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2025
Sun Y, Squires JR, Hoffmann A, Zhang Y, Minor A, Singh A, Scholten D, Mao C, Luo Y, Fang D et al..  2025.  Abstract 2420: Deep learning enables automated detection of circulating tumor cell-immune cell interactions with prognostic insights in cancer. Cancer Research. 85:2420-2420.
Squires JR, Sun Y, Hoffmann AD, Zhang Y, Minor AC, Singh A, Scholten D, Ding H, Mao C, Platanias LC et al..  2025.  Abstract B049: Deep Learning Enables Identification of Cell Types and Clusters (iCTC) in Immune Tumor Ecosystems for Prognostic Assessment in Cancer. Clinical Cancer Research. 31:B049-B049.
Shtengel G, Qiu W, Aaron J, Crowe AS, Polilov AA, Karkali K, Bleck CKE, Hess HH.  2025.  Alternating Angle Milling Suppresses Streaking Artifacts in FIB-SEM Imaging. bioRxiv.
Liu H, Squires J, Sun Y, Hoffmann ADaniel, Zhang Y, Platanias LC, Gradishar WJohn, Cristofanilli M, Stringer C.  2025.  Analysis of deep learning for automated recognition of immune cells interacting with CTCs for prognostic assessment in cancer.. Journal of Clinical Oncology. 43:e13028-e13028.
Charvat AF, Mason-Chalmers K, Grabinska-Rogala A, Shivakumar S, Gale-Day Z, Wu T, Millbern Z, Grimm J, Carroll EC, Nilsson P et al..  2025.  Aurora 2.0: A Fluorogenic Dye Library for Expanding the Capability of Protein-Adaptive Differential Scanning Fluorimetry (paDSF).. SLAS Discov. :100259.
Charvat AF, Mason-Chalmers K, Grabinska-Rogala A, Shivakumar S, Gale-Day Z, Wu T, Millbern Z, Grimm J, Carroll EC, Nilsson P et al..  2025.  Aurora 2.0: A Fluorogenic Dye Library for Expanding the Capability of Protein-Adaptive Differential Scanning Fluorimetry (paDSF).. SLAS Discov. :100259.
Antunes MMota, Oliveira AGustavo, de Paula CMaria, Chew T-L, Paula-Neto HA, Menezes GB.  2025.  Bioimaging Brasil: democratizing in vivo optical microscopy to drive scientific progress across a vast nation.. Nat Methods.
Desissaire S, Ziemczonok M, Cantat-Moltrecht T, Kuś A, Godefroy G, Hervé L, Paviolo C, Krauze W, Allier C, Mandula O et al..  2025.  Bio-inspired 3D-printed phantom: Encoding cellular heterogeneity for characterization of quantitative phase imaging. Measurement. 247:116765.
Suarez-Gomez D, Perez-Rosas NC, Miranda-Contreras GI, Colom-Braña SR, Zhang W, Mim MSahir, Tan S, Gazzo D, Tepole ABuganza, Deng Q et al..  2025.  CalciumInsights: An Open-Source, Tissue-Agnostic Graphical Interface for High-Quality Analysis of Calcium Signals. bioRxiv.
Suarez-Gomez D, Perez-Rosas NC, Miranda-Contreras GI, Colom-Braña SR, Zhang W, Mim MSahir, Tan S, Gazzo D, Tepole ABuganza, Deng Q et al..  2025.  CalciumInsights: An Open-Source, Tissue-Agnostic Graphical Interface for High-Quality Analysis of Calcium Signals. bioRxiv.
Chiu H, Robie AA, Branson K, Vippa T, Epstein S, Rubin GM, Anderson DJ, Schretter CE.  2025.  Cell type-specific contributions to a persistent aggressive internal state in female Drosophila. Elife. 12
Wolff T, Eddison M, Chen N, Nern A, Sundaramurthi P, Sitaraman D, Rubin GM.  2025.  Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation. elife.
Aaron JS, Jacobs CA, Malacrida L, Keppler A, French P, Fletcher DA, Wood C, Brown CM, Wright GD, Ogawa S et al..  2025.  Challenges of microscopy technology dissemination to resource-constrained communities.. Nat Methods.
Deb D, Both G-J, Bezzam E, Kohli A, Yang S, Chaware A, Allier C, Cai C, Anderberg G, M. Eybposh H et al..  2025.  Chromatix: a differentiable, GPU-accelerated wave-optics library. bioRxiv.
Deb D, Both G-J, Bezzam E, Kohli A, Yang S, Chaware A, Allier C, Cai C, Anderberg G, M. Eybposh H et al..  2025.  Chromatix: a differentiable, GPU-accelerated wave-optics library. bioRxiv.
Deb D, Both G-J, Bezzam E, Kohli A, Yang S, Chaware A, Allier C, Cai C, Anderberg G, M. Eybposh H et al..  2025.  Chromatix: a differentiable, GPU-accelerated wave-optics library. bioRxiv.
Glendening AM, Stephens C, Vuruputoor VS, Chaganti T, Myles MN, Stern DL, Abdelalim M, Juang Y-P, Hogenhout SA, Mathers TC et al..  2025.  Chromosome scale genomes of two invasive Adelges species enable virtual screening for selective adelgicides.. G3 (Bethesda).
Glendening AM, Stephens C, Vuruputoor VS, Chaganti T, Myles MN, Stern DL, Abdelalim M, Juang Y-P, Hogenhout SA, Mathers TC et al..  2025.  Chromosome scale genomes of two invasive Adelges species enable virtual screening for selective adelgicides.. G3 (Bethesda).
Csillag V, Forastieri C, Szücs GMartina, Vidal ITalaya, Bizzozzero MHiriart, Lavis LD, Calvigioni D, Fuzik J.  2025.  Collateral connectomes of Esr1-positive hypothalamic neurons modulate defensive behavior plasticity. bioRxiv.
Csillag V, Forastieri C, Szücs GMartina, Vidal ITalaya, Bizzozzero MHiriart, Lavis LD, Calvigioni D, Fuzik J.  2025.  Collateral connectomes of Esr1-positive hypothalamic neurons modulate defensive behavior plasticity. bioRxiv.
Park SYun, Sheridan A, An B, Jarvis E, Lyudchik J, Patton W, Axup JY, Chan SW, Damstra HGJ, Leible D et al..  2025.  Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context. bioRxiv.
Park SYun, Sheridan A, An B, Jarvis E, Lyudchik J, Patton W, Axup JY, Chan SW, Damstra HGJ, Leible D et al..  2025.  Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context. bioRxiv.
Pentimalli TMassimo, Schallenberg S, León-Periñán D, Legnini I, Theurillat I, Thomas G, Boltengagen A, Fritzsche S, Nimo J, Ruff L et al..  2025.  Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment.. Cell Syst. :101261.
Pentimalli TMassimo, Schallenberg S, León-Periñán D, Legnini I, Theurillat I, Thomas G, Boltengagen A, Fritzsche S, Nimo J, Ruff L et al..  2025.  Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment.. Cell Syst. :101261.
Stürner T, Brooks P, Capdevila LSerratosa, Morris BJ, Javier A, Fang S, Gkantia M, Cachero S, Beckett IR, Marin EC et al..  2025.  Comparative connectomics of Drosophila descending and ascending neurons.. Nature.