Publications by authors named "Timothy Tickle"

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Accelerating scRNA-seq Analysis: Automated cell type annotation using representation learning and vector search.
Stephen R Williams, Fedor Grab, Govinda M Kamath, Yerdos Ordabayev, Jeff Mellen, Timothy Tickle

bioRxiv· October 2025

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The single-cell opioid responses in the context of HIV (SCORCH) consortium.
Seth A Ament, Rianne R Campbell, Mary Kay Lobo, Joseph P Receveur, Kriti Agrawal, Timothy Tickle

Mol Psychiatry· December 2024

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The commitment of the human cell atlas to humanity.
Ido Amit, Kristin Ardlie, Fabiana Arzuaga, Gordon Awandare, Gary Bader, Timothy Tickle

Nat Commun· November 2024

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Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research.
Muskan Kapoor, Enrique Sapena Ventura, Amy Walsh, Alexey Sokolov, Nancy George, Timothy Tickle

Front Genet· November 2024

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MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data.
Irzam Sarfraz, Yichen Wang, Amulya Shastry, Wei Kheng Teh, Artem Sokolov, Timothy Tickle

Genome Biol· August 2024

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A guide to the BRAIN Initiative Cell Census Network data ecosystem.
Michael Hawrylycz, Maryann E Martone, Giorgio A Ascoli, Jan G Bjaalie, Hong-Wei Dong, Timothy Tickle

PLoS Biol· June 2023

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Targeted characterization of fusion transcripts in tumor and normal tissues via FusionInspector.
Brian J Haas, Alexander Dobin, Mahmoud Ghandi, Anne Van Arsdale, Timothy Tickle

Cell Rep Methods· May 2023

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Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data.
Yichen Wang, Irzam Sarfraz, Wei Kheng Teh, Artem Sokolov, Brian R Herb, Timothy Tickle

bioRxiv· March 2023

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Toward a data infrastructure for the Plant Cell Atlas.
Noah Fahlgren, Muskan Kapoor, Galabina Yordanova, Irene Papatheodorou, Jamie Waese, Timothy Tickle

Plant Physiol· January 2023

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The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain.
Seth A Ament, Ricky S Adkins, Robert Carter, Elena Chrysostomou, Carlo Colantuoni, Timothy L Tickle

Nucleic Acids Res· January 2023

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Multivariable association discovery in population-scale meta-omics studies.
Himel Mallick, Ali Rahnavard, Lauren J McIver, Siyuan Ma, Yancong Zhang, Timothy L Tickle

PLoS Comput Biol· November 2021

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GA4GH: International policies and standards for data sharing across genomic research and healthcare.
Heidi L Rehm, Angela J H Page, Lindsay Smith, Jeremy B Adams, Gil Alterovitz, Timothy L Tickle

Cell Genom· November 2021

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Blood and immune development in human fetal bone marrow and Down syndrome.
Laura Jardine, Simone Webb, Issac Goh, Mariana Quiroga Londoño, Gary Reynolds, Timothy L Tickle

Nature· October 2021

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A statistical model for describing and simulating microbial community profiles.
Siyuan Ma, Boyu Ren, Himel Mallick, Yo Sup Moon, Emma Schwager, Timothy L Tickle

PLoS Comput Biol· September 2021

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COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.
Toni M Delorey, Carly G K Ziegler, Graham Heimberg, Rachelly Normand, Yiming Yang, Timothy L Tickle

Nature· July 2021

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A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2.
Toni M Delorey, Carly G K Ziegler, Graham Heimberg, Rachelly Normand, Yiming Yang, Timothy L Tickle

bioRxiv· February 2021

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Author Correction: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
Michal Slyper, Caroline B M Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Timothy L Tickle

Nat Med· August 2020

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Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq.
Bo Li, Joshua Gould, Yiming Yang, Siranush Sarkizova, Marcin Tabaka, Timothy Tickle

Nat Methods· August 2020

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Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes.
Marieke Lavaert, Kai Ling Liang, Niels Vandamme, Jong-Eun Park, Juliette Roels, Timothy L Tickle

Immunity· June 2020

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A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
Michal Slyper, Caroline B M Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Timothy L Tickle

Nat Med· May 2020

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Decoding human fetal liver haematopoiesis.
Dorin-Mirel Popescu, Rachel A Botting, Emily Stephenson, Kile Green, Simone Webb, Timothy L Tickle

Nature· October 2019

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The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.
Deanne M Taylor, Bruce J Aronow, Kai Tan, Kathrin Bernt, Nathan Salomonis, Timothy L Tickle

Dev Cell· April 2019

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Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer.
Daniela Börnigen, Boyu Ren, Robert Pickard, Jingfeng Li, Enver Ozer, Timothy Tickle

Sci Rep· December 2017

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Erratum: The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation.
Antonia Wallrapp, Samantha J Riesenfeld, Patrick R Burkett, Raja-Elie E Abdulnour, Jackson Nyman, Timothy L Tickle

Nature· November 2017

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