About Khalid K. Alam, Ph.D.

Last updated August 25, 2026

Khalid K. Alam, Ph.D., biotechnologist and synthetic biology entrepreneur

Khalid K. Alam, Ph.D. is a biochemist, synthetic biologist, and entrepreneur whose work bridges biomolecular innovation and real-world translation. He earned his PhD in Biochemistry from the University of Missouri in 2016 in Donald Burke’s lab, where he developed FASTAptamer — the first open-source bioinformatic toolkit for combinatorial (SELEX-style) selection analysis, widely adopted in the aptamer community — and engineered Split-Broccoli, the first functional split fluorescent aptamer system to operate in vivo. He also led Poly-Target Selection, a strategy for discovering broad-spectrum RNA-based aptamer inhibitors against primate lentiviral reverse transcriptases.

As a postdoctoral fellow (2016–2019) in Julius B. Lucks’ lab at Northwestern University’s Center for Synthetic Biology, Khalid led the cell-free diagnostics program. With the Jewett Lab and MIT’s Collins Lab, he invented ROSALIND™ – a cell-free, RNA-output biosensor platform capable of detecting antibiotics, heavy metals, and other water contaminants in minutes. The work appeared in Nature Biotechnology (2020) and was extended through programmable DNA strand-displacement circuits in Nature Chemical Biology (2022).

In 2019, Khalid founded Stemloop, Inc. with Lucks and Michael Jewett, backed by over $4M in non-dilutive federal funding — DOE’s Chain Reaction Innovations program at Argonne National Laboratory, NIH SBIR Phase I/II awards from NIEHS, and DARPA BTO’s AI Biotechnology Same-Day Award — plus early-stage venture investment. Stemloop launched the µSense™ lead-in-water test in Q4 2022 and later concluded operations in December 2025. He continues building through Al-kimi, his personal venture portfolio.

Positions

Education

Awards & Honors

  1. DARPA BTO AI Biotechnology Same-Day Award — DARPA Biological Technologies Office (Dec 2024)
  2. Founder to Watch Award — Founder-led Biotech Summit, hosted by Pillar VC and Petri Bio (Nov 2021)
  3. MassChallenge Boston 2021 — Finalist, top 26 of ~128 cohort (2021)
  4. The Engine Blueprint — Spring 2021 cohort; later featured alumnus, Tough Tech Summit 2022 (2021)
  5. VentureCat 2020 (Northwestern) — Semi-finalist (May 2020)
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  1. Bio-Belt Ambassador — SynBioBeta (Jul 2019)
  2. 40 Under 40 Chicago Scientists — Halo Cures (Jul 2019)
  3. ORISE Entrepreneurial Fellowship — Chain Reaction Innovations Cohort 3, Argonne National Laboratory (Apr 2019 selection)
  4. Biosecurity and Synthetic Biology Fellow — Johns Hopkins Center for Health Security (Aug 2018)
  5. Kellogg BSEE Scholarship — Office of Postdoctoral Affairs, Northwestern University (May 2018)
  6. Affiliate Fellow — Multidisciplinary Training Program in Child and Adolescent Health (TL1) (2017)
  7. Outstanding Poster Contribution — Engineering Biology Research Consortium (Nov 2016)
  8. CSHL Synthetic Biology Course Scholarship — NIGMS (Aug 2015)
  9. Student Poster Scholarship — TIDES: Oligonucleotide and Peptide Therapeutics (Apr 2015)
  10. Meritorious Abstract Travel Award — American Society of Gene and Cell Therapy (Mar 2015)
  11. Travel Fellowship — RNA Society (Mar 2015)
  12. Travel Scholarship — Douglas D. Randall Young Scientists Development Fund (Feb 2015)
  13. Outstanding Poster Award — American Society of Gene and Cell Therapy (May 2014)
  14. Travel Award — MU Graduate Professional Council (May 2014)
  15. 1st Place, Molecular and Cellular Category — Missouri Life Sciences Week (Apr 2014)
  16. NAR Poster Award — 2013 Oligonucleotide Therapeutics Society Annual Meeting (Oct 2013)
  17. NSF Graduate STEM Fellow in K-12 Education (GK-12) (Jun 2012)
  18. 3rd Place, Idea Bounce Competition — 1st Annual Mid-MO Entrepreneurial Summit (Feb 2011)
  19. 1st Place, Graduate Category — Flegel Academy 6th Annual MU New Idea Venture Competition (Nov 2010)

Talks & Events

  1. “Cell-free Biosensors: From Central Dogma to Commercialization” — Northwestern University, ISEN 421 (Jan 23, 2025)
  2. NIEHS SRP Virtual Technology Fair — Lead (Pb) Detection and Treatment for Water (Oct 28, 2024)
  3. “Cell-free Biosensors: From Central Dogma to Commercialization” — Cold Spring Harbor Laboratory, Synthetic Biology Course (Jul 29, 2024)
  4. Tech Chicago Day — P33 pitch competition, Chicago, IL (Jul 2024)
  5. “Biomachines Beyond Nature” panel — SynBioBeta 2024, San Jose, CA (2024)
Show full history
  1. Session/Track Chair, Cell-Free Systems Conference 2023 (AIChE/SBE) — Austin, TX (Nov 15–17, 2023)
  2. Speaker, BioForward Wisconsin Biohealth Summit 2023 — Madison, WI (Oct 17, 2023)
  3. Pitched, EPA WaterVent — Cincinnati, OH (Oct 10, 2023)
  4. Moderator, 2Flo Ventures Health Equity Investing Symposium — Chicago, IL (Sep 14, 2023)
  5. Panelist, ThinkChicago Exchange 2023 — Chicago, IL (May 19, 2023)
  6. Guest lecturer, Northwestern ISEN 421 “Scaling Sustainable Technology” (May 2, 2023)
  7. Guest lecturer, Northwestern ISEN 421 “Deconstructing Synthetic Biology” (Jan 24, 2023)
  8. Pitched, Chicago Venture Summit 2023 (2023)
  9. Featured alumnus, The Engine’s Tough Tech Summit 2022 — Cambridge, MA (Oct 28, 2022)
  10. Speaker, SIMB 72nd Annual Meeting — San Francisco, CA (Aug 7–10, 2022)
  11. Panelist, DOE LEEP Clean Energy Summit — Inclusive Innovation Panel (Jul 12, 2022)
  12. Guest lecturer, Northwestern ISEN 421 “Scaling Sustainable Technology” (Apr 19, 2022)
  13. Panelist, University of Chicago myCHOICE — “Startups: From Idea to Founding a Company” (Apr 18, 2022)
  14. Guest lecturer, McGill University PHAR/CHEM 540 “Advances in Industrial Biotechnology” (Feb 16, 2022)
  15. “Cell-free biosensors for rapid detection of water contaminants” — DEVCOM Soldier Center (Mar 2021)
  16. Invited speaker, Islamic Foundation of Greater St. Louis — COVID Vaccine Webinar (Jan 9, 2021)
  17. “A Paper-Based Synthetic Biology Platform for the On-Demand Testing of Water Quality” — NIEHS Virtual Technology Fair (Dec 16, 2020)
  18. Moderator, SynBioBeta 2020: The Global Synthetic Biology Conference (Oct 1, 2020)
  19. Panelist, Central US Synthetic Biology Workshop 2020 — “Diagnostics and Synthetic Biology” (Sep 11, 2020)
  20. Panelist, Northwestern Center for Synthetic Biology Retreat — “Starting a company” (Aug 27, 2020)
  21. Invited speaker, “Synthetic Biology for Defense” — Arlington, VA (Sep 19, 2019)
  22. “Rapid, Low-Cost Detection of Water Contaminants Using Regulated In Vitro Transcriptions” — Synthetic Biology: Engineering, Evolution & Design, New York, NY (Jun 27, 2019)
  23. Poster: “Freeze-dried Transcription-only Diagnostics” — EBRC Spring Retreat, Evanston, IL (Mar 2017)
  24. Poster: “Split-Broccoli: A Bifurcated RNA Aptamer for Fluorescence Visualization of RNA Hybridization” — EBRC Inaugural Retreat, Pasadena, CA (Nov 2016)
  25. “Aptamer-Mediated Delivery of Large Functional RNA” — RNA Society Synthetic Biology Workshop, Madison, WI (May 27, 2015)
  26. “Aptamer-Mediated Targeted Delivery of Large RNA” — American Society of Gene and Cell Therapy 18th Annual Meeting, New Orleans, LA (May 15, 2015)
  27. Poster: “Aptamer-Mediated Delivery of Large Functional RNA” — TIDES 2015, San Diego, CA (May 4–6, 2015)
  28. Poster: “Broad-Spectrum RNA Inhibitors of Reverse Transcriptase” — RNA Society 20th Annual Meeting, Madison, WI (May 2015)
  29. Poster: “Aptamer-Mediated Delivery of Large Functional RNA” — RNA Society 20th Annual Meeting, Madison, WI (May 2015)
  30. “FASTAptamer: A Bioinformatic Toolkit for High-Throughput Sequence Analysis of Combinatorial Selections” — Missouri Informatics Symposium 2015 (Apr 28, 2015)
  31. Poster: “Broad-Spectrum RNA Inhibitors of Reverse Transcriptase” — 31st Annual Missouri Life Sciences Week (Apr 15, 2015)
  32. Poster: “Aptamer-Mediated Delivery of Large Functional RNA” — 31st Annual Missouri Life Sciences Week (Apr 13, 2015)
  33. Poster: “FASTAptamer: A Bioinformatic Toolkit for High-Throughput Sequence Analysis of Combinatorial Selections” — 10th Annual Meeting, Oligonucleotide Therapeutics Society, San Diego, CA (Oct 13, 2014)
  34. Poster: “Broad-Spectrum RNA Inhibitors of HIV-1 Reverse Transcriptase” — 10th Annual Meeting, Oligonucleotide Therapeutics Society, San Diego, CA (Oct 12, 2014)
  35. “Rapid Identification of Serum-Stable Aptamers from Existing Populations via Poly-2’ SELEX” — American Society of Gene and Cell Therapy 17th Annual Meeting, Washington, DC (May 22, 2014)
  36. Poster: “Poly-Target SELEX: A Rapid Method for Identification of Broad-Spectrum Aptamers that Inhibit HIV Reverse Transcriptase” — American Society of Gene and Cell Therapy (May 21, 2014)
  37. Poster: “Rapid In Vitro Selection of Serum-Resistant RNA Aptamers that Inhibit HIV RT” — 30th Annual Missouri Life Sciences Week (Apr 16, 2014)
  38. Poster: “FASTAptamer: A Primary Sequence Toolkit for NGS Analysis of Selections” — 30th Annual Missouri Life Sciences Week (Apr 14, 2014)
  39. Poster: “Rapid HTS Identification of Serum-Resistant and Broad-Spectrum RNA Aptamers from Pre-Enriched SELEX Libraries” — 9th Annual Meeting, Oligonucleotide Therapeutics Society, Naples, Italy (Oct 7, 2013)
  40. Poster: “Rapid HTS Identification of Serum-Resistant and Broad-Spectrum RNA Aptamers from Pre-Enriched SELEX Libraries” — Aptamers in Medicine & Perspectives, Naples, Italy (Oct 4, 2013)

Grants & Funding

  1. DARPA BTO — AI Biotechnology Same-Day Award. PI: Khalid K. Alam. Dec 2024. $100,000. “Generating ML-enabling Training Data on Allosteric Biosensors.”
  2. NIH/NIEHS — SBIR Phase I → Phase II (R43 → R44), ES031899. “A Paper-Based Synthetic Biology Platform for the On-Demand Testing of Water Quality.” PI: Khalid K. Alam. 2020–2025. $2,007,738 total across 4 award notices.
  3. NSF SBIR — Award #2032825, Phase I. “Handheld Detection of COVID-19 With Simple Biosensor Devices for Environmental Monitoring.” PI: Khalid K. Alam. 2020–2022. $276,000.
  4. DOE / Argonne — Cooperative Research and Development Agreement, CRADA A19143. Stemloop, Inc. ↔ Argonne National Laboratory. 2019–2022. $220,000. Argonne PIs: Andrzej Joachimiak, Gyorgy Babnigg.
  5. OUSD R&E BOOST program — subcontract via UES, Inc. (AFRL prime). Aug 2021 – Aug 2022. Amount not disclosed. 1 of 5 teams selected DoD-wide for “Biotechnology Enabled Rapid Water Quality Monitoring for Warfighter Hydration.”
Show full ledger

Federal, as PI: NIH/NIEHS ES031899 SBIR Phase I→II (“A Paper-Based Synthetic Biology Platform for the On-Demand Testing of Water Quality”), 4 award notices, $2,007,738 (2020–2025) · NSF SBIR #2032825 Phase I (“Handheld Detection of COVID-19 With Simple Biosensor Devices for Environmental Monitoring”), $276,000 (2020–2022) · DARPA BTO Same-Day Award (“Generating ML-enabling Training Data on Allosteric Biosensors”), $100,000 (Dec 2024)

Federal, subaward (not PI) — amounts hidden: OUSD R&E BOOST via UES, Inc./AFRL prime — “Biotechnology Enabled Rapid Water Quality Monitoring for Warfighter Hydration,” 1 of 5 DoD-wide teams (Aug 2021–Aug 2022) · NSF RAPID #2028651 via Northwestern (PI: Julius Lucks) — “Point-of-Need Detection of COVID-19 Using CRISPR-Enabled Cell-Free Synthetic Biology,” Stemloop subawardee (May 2020)

Federal, collaboration: DOE/Argonne CRADA A19143, Stemloop ↔ Argonne National Laboratory, $220,000, Argonne PIs Andrzej Joachimiak and Gyorgy Babnigg (2019–2022)

Non-federal non-dilutive: Fortune 100 corporate research gift, administered by Northwestern — amount confidential · Walder Foundation, Chicagoland Coronavirus Assessment Network, $20,000 (via Northwestern) · VentureWell E-Teams Phase I, $5,000 · VentureCat 2020 (Northwestern), Semi-finalist, $2,000

Accelerators / tough-tech (no cash): MassChallenge Boston 2021, Finalist · The Engine’s Blueprint, Spring 2021 cohort, featured alumnus at Tough Tech Summit 2022 · Querrey InQbation Lab, Northwestern INVO

Equity (pre-seed): Northwestern N.XT Fund (May 2020) · TitletownTech (Apr 2022) — investor names public, per-investor amounts confidential

R&D-services revenue: LanzaTech, Solesence, UES — customer names public, per-customer amounts confidential; $155,788 aggregate across 3 customers (Apr 2021–Feb 2023)

Affiliations & Service