Karl Lundquist

Bioinformatics Data Scientist

EMD Serono

About me

I am passionate about leveraging data analytics and machine learning to tackle complex problems related to human health.

I have a BS and PhD in Physics / Computational Biology and completed a postdoc in structural biology. My past academic work revolved around the use of high-performance computation, simulation, and cryoEM to elucidate the assembly mechanism of bacterial membrane proteins aiding in the development of novel antibiotics.

In my professional journey I’ve sought out experiences which draw upon my past scientific work and expertise while working to gain exposure to and embrace the use of modern AI/ML methods to positively impact human health. I gained a firm foundation in AI/ML by completing a Fellowship at the NYC Data Science Academy before beginning a role at Calyxt where I developed several analytic tools to help researchers identify metabolic pathways in plants and optimally deliver genetic material to maximize rare-compound production. In May 2023 I started a new position at EMD Serono in bioinformatics for translational medicine.

Interests

Computational Protein Design
Protein Language Models
Molecular Dynamics Simulation

Education

PhD in Physics and Chemistry, 2019
Georgia Institute of Technology
MS in Physics, 2015
Georgia Institute of Technology
BS in Physics and Mathematics, 2012
University of Michigan

Projects

An exploration of protein secondary structure prediction with RNNs and Transformers

We explore the characteristics and efficiency of sequencial models as applied to protein secondary structure prediction

An exploration of protein secondary structure prediction with RNNs and Transformers

Drug Target Prioritization with Text Mining

Time series modeling of gene mentions across literature to develop a trendiness metric for use in the drug target prioritization pipeline

Drug Target Prioritization with Text Mining

Graph generation to identify novel synthesis pathways

Enzyme and compound properties obtained from PlantCyc and integrated into a graph visualization to identify the shortest synthesis pathways for compounds of interest

Graph generation to identify novel synthesis pathways

Experience

Bioinformatics Data Scientist

Merck (EMD Serono)

May 2023 – Present

Performed text mining and time-series analysis to identify high-interest genes for drug target prioritization pipeline

Data Scientist

May 2022 – January 2023

Developed ML models to predict rearrangement of genetic elements that maximizes production of rare compounds in plants

Postdoctoral Research Associate

Purdue University

September 2019 – Present

Studied membrane protein assembly with cryoEM, biochemical assays and molecular dynamics

Publications

Victor G Lui, Manfred Hoenig, Berenice Cabrera-Martinez, Ryan M Baxter, Josselyn E Garcia-Perez, Olivia Bailey, Atanu Acharya, Karl Lundquist, Jesusa Capera, Paul Matusewicz, others (2023). A partial human LCK defect causes a T cell immunodeficiency with intestinal inflammation. Journal of Experimental Medicine.

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Katie M Kuo, David Ryoo, Karl Lundquist, James C Gumbart (2022). Modeling intermediates of BamA folding an outer membrane protein. Biophysical Journal.

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Ashley Nicole Greenawalt, Julie Stoudenmire, Karl Lundquist, Nicholas Noinaj, James C Gumbart, Cynthia Nau Cornelissen (2022). Point Mutations in TbpA Abrogate Human Transferrin Binding in Neisseria gonorrhoeae. Infection and Immunity.

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Runrun Wu, Jeremy W Bakelar, Karl Lundquist, Zijian Zhang, Katie M Kuo, David Ryoo, Yui Tik Pang, Chen Sun, Tommi White, Thomas Klose, others (2021). Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM. Nature Communications.

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Evan Billings, Karl Lundquist, Claire Overly, Karthik Srinivasan, Nicholas Noinaj (2021). Structure determination of membrane proteins using X-ray crystallography. Structure and Function of Membrane Proteins.

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Karl Lundquist, Evan Billings, Maxine Bi, James Wellnitz, Nicholas Noinaj (2021). The assembly of β-barrel membrane proteins by BAM and SAM. Molecular microbiology.

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David Ryoo, Marcella Orwick Rydmark, Yui Tik Pang, Karl P Lundquist, Dirk Linke, James C Gumbart (2020). BamA is required for autotransporter secretion. Biochimica et Biophysica Acta (BBA)-General Subjects.

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Michael T Kammerman, Aloke Bera, Runrun Wu, Simone A Harrison, C Noel Maxwell, Karl Lundquist, Nicholas Noinaj, Walter J Chazin, Cynthia Nau Cornelissen (2020). Molecular insight into TdfH-mediated zinc piracy from human calprotectin by Neisseria gonorrhoeae. Mbio.

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Karl P Lundquist, James C Gumbart (2020). Presence of substrate aids lateral gate separation in LptD. Biochimica et Biophysica Acta (BBA)-Biomembranes.

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Jeremy Guerin, Istvan Botos, Zijian Zhang, Karl Lundquist, James C Gumbart, Susan K Buchanan (2020). Structural insight into toxin secretion by contact-dependent growth inhibition transporters. Elife.

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Isabel Z Fernandez, Ryan M Baxter, Josselyn E Garcia-Perez, Elena Vendrame, Thanmayi Ranganath, Daniel S Kong, Karl Lundquist, Tom Nguyen, Sidney Ogolla, Jennifer Black, others (2019). A novel human IL2RB mutation results in T and NK cell--driven immune dysregulation. Journal of Experimental Medicine.

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Curtis Balusek, Hyea Hwang, Chun Hon Lau, Karl Lundquist, Anthony Hazel, Anna Pavlova, Diane L Lynch, Patricia H Reggio, Yi Wang, James C Gumbart (2019). Accelerating membrane simulations with hydrogen mass repartitioning. Journal of chemical theory and computation.

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Karl Lundquist, Jeremy Bakelar, Nicholas Noinaj, James C Gumbart (2018). C-terminal kink formation is required for lateral gating in BamA. Proceedings of the National Academy of Sciences.

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Curtis Balusek, Hyea Hwang, Anthony Hazel, Karl Lundquist, Anna Pavlova, James C Gumbart (2018). Diverse protein-folding pathways and functions of β-hairpins and β-sheets. Quantitative Models for Microscopic to Macroscopic Biological Macromolecules and Tissues.

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Rebecca S Bamert, Karl Lundquist, Hyea Hwang, Chaille T Webb, Takoya Shiota, Christopher J Stubenrauch, Mathew J Belousoff, Robert JA Goode, Ralf B Schittenhelm, Richard Zimmerman, others (2017). Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery. Molecular microbiology.

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Karl Lundquist, Conner Herndon, Tyson H Harty, James C Gumbart (2016). Accelerating the use of molecular modeling in the high school classroom with VMD Lite. Biochemistry and molecular biology education.

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Anna Pavlova, Hyea Hwang, Karl Lundquist, Curtis Balusek, James C Gumbart (2016). Living on the edge: Simulations of bacterial outer-membrane proteins. Biochimica et Biophysica Acta (BBA)-Biomembranes.

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Istvan Botos, Nadim Majdalani, Stephen J Mayclin, Jennifer Gehret McCarthy, Karl Lundquist, Damian Wojtowicz, Travis J Barnard, James C Gumbart, Susan K Buchanan (2016). Structural and functional characterization of the LPS transporter LptDE from Gram-negative pathogens. Structure.

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M Traxler, RE Sapiro, K Lundquist, EP Power, G Raithel (2013). Coupled internal-state and center-of-mass dynamics of Rydberg atoms in a magnetic guide. Physical Review A.

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M Traxler, RE Sapiro, C Hempel, K Lundquist, EP Power, G Raithel (2012). Guiding of Rydberg atoms in a high-gradient magnetic guide. Physical Review A.

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