Joshua K. Thackray

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Joshua K. Thackray

My research spans genetics, neuroscience, and molecular biology, with a primary focus on developing machine learning and computer vision approaches to understand pain, injury, and recovery in rodent models. I've made significant contributions to Tourette Syndrome research by creating the first mouse models with construct validity based on human patient mutations and using computational methods to identify behavioral and dopamine-signaling phenotypes. Additionally, my work has advanced our understanding of Sirtuin biology, particularly its roles in DNA repair, transposable element regulation, and X-chromosome inactivation. Despite my computational expertise, I have a strong foundation in conducting wet-lab experiments to validate my findings and ensure their biological relevance.

Interests

  • Genetics and Genomics
  • Neuroscience and Ethology
  • Bioinformatics and Machine Learning
  • Solving Problems and Building Useful Things

Education

School of Environmental and Biological Sciences, Rutgers University
September 2005 — January 2012
New Brunswick, NJ
  1. Major in Biological Sciences
  2. Minor in Computer Science
Ewing High School
September 2001 — June 2005
Ewing, NJ
  1. High School Diploma

Professional Experience

Scientific Programmer (Consulting)
January 2025 - Present
Tactorum, Inc.
Overhaul user interface and device control software for the Arm, a robotic device used to automate and standardize pre-clinical pain testing in rodents. Synchronizing high-speed videography, streaming force sensor measurement and refinement with Kalman filters. Improve user input via gamepads and add additional user input strategies.
PythonOpenCVTkinterSpinnakerZaberPySerialPyKalmanPyInstallerHigh-speed VideographyForce MeasurementRoboticsClosed-loop SystemsUser Interface Design
Laboratory Researcher II
September 2022 - Present
Rutgers University
Working in the Human Genetics Institute of New Jersey, the Department of Genetics, the WM Keck Center for Collaborative Neuroscience, and the Department of Cell Biology and Neuroscience. Computational analysis of animal behavior data and integration with physiological recordings including EMG, fiber photometry, and optogenetics. Built a framework for analysis of operant conditioning data and fiber photometry data. Built a realtime closed-loop system for delivery of pose-triggered optogenetic stimulus. Developed a deep learning model for segmentation and tracking of 3D depth video of rodent behavior. Built rig for multi-view video capture and framework for 3D keypoint projection and pose analysis. Development of pipelines to analyze high-throughput sequencing data such as ChIP-seq, RNA-seq, etc. Design and execution of validation assays for CNV and variant analysis in human cohorts. Design and validation of CRISPR-engineered mice harboring mutations found in human disease populations.
Signal ProcessingFiber PhotometryOptogeneticsOperant ConditioningEMGHigh-speed VideographyMulti-view/3D VideographyPose-EstimationAction-RecognitionEthologyChIP-seqRNA-seqCNV AnalysisMachine LearningDeep LearningComputational PipelinesData Management
Scientific Programmer (Consulting)
July 2019 - Present
Premier Medical Laboratory
Designed and implemented a cloud-based software platform for calling results of clinical molecular testing assays, technician review, and integration with the Laboratory Information System. Developed assays covering urinary tract infections, nail fungal infections, antibiotic resistance, and combined assays. Provide ongoing support.
TypeScriptWebpackGoogle App ScriptClaspGoogleSheetsJestqPCROpen ArrayLaboratory Information System (LIS)Clinical Molecular TestingCloud Computing
Laboratory Researcher III
May 2011 - September 2022
Rutgers University
Established techniques in the lab for ChIP-seq, RNA-seq and other sequencing experiments, and implemented corresponding analytical procedures according to current best-practices. Developed novel techniques for 3D-FISH and laser-induced DNA damage in live cells. Designed and implemented software for high-throughput, semi-supervised, distributed image analysis. Implemented machine learning based methods for analysis of animal model behavioral assays.
Confocal MicroscopyWidefield MicroscopyLive-Cell Imaging3D-FISHImmunostainingHigh-Throughput ImagingComputational Image AnalysisChIP-seqRNA-seqSequencing Library PrepRT-PCRWestern BlottingCloningViral TransductionComputational PipelinesCell CultureCRISPR/Cas9Data Management
Application Developer
March 2010 - January 2012
Rutgers University
Application development for the School of Communication and Information and Department of Library Information Sciences at Rutgers University reporting to the dean of Information Technology. Developed and implemented custom applications (mostly web-based) for the school website and Information Technology Office.
PHPMySQLJoomlaJavaScriptjQueryHTMLCSSApacheIISLinuxLDAPC#
LC/MS Data Analyst
September 2009 - September 2010
Rutgers University
Analysis of data generated by the LC/MS core facility at the Rutgers Center for Lipid Research within the Nutritional Sciences Department at the School of Environmental and Biological Sciences (SEBS). Data generated included lipid identification and quantification from various sources (plant and mammalian tissues), and was used by a variety of projects and PIs, including engineered plant biofuels, cardiovascular disease, and adipocyte function.
LC/MSHPLCLipid ExtractionMarkerView (AB/SCIEX)Lipid View (AB/SCIEX)Analyst (AB/SCIEX)
Research Assistant
September 2005 - August 2009
Rutgers University
Working in the Nutritional Sciences Department at the School of Environmental and Biological Sciences (SEBS), performed analysis of LDL and VLDL particle lipid and protein composition in the context of cardiovascular disease and lipidemia. Performed general laboratory work, as well as mentoring and teaching laboratory techniques to junior students.
LC/MSFPLCHPLCTLCLipid ExtractionProtein ExtractionGel ElectrophoresisWestern BlottingCell Culture
Clinical Veterinary Technician
December 2005 - June 2008
West Trenton Animal Hospital
Setup and monitor surgical/dental procedures daily, ensuring smooth/uneventful patient recoveries. Communication with clients. Administered vaccines, microchips, and other medications and collected lab specimens (radiographs, blood draw, urine, etc) and prepared for external lab analysis or performed in-house lab analysis.
Veterinary MedicineSurgical AssistanceDental ProceduresClient CommunicationSpecimen CollectionLaboratory AnalysisAnesthesia MonitoringFilm DevelopmentRadiography

Projects

MoSeq-Reports: Interactive interrogation of MoSeq models
https://github.com/tischfieldlab/moseq-reports
A no-code platform for interactive MoSeq analysis that democratizes access to sophisticated behavioral analytics while maintaining full analytical power.
ElectronTypescriptVueVitePiniaD3.jsAxios
Fiber Photometry Analysis: `fptools`
https://github.com/tischfieldlab/fptools
A Python package for analyzing fiber photometry and behavior data, including tools for signal processing and visualization.
PythonNumPySciPySeabornPandasTDTMed-Associates
moseq2-detectron-extract
https://github.com/tischfieldlab/moseq2-detectron-extract
A Python package for extracting and analyzing mouse behavior from videos using Detectron2, designed to work with the MoSeq2 framework.
PythonPyTorchDetectron2OpenCVNumPySciPyPandasMatplotlibPyKalmanstats-modelsImage AugmentationFFMPEG
Front-Tracking-Toolkit
https://github.com/tischfieldlab/front_tracking_toolkit
Toolkit for tracking fluorescent tracers during transcranial imagining.
PythonNumPySciPyOpenCVMatplotlibPandasImage Registration
See more projects on my GitHub Profile.

Publications

citations1057
h-index12
i10-index14

    Upcoming Manuscripts

  1. MoSeq-Reports: An Open-Source Platform for Interactive Analysis of MoSeq Models.
    JK Thackray, K Narra, JM Chester, M Haas, JT Eisdorfer, S Lin, M Bohic, C Nasello, LA Poppi, J Wu, SR Datta, JA Tischfield, MA Tischfield, VE Abraira.
    In preparation for submission to eNeuro.
  2. Inapparent maternal ZIKV infection impacts fetal brain development and postnatal behavior.
    TW Chou, M McCourt, M Lindman, I Estevez, BD Buckley, JK Thackray, K Rodriguez, M Nissenbaum, C Mishra, C Atkins, AW Kusnecov, MA Tischfield, BP Daniels.
    Submitted to PLOS Pathogens.
    June 11, 2025.
  3. Remote automated delivery of mechanical stimuli coupled to brain recordings in behaving mice.
    J Burdge, A Jhumka, A Khan, S Ogundare, N Baer, S Fulton, A Kaplan, B Bistis, W Foster, JK Thackray, A Toussaint, M Li, YM Morizawa, J Nazarian, L Yadessa, AJ George, A Delinois, W Mayiseni, N Loran, G Yang, DJ Margolis, VE Abraira, I Abdus-Saboor.
    Submitted to eLife.
    June 5, 2025.
    • Remote automated delivery of mechanical stimuli coupled to brain recordings in behaving mice.
      J Burdge, A Jhumka, A Khan, S Ogundare, N Baer, S Fulton, A Kaplan, B Bistis, W Foster, JK Thackray, A Toussaint, M Li, YM Morizawa, J Nazarian, L Yadessa, AJ George, A Delinois, W Mayiseni, N Loran, G Yang, DJ Margolis, VE Abraira, I Abdus-Saboor.
      bioRxiv.
      June 8, 2025.
      10.1101/2024.05.06.592101.
  4. Sirtuin 7 regulates Xa-hyperactivation to balance the X-chromosome against the genome.
    NG Simonet, JK Thackray, B Kesner, F Serra, M Espinosa-Alcantud, A Lappala, A Guitart, L Marin, U Weissbein, D Wang, J Castelló, L Rovirosa, L Serrano, BN Vazquez, A Ruiz-Herrera, B Payer, BM Javierre, A Vaquero, JT Lee.
    Second round of review at Nature.
    February 2024.

    5. Published Manuscripts

  5. Using DeepLabCut-Live to probe state dependent neural circuits of behavior with closed-loop optogenetic stimulation.
    M Gonzalez, MA Gradwell, JK Thackray, KK Temkar, KR Patel, VE Abraira.
    Journal of Neuroscience Methods.
    May 26, 2025.
    10.1016/j.jneumeth.2025.110495.
    • Using DeepLabCut-Live to probe state dependent neural circuits of behavior with closed-loop optogenetic stimulation.
      M Gonzalez, MA Gradwell, JK Thackray, KK Temkar, KR Patel, VE Abraira.
      bioRxiv.
      August 19, 2024.
      10.1101/2024.07.28.605489.
  6. The dorsal column nuclei scale mechanical sensitivity in naive and neuropathic pain states.
    A Upadhyay, MA Gradwell, TJ Vajtay, J Conner, AA Sanyal, C Azadegan, KR Patel, JK Thackray, M Bohic, F Imai, SO Ogundare, Y Yoshida, I Abdus-Saboor, E Azim, VE Abraira.
    Cell Reports.
    April 22, 2025.
    10.1016/j.celrep.2025.115556.
    • The Dorsal Column Nuclei Scales Mechanical Allodynia During Neuropathic Pain.
      A Upadhyay, MA Gradwell, TJ Vajtay, J Conner, AA Sayal, C Azadegan, KR Patel, JK Thackray, M Bohic, F Imai, SO Ogundare, Y Yoshida, I Abdus-Saboor, E Azim, VE Abraira.
      bioRxiv.
      February 23, 2024.
      10.1101/2024.02.20.581208.
  7. Functional synaptic connectivity of engrafted spinal cord neurons with locomotor circuitry in the injured spinal cord.
    A Tucker, JT Eisdorfer, JK Thackray, K Vo, H Thomas, A Tandon, J Moses, B Singletary, T Gillespie, A Smith, A Pauken, S Nadella, M Pitonak, S Letchuman, J Jang, M Totty, FL Jalufka, M Aceves, AF Adler, S Maren, H Blackmon, DA McCreedy, VE Abraira, JN Dulin.
    bioRxiv.
    April 5, 2025.
    10.1101/2025.04.05.644402.
  8. A SIRT7-dependent acetylation switch regulates early B-cell differentiation and lineage commitment through PAX5.
    A Gamez-Garcia, A Bueno-Costa, E Alari-Pahissa, JK Thackray, M Espinosa-Alcantud, C Ray, C Berenguer, P Kumari, JJ Bech, T Braun, A Ianni, JA Tischfield, JL Sardina, L Serrano, M Esteller, C De La Torre, M Sigvardsson, BN Vazquez, A Vaquero.
    Nature Immunology.
    October 18, 2024.
    10.1038/s41590-024-01995-7.
  9. Human mutations in high-confidence Tourette disorder genes affect sensorimotor behavior, reward learning, and striatal dopamine in mice.
    C Nasello, LA Poppi, J Wu, TF Kowalski, JK Thackray, R Wang, A Persaud, M Mahboob, S Lin, R Spaseska, CK Johnson, D Gordon, F Tissir, GA Heiman, JA Tischfield, M Bocarsly, MA Tischfield.
    Proceedings of the National Academy of Sciences.
    April 29, 2024.
    10.1073/pnas.2307156121.
    • Human mutations in high-confidence Tourette disorder genes affect sensorimotor behavior, reward learning, and striatal dopamine in mice.
      C Nasello, LA Poppi, J Wu, TF Kowalski, JK Thackray, R Wang, A Persaud, M Mahboob, S Lin, R Spaseska, CK Johnson, D Gordon, F Tissir, GA Heiman, JA Tischfield, M Bocarsly, MA Tischfield.
      bioRxiv.
      November 28, 2023.
      10.1101/2023.11.28.569034.
  10. Multimodal sensory control of motor performance by glycinergic interneurons of the mouse spinal cord deep dorsal horn.
    MA Gradwell, N Ozeri-Engelhard, JT Eisdorfer, OD Laflamme, M Gonzalez, A Upadhyay, L Medlock, T Shrier, KR Patel, A Aoki, M Gandhi, G Abbas-Zadeh, O Oputa, JK Thackray, M Ricci, A George, N Yusuf, J Keating, Z Imtiaz, SA Alomary, M Bohic, M Haas, Y Hernandez, SA Prescott, T Akay, VE Abraira.
    Neuron.
    March 6, 2024.
    10.1016/j.neuron.2024.01.027.
    • Multimodal sensory control of motor performance by glycinergic interneurons of the spinal cord deep dorsal horn.
      MA Gradwell, N Ozeri-Engelhard, JT Eisdorfer, OD Laflamme, M Gonzalez, A Upadhyay, A Aoki, T Shrier, M Gandhi, G Abbas-Zadeh, O Oputa, JK Thackray, M Ricci, N Yusuf, J Keating, M Bohic, Z Imtiaz, SA Alomary, J Katz, M Haas, Y Hernandez, T Akay, V Abraira.
      bioRxiv.
      May 21, 2022.
      10.1101/2022.05.21.492933.
  11. SIRT7 and p53 interaction in embryonic development and tumorigenesis.
    BN Vazquez, I Fernández-Duran, Y Hernandez, S Tarighi, JK Thackray, M Espinosa-Alcantud, P Kumari, A Ianni, L Cesaire, T Braun, M Esteller, J Tischfield, A Vaquero, L Serrano.
    Frontiers in Cell Developmental Biology.
    January 3, 2024.
    10.3389/fcell.2023.1281730.
  12. Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD.
    S Wang, B Wang, V Drury, S Drake, N Sun, H Alkhairo, J Arbelaez, C Duhn, Tourette International Collaborative Genetics (TIC Genetics), VH Bal, K Langley, J Martin, PJ Hoekstra, A Dietrich, J Xing, GA Heiman, JA Tischfield, TV Fernandez, MJ Owen, MC O'Donovan, A Thapar, MW State, AJ Willsey.
    Nature Communications.
    December 6, 2023.
    10.1038/s41467-023-43776-0.
  13. Using behavioral biomarkers to redefine epochs of spontaneous recovery following spinal cord injury.
    JT Eisdorfer*, JK Thackray*, T Theis, A Vivinetto, MT Ricci, S Lin, O Oputa, AM Martinez, HD Nacht, M Tschang, M Mahmood, A Tucker, C Ruven, M Bohic, S Pusuloori, L Zmoyro, S Kumar, Abraira Lab Computational Group, M Schachner, V Sahni, P Popovich, AR Ferguson, D McTigue, VM Tysseling, J Dulin, E Hollis II, SR Datta, VE Abraira. (* Equal contributions)
    bioRxiv.
    November 5, 2023.
    10.1101/2023.10.31.564826.
  14. Piezo1 agonist restores meningeal lymphatic vessels, drainage, and brain-CSF perfusion in craniosynostosis and aged mice.
    MJ Matrongolo, PS Ang, J Wu, A Jain, JK Thackray, A Reddy, CC Sung, G Barbet, YK Hong, and MA Tischfield.
    Journal of Clinical Investigation.
    November 2, 2023.
    10.1172/JCI171468.
  15. Mapping the neuroethological signatures of pain, analgesia and recovery in mice.
    M Bohic, LA Pattison, ZA Jhumka, H Rossi, JK Thackray, M Ricci, N Mossazghi, W Foster, S Ogundare, CR Twomey, H Hilton, J Arnold, MA Tischfield, EA Yttri, E St John Smith, I Abdus-Saboor, VE Abraira.
    Neuron.
    July 12, 2023.
    10.1016/j.neuron.2023.06.008.
    • Behavioral and nociceptor states of inflammatory pain across timescales in 2D and 3D.
      M Bohic, LA Pattison, Z Anissa Jhumka, H Rossi, JK Thackray, M Ricci, W Foster, J Arnold, N Mossazghi, EA Yttri, MA Tischfield, E St. John Smith, I Abdus-Saboor, VE Abraira.
      bioRxiv.
      June 17, 2021.
      10.1101/2021.06.16.448689.
  16. A cadherin mutation in Celsr3 linked to Tourette Disorder affects dendritic patterning and excitability of cholinergic interneurons.
    LA Poppi, KT Ho-Nguyen, J Wu, M Matrongolo, JK Thackray, C Nasello, A Shi, M Ricci, J McGinnis, NL Carayannopoulos, N Cheedalla, S Schaper, C Daut, J Hernandez, GA Heiman, JA Tischfield, MA Tischfield.
    bioRxiv.
    March 7, 2022.
    10.1101/2022.03.06.483205.
  17. A machine-vision approach for automated locomotor recovery at millisecond timescales.
    T Theis, JK Thackray, M Ricci, V Abraira.
    Journal of Neurotrauma. Volume 38, Issue 14, Page A82.
    July 15, 2021.
  18. Whole-exome sequencing identifies genes associated with Tourette's Disorder in multiplex families.
    X Cao, Y Zhang, M Abdulkadir, L Deng, TV Fernandez, B Garcia-Delgar, J Hagstrøm, PJ Hoekstra, RA King, J Koesterich, S Kuperman, A Morer, C Nasello, KJ Plessen, JK Thackray, L Zhou, Tourette International Collaborative Genetics Study (TIC Genetics), A Dietrich, JA Tischfield, GA Heiman, J Xing.
    Molecular Psychiatry.
    April 9, 2021.
    10.1038/s41380-021-01094-1.
  19. SirT7 auto-ADPribosylation regulates glucose starvation response through macroH2A1.
    NG Simonet, JK Thackray, BN Vazquez, A Ianni, M Espinosa-Alcantud, JI Morales-Sanfrutos, S Hurtado-Bagès, E Sabidó, M Buschbeck, J Tischfield, C de la Torre, M Esteller, T Braun, M Olivella, L Serrano, A Vaquero.
    Science Advances.
    July 2020.
    10.1126/sciadv.aaz2590.
    • SirT7 auto-ADPribosylation regulates glucose starvation response through macroH2A1.
      NG Simonet, JK Thackray, BN Vazquez, A Ianni, M Espinosa-Alcantud, JI Morales-Sanfrutos, S Hurtado-Bagès, E Sabidó, M Buschbeck, J Tischfield, C de la Torre, M Esteller, T Braun, M Olivella, L Serrano, A Vaquero.
      bioRxiv.
      August 5, 2019.
      10.1101/719559.
  20. SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina.
    BN Vazquez*, JK Thackray*, NG Simonet, S Chahar, N Kane-Goldsmith, SJ Newkirk, S Lee, J Xing, MP Verzi, W An, A Vaquero, JA Tischfield, L Serrano. (* Equal contributions)
    Nucleic Acids Research.
    June 2, 2019.
    10.1093/nar/gkz519.
  21. De Novo Sequence and Copy Number Variants are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis.
    S Wang, JD Mandell, Y Kumar, N Sun, MT Morris, J Arbelaez, C N, S Dong, C Duhn, X Zhao, Z Yang, SS Padmanabhuni, D Yu, RA King, A Dietrich, AY Huang, BM Neale, G Coppola, CA Mathews, JM Scharf, Tourette International Collaborative Genetics (TIC Genetics), Tourette Syndrome Genetics Southern and Eastern Europe Initiative (TSGENESEE), Tourette Association of America International Consortium for Genetics (TAAICG), L Wei, TV Fernandez, J Xing, GA Heiman, JA Tischfield, P Paschou, AJ Willsey, MW State.
    Cell Reports.
    September 25, 2018.
    10.1016/j.celrep.2018.08.082.
  22. Degree of Tissue Differentiation Dictates Susceptibility to BRAF-driven Colorectal Cancer.
    K Tong, O Pellón-Cárdenas, VR Sirihorachai, BN Warder, OA Kothari, AO Perekatt, EE Fokas, RL Fullem, A Zhou, JK Thackray, H Tran, L Zhang, J Xing, MP Verzi.
    Cell Reports.
    December 2017.
    10.1016/j.celrep.2017.11.104.
  23. Mammalian HP1 isoforms have specific roles in heterochromatin structure and organization.
    L Bosch-Presegué, H Raurell-Vila, JK Thackray, J González, C Casal, N Kane-Goldsmith, MN Vizoso, JP Brown, A Gómez, J Ausió, T Zimmermann, M Esteller, G Schotta, PB Singh, L Serrano, A Vaquero.
    Cell Reports.
    November 2017.
    10.1016/j.celrep.2017.10.092.
  24. Sirtuins and DNA damage repair: SIRT7 comes to play.
    BN Vazquez, JK Thackray, L Serrano.
    Nucleus.
    February 2017.
    10.1080/19491034.2016.1264552.
  25. SIRT7 promotes genome integrity and modulates non-homologous end joining DNA repair.
    BN Vazquez, JK Thackray, NG Simonet, N Kane-Goldsmith, P Martinez-Redondo, T Nguyen, S Bunting, A Vaquero, JA Tischfield, L Serrano.
    The EMBO Journal.
    May 2016.
    10.15252/embj.201593499.
  26. Chromatin profiling reveals regulatory network shifts and a protective role for hepatocyte nuclear factor 4α during colitis.
    S Chahar, V Gandhi, S Yu, K Desai, R Cowper-Sal, Y Kim, AO Perekatt, N Kumar, JK Thackray, A Musolf, N Kumar, A Hoffman, D Londono, BN Vazquez, L Serrano, H Shin, M Lupien, N Gao, MP Verzi.
    Molecular and Cellular Biology.
    September 2014.
    10.1128/MCB.00349-14.

Awards and Honors

Best Image Award—Microscopy and Cytology Category
April 2012
Human Genetics Institute of New Jersey, Rutgers University
Eagle Scout
January 2005
Boy Scouts of America