemical synthesis. As a Synthetic Chemistry Methodologist, Terry develops new synthesis on Octant’s high-throughput chemistry platform and enables new chemical space for drug discovery.

Prior to joining Octant, Terry was a postdoctoral fellow in Scripps Research working with Prof Phil Baran. He obtained his DPhil degree from the University of Oxford in the UK, under Prof Michael Willis’ supervision. During his undergraduate study, Terry also worked in Prof Chi-Ming Che’s and Prof Steve Ley’s group in the University of Hong Kong and University of Cambridge, respectively.

Outside of the lab, Terry enjoys cooking, traveling and working out in the gym.

Theo is a biologist in the Platform group with experience in assay development and the study of cancer therapies. He received a B.S. in Biology, with a minor in Biochemistry, at the University of San Francisco. At Roche Molecular Systems, he participated in the research and development of medical diagnostic assays for targets such as HIV and genetic mutations implicated in lung cancer. Then, at UCSF under Dr. Catherine Smith, he researched mechanisms of response and resistance to targeted drug therapy for acute myeloid leukemia. Outside of the lab, Theo enjoys golfing, hiking, and following his Bay Area sports teams.

Publications

Smith, C.C., Viny, A.D., Massi, E., Kandoth, C., Socci, N.D., Rapaport, F., Najm, M., Medina-Martinez, J.S.,Papaemmanuil, E. Tarver, T.C., Hsu, H.H., Le, M.H., West, B., Bollag, G., Taylor, B.S., Levine. R.L., & Shah, N.P. Recurrent Mutations in Cyclin D3 Confer Clinical Resistance to FLT3 Inhibitors in Acute Myeloid Leukemia. Clinical Cancer Research (2021) 27 (14), 14, 4003-4011

Tarver, T., Hill, J. Rahmat, L., Perl, A., Bahceci, E., Mori, K., & Smith, C C. Gilteritinib is a clinically active FLT3 inhibitor with broad activity against FLT3 kinase domain mutations. Blood Adv (2020) 4 (3): 514–524.

Smith, C. C., Paguirigan, A., Jeschke, G. R., Lin, K. C., Massi, E., Tarver, T., Chin, C. S., Asthana, S., Olshen, A., Travers, K. J., Wang, S., Levis, M. J., Perl, A. E., Radich, J. P., & Shah, N. P. (2017). Heterogeneous resistance to quizartinib in acute myeloid leukemia revealed by single-cell analysis. Blood (2017), 130 (1), 48–58.

Yuning is a chemist with a background in novel transition metal catalyzed methodology development enabled by high throughput chemistry.

Yuning obtained her PhD in medicinal chemistry from University of Michigan under the supervision of Dr. Tim Cernak. Her research focused on identifying new reactivity, achieved by copper catalysis for amine–acid coupling facilitated by cheminformatic analysis. Such method development is enabled by nanoscale synthesis on a high throughput chemistry platform that was established in Tim’s lab.  

Outside of lab, she likes to play video games and spend time with her cats.

Papers

Shen, Y., Mahjour B. and Cernak, T., Development of deaminative esterification using high-throughput experimentation. Commun. Chem., 5, 83 (2022).

Shen, Y., Borowski, J.E., Hardy, M.A., Sarpong, R., Doyle, A.G. and Cernak, T., Automation and computer-assisted planning for chemical synthesis. Nat. Rev. Methods Primers, 1,1-23 (2021).

Mahjour, B., Shen, Y. and Cernak, T., Ultrahigh-Throughput Experimentation for Information-Rich Chemical Synthesis. Acc. Chem. Res., 54, 2337-2346, (2021).

Lin, Y., Zhang, Z., Mahjour, B., Wang, D., Zhang, R., Shim, E., McGrath, A., Shen, Y., Brugger, N., Turnbull, R. and Trice, S., Reinforcing the supply chain of umifenovir and other antiviral drugs with retrosynthetic software. Nat. Commun., 12, (2021).

Mahjour, B., Shen, Y., Liu, W., & Cernak, T., A map of the amine–carboxylic acid coupling system. Nature, 580, 71-75 (2020).

Shen, Y., Lee, W.C.C., Gutierrez, D.A. and Li, J.J., Palladium-Catalyzed Direct C(sp2)–H ortho-Arylation of Anilides Using 2-Aminophenylpyrazole as the Directing Group. J. Org. Chem., 82, 11620-11625 (2017).

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Zach recently started at Octant as a Research Associate working on high-throughput chemical assembly and screening. He graduated from James Madison University with a B.S. in Biotechnology in 2021. While at JMU, Zach was a research assistant in the lab of George Vidal where he studied the effect of integrin beta-3 deficiency on the morphology of cortical neurons in the developing mouse brain.

Outside of the lab, Zach enjoys, hiking, playing board games, and slaying monsters in Dungeons and Dragons.

Charles S. Zuker is an American molecular geneticist and neurobiologist of Chilean descent. His lab, in collaboration with Nick Ryba at the NIH, have transformed our understanding of cell signaling and mammalian taste. Zuker is an Investigator of the Howard Hughes Medical Institute and a Senior Fellow at the Janelia Research Campus. Zuker is a member of the National Academy of Sciences, the National Academy of Medicine, and the American Academy of Arts and Sciences. After more than 20 years at the University of California, San Diego, he began his appointment at Columbia University in 2009.

Vijay Pande, PhD, is a general partner at Andreessen Horowitz, where he focuses on investments in biopharma and healthcare. As the founding investor of a16z’s Bio Fund, Vijay leads the firm’s investments at the cross section of biology and computer science, including applications in computation, machine learning, and artificial intelligence in healthcare; digital therapeutics; diagnostics; and other novel transformative scientific advances applied to industry that take bio beyond healthcare. Op-eds by Vijay defining trends and issues in this emerging space have been published by The New York Times, Scientific American, and Forbes, among others. He is also an Adjunct Professor of Bioengineering at Stanford University.

Previously, Vijay was the Henry Dreyfus Professor of Chemistry and Professor of Structural Biology and of Computer Science at Stanford University, where he led a team of researchers pioneering computational methods and their application to medicine and biology (resulting in over 300 publications, two patents, and two novel drug candidates). Vijay was also concurrently the director of the Biophysics program at Stanford, where he led a team of more than 50 faculty members and propelled the program to the top in the country.

During his time at Stanford, Vijay co-founded Globavir Biosciences, where he translated his research advances into a successful startup that aimed to discover cures for Dengue Fever and Ebola. Vijay also founded the Folding@Home Distributed Computing Project for disease research, which pushed the boundaries of computer science techniques (distributed systems, machine learning, and exotic computer architectures) into biology and medicine, in both research as well as the development of new therapeutics.

Vijay holds a BA in Physics from Princeton University and a PhD in Physics from MIT. He has been awarded the DeLano Prize in Computation; a Guinness World Record for Folding@Home; the American Chemical Society Thomas Kuhn Paradigm Shift Award; and was selected for MIT TR10. In his teens, Vijay was the first employee at video game startup Naughty Dog Software, maker of Crash Bandicoot.

After studying at City College of San Francisco, Hosea obtained a B.S. in Chemistry from University of California Berkeley and a Ph.D. from the California Institute of Technology in 2012 under the mentorship of Brian Stoltz. After postdoctoral training at University of California Berkeley with Dean Toste, Hosea joined the UCLA faculty in 2015 as an assistant professor. In 2021 he moved his group to Caltech where they currently focus on developing enabling technologies for the biomedical sciences. More specifically they utilize cutting-edge electron microscopy methods to identify new bioactive small molecules and main group metal catalysis to prepare complex molecules through novel chemical reactions.

Debora is a mathematician and computational biologist with a track record of using novel algorithms and statistics to successfully address unsolved biological problems. She has a passion for interpreting genetic variation in a way that impacts biomedical applications. During her PhD, she quantified the potential pan-genomic scope of microRNA targeting and combinatorial regulation of protein expression and co-discovered the first microRNA in a virus. As a postdoc she and her colleagues cracked the classic, unsolved problem of ab initio 3D structure prediction of proteins using a maximum entropy probability model for evolutionary sequences. She has developed this approach to determine functional interactions, biomolecular structures, including the 3D structure of RNA and RNA-protein complexes and the conformational ensembles of apparently disordered proteins. Her new lab at Harvard is interested in developing methods in deep learning to address a wide range of biological challenges including predicting the effects of genetic variation and sequence design for biosynthetic applications.

Mark Murcko was an early leader in structure-based drug design and has directly contributed to nine marketed drugs spanning HIV, HCV, cystic fibrosis, and glaucoma. He is a Founder, Board member, and was the interim CSO at Relay Therapeutics. More recently he was the founding CSO and remains a board member and advisor to Dewpoint Therapeutics.  In addition, Mark is a senior lecturer in the Department of Biological Engineering at MIT, and has served on numerous scientific advisory boards and corporate boards of directors for a diverse range of organizations.  Mark was chief technology officer and chair of the SAB of Vertex Pharmaceuticals and was responsible for the identification, validation and implementation of disruptive technologies across R&D. Mark is a co-inventor of the HCV protease inhibitor Incivek (telaprevir), as well as Agenerase (amprenavir) and Lexiva (fosamprenavir), Vertex’s two marketed drugs for the treatment of HIV. In addition, he guided the early efforts of Vertex’s cystic fibrosis program that has produced four marketed drugs.

Prior to Vertex, Mark worked at Merck Sharpe & Dohme, where he helped discover multiple clinical candidates, including Dorzolamide, a carbonic anhydrase inhibitor for the treatment of glaucoma which was commercialized in two approved drugs, Trusopt and Cosopt.  Trusopt was the first medicine in history to come from a structure-based drug design program.  He is a member of the Board of Trustees of the GRC and the Board of Advisors of the Boston Museum of Science.  He is a co-inventor on more than 50 issued patents and has co-authored more than 85 scientific articles. Mark holds a Ph.D. in organic chemistry from Yale University.

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Feng Zhang is a core institute member of the Broad Institute of MIT and Harvard, as well as an investigator at the McGovern Institute for Brain Research at MIT, the James and Patricia Poitras Professor of Neuroscience at MIT, and a professor at MIT, with joint appointments in the departments of Brain and Cognitive Sciences and Biological Engineering. Zhang is also an investigator at the Howard Hughes Medical Institute.

Zhang is a molecular biologist developing and applying novel molecular technologies for studying the brain. Zhang pioneered the development of genome editing tools for use in eukaryotic cells – including human cells – from natural microbial CRISPR-Cas9 systems. He and his team have adapted multiple other CRISPR systems for use as genome engineering tools, including RNA-targeting CRISPR-Cas13 systems and CRISPR-associated transposon systems, which can be used for gene insertion.

Zhang leverages CRISPR and other methods to study the genetics and epigenetics of human diseases, especially complex disorders, such as psychiatric and neurological diseases that are caused by multiple genetic and environmental risk factors and are difficult to model using conventional methods. His lab’s tools, which he has made widely available, are also being used in the fields of immunology, clinical medicine, and cancer biology, among others. His long-term goal is to develop novel therapeutic strategies for disease treatment.

Zhang is a recipient of many awards including the Canada Gairdner International Award, the Tang Prize, the Blavatnik National Award for Young Scientists, the Albany Medical Center Prize in Medicine and Biomedical Research, the Lemelson-MIT Prize, and the Keio Medical Science Prize. He has also received technology innovation awards from the Paul G. Allen Family, McKnight, New York Stem Cell, and Damon Runyon foundations. Zhang is an elected member of the National Academy of Sciences and the American Academy of Arts and Sciences.

Zhang received his A.B. in chemistry and physics from Harvard College and his Ph.D. in chemistry from Stanford University.