Sequencing, at scale

Publications

1. Paper2026· ARUP Laboratories / University of Utah

   Evaluation of the Ultima Genomics UG 100 sequencer for low-cost, high-sensitivity metagenomic pathogen detection from cerebrospinal fluid

   R. C. Shean, K. D. Tardif, A. Rangel, …, N. Iremadze, …, B. T. Bradley · author 8 of 11

   Microbiology Spectrum, 14(4), e01874-25 (2026)

   Tested whether low-cost UG 100 sequencing can find pathogens directly in spinal fluid; it agreed with standard tests in 26 of 28 cases.

   My part: Ultima-side sequencing

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2. Abstract2026· Alter Lab, University of Utah

   Abstract 6884: Quantum mechanics-based multi-tensor AI/ML correctly predicts glioblastoma patients' overall survival, gene targets to sensitize the tumors, and the tumors' response to their targeting from their whole genomes

   O. Alter, S. P. Ponnapalli, M. Coppola, …, N. Iremadze, …, J. W. Tsai · author 11 of 25

   Cancer Research, 86(7 Suppl), 6884 (2026)

   An AI model applied to tumor whole genomes predicts glioblastoma survival and suggests gene targets to make the tumors more treatable.

   My part: Ultima-side sequencing

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3. Abstract2026· Swanton Lab, Francis Crick Institute / UCL

   Abstract LB116: Error-corrected plasma whole-genome sequencing for personalised and tumor-agnostic minimal residual disease detection in NSCLC

   J. Wan, S. Ward, A. A. Azizi, …, N. Iremadze, …, C. Swanton · author 8 of 17

   Cancer Research, 86(8 Suppl), LB116 (2026)

   Ultra-sensitive blood tests based on whole-genome sequencing spot leftover lung cancer after surgery; patients who test positive relapse sooner.

   My part: Ultima-side sequencing

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4. Paper2025· NIST Genome in a Bottle consortium

   Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

   J. H. McDaniel, V. Patel, N. D. Olson, …, N. Iremadze, …, J. M. Zook · author 65 of 96

   Scientific Data, 12, 1195 (2025)

   A public reference tumor/normal cell-line pair, sequenced on many platforms, that labs can use to benchmark cancer genomics methods.

   My part: Ultima-side sequencing data

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5. Paper2025· Satija Lab, New York Genome Center / NYU

   Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens

   L. Jiang, C. Dalgarno, E. Papalexi, …, N. Iremadze, …, R. Satija · author 7 of 10

   Nature Cell Biology, 27(3), 505–517 (2025)

   More than 1,500 genetic perturbations across six cell lines, read out by single-cell sequencing, to map what signaling regulators actually control.

   My part: Ran the Ultima sequencing

   DOI ↗Free full text ↗Copy BibTeXSubscription (free copy in PMC)
6. Paper2025· Adey Lab, OHSU

   Atlas-scale single-cell DNA methylation profiling with sciMETv3

   R. V. Nichols, L. E. Rylaarsdam, B. L. O'Connell, …, N. Iremadze, …, A. C. Adey · author 5 of 7

   Cell Genomics, 5(1), 100726 (2025)

   A method that profiles DNA methylation in hundreds of thousands of single cells per experiment, used to build a human brain atlas.

   My part: Ultima sequencing and primary data processing

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7. Preprint2025· Greenleaf Lab, Stanford

   An automated ATAC-seq method reveals sequence determinants of transcription factor dose response in the open chromatin

   B. B. Liu, M. Shimasawa, S. Vermeulen, …, N. Iremadze, …, W. J. Greenleaf · author 5 of 8

   bioRxiv (2025)

   An automated chromatin-accessibility workflow run across hundreds of samples to learn how DNA sequence shapes the way genes respond to transcription-factor dose.

   My part: Ultima-side sequencing

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8. Preprint2025· Shoshani Lab, Weizmann Institute of Science

   Aberrant inheritance of extrachromosomal DNA amplifications promotes cancer evolution

   S. Marom, I. Lifshits Dayan, V. Narasimha Kadali, …, N. Iremadze, …, O. Shoshani · author 17 of 25

   bioRxiv, 2025.09.19.677276 (2025)

   Extra DNA circles in cancer cells are passed unevenly to daughter cells, which increases tumor diversity and helps cancers adapt.

   My part: Ultima-side sequencing

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9. Abstract2024· Watchmaker Genomics

   Abstract 315: Cost-effective, comprehensive detection of gene fusions from DNA and RNA using the UG100 sequencer

   G. Lithwick-Yanai, S. R. Pollock, D. Lebanony, …, N. Iremadze, …, D. Lipson · author 7 of 14

   Cancer Research, 84(6 Suppl), 315 (2024)

   Combined DNA and RNA sequencing on the UG100 recovered 93% of known cancer gene fusions across five cell lines, at low cost.

   My part: Ultima-side sequencing

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10. Abstract2024· Maruvka Lab, Technion

    Abstract 7560: Microsatellite instability (MSI) detection using flow-based sequencing

    G. Lithwick-Yanai, H. Benjamin, J. Cano-Nistal, …, N. Iremadze, …, Y. E. Maruvka · author 6 of 14

    Cancer Research, 84(6 Suppl), 7560 (2024)

    Whole-genome sequencing on the UG100 correctly called microsatellite instability, a key cancer biomarker, in cell lines and tumor samples.

    My part: Ultima-side sequencing

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11. Paper2023· Broad Institute

    Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing

    S. K. Simmons, G. Lithwick-Yanai, X. Adiconis, …, N. Iremadze, …, J. Z. Levin · author 5 of 14

    Nature Biotechnology, 41(2), 204–211 (2023)

    Showed that Ultima's lower-cost chemistry, built mostly on natural nucleotides, gives single-cell RNA-seq data on par with the incumbent platform.

    My part: Ultima-side sequencing

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12. Abstract2023· Weizmann Institute of Science

    Abstract 5467: Single-cell analysis of CD34-enriched blood cells reveals early prognostic markers of myelodysplastic syndromes

    E. Meiri, N. Saar-Furer, N. Rappoport, …, N. Iremadze, …, L. Shlush · author 7 of 10

    Cancer Research, 83(7 Suppl), 5467 (2023)

    Single-cell RNA sequencing of 685,000 blood stem and progenitor cells, looking for early warning signs of a bone-marrow cancer.

    My part: Ultima-side sequencing

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13. Abstract2023· Ultima Genomics (internal)

    Abstract 3134: Calling somatic variants from UG100 data using deep learning

    M. Levy, D. Shem-Tov, H. Benjamin, …, N. Iremadze, …, O. Barad · author 8 of 11

    Cancer Research, 83(7 Suppl), 3134 (2023)

    A deep-learning method for finding tumor-specific mutations in UG100 sequencing data.

    My part: Ultima-side sequencing

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14. Paper2022· Weissman Lab, Whitehead Institute / MIT

    Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

    J. M. Replogle, R. A. Saunders, A. N. Pogson, …, N. Iremadze, …, J. S. Weissman · author 11 of 17

    Cell, 185(14), 2559–2575.e28 (2022)

    Knocked down every expressed human gene and read out each cell's full transcriptional response, building a genome-wide map of what genes do.

    My part: Ultima-side sequencing

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15. Preprint2022· Snyder Lab, Stanford

    Ultra high-throughput whole-genome methylation sequencing reveals trajectories in precancerous polyps to early colorectal adenocarcinoma

    H. Lee, G. Krieger, T. Clark, …, N. Iremadze, …, M. P. Snyder · author 16 of 23

    bioRxiv, 2022.05.30.494076 (2022)

    Mapped DNA methylation across the whole genome as colorectal polyps progress toward early cancer, revealing early markers of the transition.

    My part: Ultima-side sequencing

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