DH
David Haussler
Genome, HumanGenomeDatabases, GeneticEvolution, MolecularGenomicsSoftwareAlgorithmsPhylogenyneurosciencegenomics
On Valency
published · living versionsW_rhtyetpx·v1 · currentpublished
Sensorimotor behaviour from an untrained brain-and-nerve-cord connectome
with John R. Minnick, Jesus Gonzalez-Ferrer, Jinghui Geng, Jason K. Eshraghian +2
1 version
W_26xzgw86·v1published
Preprints & journals
315 papers in the corpus · 1974–2026AI Agents for CRISPR Diagnostics: From Automation to Bounded Autonomy10.26434/chemrxiv.15010042/v1 · Sina Jamalzadegan, Mahsa Bagi, Sepehr Soltani et al.2026 · 0 citationsChemRxiv
Decoding brain anatomy from neuronal neighborhoods with MYCEL.42856415 · Gonzalez-Ferrer, Jesus, Moreno-Ochando, Avelina, Minnick, John R et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
HIPPIE: a generative model for electrophysiological analysis across species, technologies, and modalities.42764354 · Gonzalez-Ferrer, Jesus, Lehrer, Julian, Alvarez-Esteban, Bruno et al.2026 · 1 citationNature communications. 2026;17(1)
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.42539208 · Lucas, Julian K, Hebbar, Prajna, Liao, Wen-Wei et al.2026 · 9 citationsbioRxiv : the preprint server for biology. 2026
Servo-Actuated 3D-Printed Disposable Microvalves for Automated, Scalable Organoid Culture in Standard Incubators.42367962 · Zeraatkar, Mojtaba, Ehrlich, Drew, Hernandez, Sebastian et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
SpikeProphecy: A Large-Scale Benchmark for Autoregressive Neural Population Forecasting2605.12992v1 · John R. Minnick, Jinghui Geng, Kamran Hussain et al.2026 · 0 citationsarXiv
Implicit Behavioral Decoding from Next-Step Spike Forecasts at Population Scale2605.12999v1 · John R. Minnick, Jesus Gonzalez-Ferrer, Kamran Hussain et al.2026 · 0 citationsarXiv
SpikeLab: Agentic tools for spike data analysis.42094562 · van der Molen, Tjitse, Cheney, Luka, Hussain, Kamran et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
Microfluidic Control of Dorsal-Ventral Patterning Within a Single Forebrain Organoid.41993407 · Torres-Montoya, Sebastian, Vera-Choqqueccota, Samira, Seiler, Spencer T et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Automated Optofluidic Analysis of Single Extracellular Vesicles for Organoid Culture Monitoring.42609747 · Losakul, Ravipa, Voitiuk, Kateryna, Xu, Ruiting et al.2026 · 1 citationIEEE journal of selected topics in quantum electronics : a publication of the IEEE Lasers and Electro-optics Society. 2026;32(4)
A modular platform for automated organoid culture and longitudinal imaging.41703003 · Torres-Montoya, Sebastian, Hernandez, Sebastian, Seiler, Spencer T et al.2026 · 3 citationsScientific reports. 2026;16(1)
A Modular In-Incubator Microscope for Longitudinal Live Cell Microscopy.41648487 · Ehrlich, Drew, Rosen, Yohei, Arul, Santhosh et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
CytoVerse: Single-Cell AI Foundation Models in the Browser.41659670 · Currie, Robert, Gonzalez-Ferrer, Jesus, Mostajo-Radji, Mohammed A et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Cloud-Connected Pluripotent Stem Cell Platform Enhances Scientific Identity in Underrepresented Students.41648443 · Vera-Choqqueccota, Samira, Ehrlich, Drew, Luna-Gomez, Vladimir et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
Scalable high-fidelity human vascularized cortical assembloids recapitulate neurovascular co-development and cell specialization10.64898/2026.01.09.698753v1 · Bhalla, S., Gulsuyu, B., Sanchez, D. et al.2026 · 1 citationbioRxiv
The UCSC Genome Browser database: 2026 update.41251146 · Casper, Jonathan, Speir, Matthew L, Raney, Brian J et al.2026 · 151 citationsNucleic acids research. 2026;54(D1):D1331-D1335
Microscale maps of bursting dynamics across human hippocampal slices from patients with epilepsy.41385612 · Elliott, Matthew A T, Andrews, John P, van der Molen, Tjitse et al.2026 · 1 citationJournal of neurophysiology. 2026;135(1):273-285
Single molecule nanopore counting assay targeting small extracellular vesicle cargo for non-invasive monitoring of cerebral organoid development and health.41387532 · Saiduzzaman, S M, Xu, Ruiting, Sampad, Mohammad Julker Neyen et al.2025 · 3 citationsScientific reports. 2025;15(1):45806
Incubator-Free Organoid Culture in a Sealed Recirculatory System.40950033 · Rosen, Yohei, Doganyigit, Kivilcim, Arul, Santhosh et al.2025 · 3 citationsbioRxiv : the preprint server for biology. 2025
Consistently processed RNA sequencing data from 50 sources enriched for pediatric data.40603900 · Beale, Holly C, Learned, Katrina, Kephart, Ellen T et al.2025 · 2 citationsScientific data. 2025;12(1):1134
Weighted Graph for Longitudinal Tracking of Neurons in Cortical Organoids on a High-Density Microelectrode Array.41335812 · Geng, Jinghui, Gonzalez-Ferrer, Jesus, Voitiuk, Kateryna et al.2025 · 0 citationsAnnual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference. 2025;2025:1-5
Microfluidic Topography Biases Neural Organoid Morphogenesis.41337041 · Minnick, John, Ehrlich, Drew, Moarefian, Maryam et al.2025 · 0 citationsAnnual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference. 2025;2025:1-7
Comparative analysis of RNA expression identifies effective targeted drug in myoepithelial carcinoma.40379813 · Vasquez, Yvonne A, Sanders, Lauren, Beale, Holly C et al.2025 · 1 citationNPJ precision oncology. 2025;9(1):145
Self-Organizing Neural Networks in Organoids Reveal Principles of Forebrain Circuit Assembly.40654898 · Hernandez, Sebastian, Schweiger, Hunter E, Cline, Isabel et al.2026 · 9 citationsbioRxiv : the preprint server for biology. 2025
Protocol for deep-learning-driven cell type label transfer in single-cell RNA sequencing data.40232935 · Zabetian, Zoe, Gonzalez-Ferrer, Jesus, Lehrer, Julian et al.2025 · 2 citationsSTAR protocols. 2025;6(2):103768
Comparative analysis of RNA expression in a single institution cohort of pediatric cancer patients.40119139 · Vasquez, Yvonne A, Beale, Holly C, Sanders, Lauren et al.2025 · 1 citationNPJ precision oncology. 2025;9(1):81
Microscope Upcycling: Transforming legacy microscopes into automated cloud-integrated imaging systems.40213781 · Ehrlich, Drew, Rosen, Yohei, Parks, David F et al.2025 · 1 citationHardwareX. 2025;22:e00637
Pathological microcircuits and epileptiform events in patient hippocampal slices.39605666 · Elliott, Matthew A T, Andrews, John P, van der Molen, Tjitse et al.2025 · 1 citationbioRxiv : the preprint server for biology. 2025
HIPPIE: A Multimodal Deep Learning Model for Electrophysiological Classification of Neurons.40161713 · Gonzalez-Ferrer, Jesus, Lehrer, Julian, Schweiger, Hunter E et al.2026 · 4 citationsbioRxiv : the preprint server for biology. 2025
Multiscale Cloud-Based Pipeline for Neuronal Electrophysiology Analysis and Visualization.39605518 · Geng, Jinghui, Voitiuk, Kateryna, Parks, David F et al.2025 · 5 citationsbioRxiv : the preprint server for biology. 2024
Goal-Directed Learning in Cortical Organoids.39713376 · Robbins, Ash, Schweiger, Hunter E, Hernandez, Sebastian et al.2026 · 24 citationsbioRxiv : the preprint server for biology. 2024
A feedback-driven brain organoid platform enables automated maintenance and high-resolution neural activity monitoring.38559212 · Voitiuk, Kateryna, Seiler, Spencer T, Pessoa de Melo, Mirella et al.2026 · 22 citationsbioRxiv : the preprint server for biology. 2024
RT-Sort: An action potential propagation-based algorithm for real time spike detection and sorting with millisecond latencies.39637133 · van der Molen, Tjitse, Lim, Max, Bartram, Julian et al.2024 · 8 citationsPloS one. 2024;19(12):e0312438
Multimodal evaluation of network activity and optogenetic interventions in human hippocampal slices.39548326 · Andrews, John P, Geng, Jinghui, Voitiuk, Kateryna et al.2024 · 42 citationsNature neuroscience. 2024;27(12):2487-2499
The UCSC Genome Browser database: 2025 update.39460617 · Perez, Gerardo, Barber, Galt P, Benet-Pages, Anna et al.2025 · 616 citationsNucleic acids research. 2025;53(D1):D1243-D1249
Model-agnostic neural mean field with a data-driven transfer function.39310743 · Spaeth, Alex, Haussler, David, Teodorescu, Mircea2025 · 1 citationNeuromorphic computing and engineering. 2024;4(3):034013
Reducing education inequalities through cloud-enabled live-cell biotechnology.39209603 · Vera-Choqqueccota, Samira, Belmekki, Baha Eddine Youcef, Alouini, Mohamed-Slim et al.2025 · 7 citationsTrends in biotechnology. 2025;43(1):43-60
Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders.38382530 · Shin, David, Kim, Chang N, Ross, Jayden et al.2024 · 44 citationsCell stem cell. 2024;31(3):421-432.e8
Model-Agnostic Neural Mean Field With The Refractory SoftPlus Transfer Function.38370695 · Spaeth, Alex, Haussler, David, Teodorescu, Mircea2024 · 0 citationsbioRxiv : the preprint server for biology. 2024
The UCSC Genome Browser database: 2024 update.37953330 · Raney, Brian J, Barber, Galt P, Benet-Pagès, Anna et al.2024 · 340 citationsNucleic acids research. 2024;52(D1):D1082-D1088
Unraveling Neuronal Identities Using SIMS: A Deep Learning Label Transfer Tool for Single-Cell RNA Sequencing Analysis.36909548 · Gonzalez-Ferrer, Jesus, Lehrer, Julian, O'Farrell, Ash et al.2026 · 15 citationsbioRxiv : the preprint server for biology. 2023
Internet-connected cortical organoids for project-based stem cell and neuroscience education.37503236 · Elliott, Matthew A T, Schweiger, Hunter E, Robbins, Ash et al.2025 · 21 citationsbioRxiv : the preprint server for biology. 2023
A non-oscillatory, millisecond-scale embedding of brain state provides insight into behavior.37333381 · Parks, David F, Schneider, Aidan M, Xu, Yifan et al.2025 · 25 citationsbioRxiv : the preprint server for biology. 2023
Isoform-specific translational control is evolutionarily conserved in primates.37131629 · Draper, Jolene M, Philipp, Julia, Neeb, Zachary T et al.2025 · 2 citationsbioRxiv : the preprint server for biology. 2023
A draft human pangenome reference.37165242 · Liao, Wen-Wei, Asri, Mobin, Ebler, Jana et al.2023 · 1,170 citationsNature. 2023;617(7960):312-324
Open-loop lab-on-a-chip technology enables remote computer science training in Latinx life sciences students.37205466 · Sano, Tyler, Sampad, Mohammad Julker Neyen, Gonzalez-Ferrer, Jesus et al.2024 · 7 citationsbioRxiv : the preprint server for biology. 2023
GenArk: Towards a million UCSC Genome Browsers.37066427 · Clawson, Hiram, Lee, Brian T, Raney, Brian J et al.2025 · 17 citationsResearch square. 2023
The UCSC Genome Browser database: 2023 update.36420891 · Nassar, Luis R, Barber, Galt P, Benet-Pagès, Anna et al.2023 · 602 citationsNucleic acids research. 2023;51(D1):D1188-D1195
Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors.36513728 · Sanders, Lauren M, Chandra, Rahul, Zebarjadi, Navid et al.2022 · 15 citationsCommunications biology. 2022;5(1):1367
Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids.36418910 · Seiler, Spencer T, Mantalas, Gary L, Selberg, John et al.2022 · 62 citationsScientific reports. 2022;12(1):20173
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