# Publications Sort & Filters close ## Filters Organism expand\_more - Aedes aegypti (3) - Culex quinquefasciatus (4) - Ixodes scapularis (tick) (3) - Aedes albopictus (3) - Anopheles gambiae (4) - C. elegans (worm) (14) - Drosophila (fly) (185) - Human (57) - Mouse (29) - Rat (9) - Xenopus (frog) (9) - Yeast (S. cerevisiae) (16) - Yeast (S. pombe) (9) - Zebrafish (13) Publication Type expand\_more - Bioinformatics (44) - Dataset or data portal (13) - DRSC-BTRR (27) - Method or protocol (39) - Research report (115) - Review article (18) Technology expand\_more - Cell-based assays (114) - DRSC-BTRR (30) - Protein binders (3) - Proximity labeling (1) - CRISPR gRNA design (17) - Cell-based CRISPR (28) - in vivo fly CRISPR (15) - Primary cell culture (6) - Cell-based RNAi (116) - in vivo fly RNAi (28) Topics expand\_more - Apoptosis (4) - Autophagy (2) - Cell cycle and checkpoints (7) - Cell morphology (13) - Chromosome pairing (1) - Circadian rhythms (1) - CRISPRa (7) - CRISPR genome editing (26) - CRISPR gRNA design (18) - CRISPRi (3) - Cytoskeletal proteins (9) - Data mining (43) - Data visualization (28) - Disease-related studies (43) - Disease models (15) - DRSC-BTRR (30) - Drug screens (1) - Enrichment analysis (23) - Epigenetics and chromatin factors (12) - Essential genes (6) - Genome-wide screen (85) - High-throughput data analysis (65) - Host-pathogen interactions (13) - Image analysis (18) - Immunity and immune signaling (8) - Ion transport (11) - Lipid storage (4) - Metabolism (6) - miRNAs (5) - Neurobiology (5) - Off-target analysis (20) - Organelles (17) - Ortholog identification (7) - Phosphoproteomics (5) - Physiology (2) - Primary cells (6) - Protein binders (2) - Protein interactions (5) - Protein labeling (2) - Protein localization (4) - Protein secretion (3) - Proximity labeling (1) - RNA biology (8) - RNAi reagent design (18) - RNAi rescue (10) - RNAi validation (33) - Screening technologies (46) - Signal transduction (42) - Single-cell isolation (5) - Stem cells (1) - Synthetic lethality (4) - Transcription (11) - Translation (7) Search Within Results Search Within Results search ## 221 results Show filters filter\_alt Sort by Year of PublicationAlphabetical A-Z sort ## 221 results Download 221 citations download- [BibTeX](/node/1589131/export?format=bibtex) - [EndNote X3 XML](/node/1589131/export?format=endnote8) - [EndNote 7 XML](/node/1589131/export?format=endnote7) - [Endnote tagged](/node/1589131/export?format=tagged) - [Marc](/node/1589131/export?format=marc) - [PubMedId](/node/1589131/export?format=pubmed_id) - [RIS](/node/1589131/export?format=ris) ### 2026 Matthew Butnaru, William McKenna, Srishti Goswami, Alejandra Wu-Chuang, Enzo Mameli, Abigail Wilcox, Leopoldine Quennesson, Ah-Ram Kim, Austin Veal, Weihang Chen, Hugo Verzone, Elizabeth A Lane, Hanna J Laukaitis-Yousey, Chad Araneo, Nisha Singh, Joao Pedra, Yanhui Hu, Raghuvir Viswanatha, Norbert Perrimon, and Stephanie E Mohr. 2026. “[Genome-Wide CRISPR Knockout Cell Screening Platform for the Disease Vector Tick Species Ixodes Scapularis](/publication/genome-wide-crispr-knockout-cell-screening-platform-disease-vector-tick-species-ixodes)”. BioRxiv. doi:10.64898/2026.05.05.721418 Matthew Butnaru, William McKenna, Srishti Goswami, Alejandra Wu-Chuang, Enzo Mameli, Abigail Wilcox, Leopoldine Quennesson, Ah-Ram Kim, Austin Veal, Weihang Chen, Hugo Verzone, Elizabeth A Lane, Hanna J Laukaitis-Yousey, Chad Araneo, Nisha Singh, Joao Pedra, Yanhui Hu, Raghuvir Viswanatha, Norbert Perrimon, and Stephanie E Mohr. 2026. “[Genome-Wide CRISPR Knockout Cell Screening Platform for the Disease Vector Tick Species Ixodes Scapularis](/publication/genome-wide-crispr-knockout-cell-screening-platform-disease-vector-tick-species-ixodes)”. BioRxiv. doi:10.64898/2026.05.05.721418 - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2026/05/07/2026.05.05.721418) The black legged tick, Ixodes scapularis, is a vector of the bacterium that causes Lyme disease and several other illnesses, including anaplasmosis, babesiosis, and tick-borne encephalitis. Although high-quality genome annotations are available for I... - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2026/05/07/2026.05.05.721418) ### 2025 Baolong Xia, Ah-Ram Kim, Feimei Liu, Myeonghoon Han, Emily Stoneburner, Stephanie Makdissi, Francesca Di Cara, Stephanie E Mohr, Aaron Ring, and Norbert Perrimon. 2025. “[Phage-Displayed Synthetic Library and Screening Platform for Nanobody Discovery.](/publication/phage-displayed-synthetic-library-and-screening-platform-nanobody-discovery)”. ELife, 14. doi:10.7554/eLife.105887 Baolong Xia, Ah-Ram Kim, Feimei Liu, Myeonghoon Han, Emily Stoneburner, Stephanie Makdissi, Francesca Di Cara, Stephanie E Mohr, Aaron Ring, and Norbert Perrimon. 2025. “[Phage-Displayed Synthetic Library and Screening Platform for Nanobody Discovery.](/publication/phage-displayed-synthetic-library-and-screening-platform-nanobody-discovery)”. ELife, 14. doi:10.7554/eLife.105887 - add\_circle do\_not\_disturb\_on Abstract Nanobodies, single-domain antibodies derived from camelid heavy-chain antibodies, are known for their high affinity, stability, and small size, which make them useful in biological research and therapeutic applications. However, traditional nanobody... Justin A Bosch, Pierre Michel Jean Beltran, Cooper Cavers, James Thai LaGraff, Randy Melanson, Ankita Singh, Weihang Chen, Yanhui Hu, Sudhir Gopal Tattikota, Ying Liu, Yousuf Hashmi, John M Asara, Tess Branon, Alice Y Ting, Steven A Carr, and Norbert Perrimon. 2025. “[Multi-Omic Mapping of Protein Secretomes Reveals Tissue-Specific Origins and Inter-Organ Trafficking.](/publication/multi-omic-mapping-protein-secretomes-reveals-tissue-specific-origins-and-inter-organ)”. BioRxiv : The Preprint Server for Biology. doi:10.1101/2025.07.09.659702 Justin A Bosch, Pierre Michel Jean Beltran, Cooper Cavers, James Thai LaGraff, Randy Melanson, Ankita Singh, Weihang Chen, Yanhui Hu, Sudhir Gopal Tattikota, Ying Liu, Yousuf Hashmi, John M Asara, Tess Branon, Alice Y Ting, Steven A Carr, and Norbert Perrimon. 2025. “[Multi-Omic Mapping of Protein Secretomes Reveals Tissue-Specific Origins and Inter-Organ Trafficking.](/publication/multi-omic-mapping-protein-secretomes-reveals-tissue-specific-origins-and-inter-organ)”. BioRxiv : The Preprint Server for Biology. doi:10.1101/2025.07.09.659702 - add\_circle do\_not\_disturb\_on Abstract Secreted proteins regulate many aspects of animal biology and are attractive targets for biomarkers and therapeutics. However, comprehensively identifying the "secretome", along with their tissues of origin, remains extremely challenging. To address this... Raghuvir Viswanatha, Samuel Entwisle, Yanhui Hu, Ah-Ram Kim, Kelly Reap, Matthew Butnaru, Mujeeb Qadiri, Stephanie E Mohr, and Norbert Perrimon. 2025. “[Higher Resolution Pooled Genome-Wide CRISPR Knockout Screening in Drosophila Cells Using Integration and Anti-CRISPR (IntAC).](/publication/higher-resolution-pooled-genome-wide-crispr-knockout-screening-drosophila-cells-using-0)”. Nature Communications, 16, 1, Pp. 6498. doi:10.1038/s41467-025-61692-3 Raghuvir Viswanatha, Samuel Entwisle, Yanhui Hu, Ah-Ram Kim, Kelly Reap, Matthew Butnaru, Mujeeb Qadiri, Stephanie E Mohr, and Norbert Perrimon. 2025. “[Higher Resolution Pooled Genome-Wide CRISPR Knockout Screening in Drosophila Cells Using Integration and Anti-CRISPR (IntAC).](/publication/higher-resolution-pooled-genome-wide-crispr-knockout-screening-drosophila-cells-using-0)”. Nature Communications, 16, 1, Pp. 6498. doi:10.1038/s41467-025-61692-3 - add\_circle do\_not\_disturb\_on Abstract CRISPR screens enable systematic, scalable genotype-to-phenotype mapping. We previously developed a CRISPR screening method for Drosophila melanogaster and mosquito cell lines using plasmid transfection and site-specific integration to introduce single... Yanhui Hu, Jonathan Rodiger, Yifang Liu, Chenxi Gao, Ying Liu, Mujeeb Qadiri, Austin Veal, Martha L Bulyk, and Norbert Perrimon. 2025. “[TF2TG: An Online Resource Mining the Potential Gene Targets of Transcription Factors in Drosophila.](/publication/tf2tg-online-resource-mining-potential-gene-targets-transcription-factors-drosophila)”. Genetics. doi:10.1093/genetics/iyaf082 Yanhui Hu, Jonathan Rodiger, Yifang Liu, Chenxi Gao, Ying Liu, Mujeeb Qadiri, Austin Veal, Martha L Bulyk, and Norbert Perrimon. 2025. “[TF2TG: An Online Resource Mining the Potential Gene Targets of Transcription Factors in Drosophila.](/publication/tf2tg-online-resource-mining-potential-gene-targets-transcription-factors-drosophila)”. Genetics. doi:10.1093/genetics/iyaf082 - add\_circle do\_not\_disturb\_on Abstract Sequence-specific transcription factors (TFs) are key regulators of many biological processes, controlling the expression of their target genes through binding to the cis- regulatory regions such as promoters and enhancers. Each TF has unique DNA binding... Alejandra Wu-Chuang, Hanna J Laukaitis-Yousey, Matthew Butnaru, Stephanie E Mohr, Norbert Perrimon, and Joao H F Pedra. 2025. “[Decoding Arthropod Vector Immunology through Bona Fide Pathogens.](/publication/decoding-arthropod-vector-immunology-through-bona-fide-pathogens)”. Trends in Parasitology, 41, 5, Pp. 351-60. doi:10.1016/j.pt.2025.03.004 Alejandra Wu-Chuang, Hanna J Laukaitis-Yousey, Matthew Butnaru, Stephanie E Mohr, Norbert Perrimon, and Joao H F Pedra. 2025. “[Decoding Arthropod Vector Immunology through Bona Fide Pathogens.](/publication/decoding-arthropod-vector-immunology-through-bona-fide-pathogens)”. Trends in Parasitology, 41, 5, Pp. 351-60. doi:10.1016/j.pt.2025.03.004 - add\_circle do\_not\_disturb\_on Abstract The interrelationship between the microbiota, metabolism, and the arthropod immune system has evolved to maintain physiological equilibrium. Arthropods rely on this delicate balance when encountering fitness challenges. The understanding of life history... Yanhui Hu, Jonathan Rodiger, Yifang Liu, Chenxi Gao, Ying Liu, Mujeeb Qadiri, Austin Veal, Martha L Bulyk, and Norbert Perrimon. 2025. “[TF2TG: An Online Resource Mining the Potential Gene Targets of Transcription Factors in .](/publication/tf2tg-online-resource-mining-potential-gene-targets-transcription-factors)”. BioRxiv : The Preprint Server for Biology. doi:10.1101/2025.02.13.638157 Yanhui Hu, Jonathan Rodiger, Yifang Liu, Chenxi Gao, Ying Liu, Mujeeb Qadiri, Austin Veal, Martha L Bulyk, and Norbert Perrimon. 2025. “[TF2TG: An Online Resource Mining the Potential Gene Targets of Transcription Factors in .](/publication/tf2tg-online-resource-mining-potential-gene-targets-transcription-factors)”. BioRxiv : The Preprint Server for Biology. doi:10.1101/2025.02.13.638157 - add\_circle do\_not\_disturb\_on Abstract Sequence-specific transcription factors (TFs) are key regulators of many biological processes, controlling the expression of their target genes through binding to the cis- regulatory regions such as promoters and enhancers. Each TF has unique DNA binding... Ben Ewen-Campen, Neha Joshi, Ashley Suraj Hermon, Tanuj Thakkar, Jonathan Zirin, and Norbert Perrimon. 2025. “[A Collection of Split-Gal4 Drivers Targeting Conserved Signaling Ligands in Drosophila.](/publication/collection-split-gal4-drivers-targeting-conserved-signaling-ligands-drosophila)”. G3 (Bethesda, Md.), 15, 2. doi:10.1093/g3journal/jkae276 Ben Ewen-Campen, Neha Joshi, Ashley Suraj Hermon, Tanuj Thakkar, Jonathan Zirin, and Norbert Perrimon. 2025. “[A Collection of Split-Gal4 Drivers Targeting Conserved Signaling Ligands in Drosophila.](/publication/collection-split-gal4-drivers-targeting-conserved-signaling-ligands-drosophila)”. G3 (Bethesda, Md.), 15, 2. doi:10.1093/g3journal/jkae276 - add\_circle do\_not\_disturb\_on Abstract Communication between cells in metazoan organisms is mediated by a remarkably small number of highly conserved signaling pathways. Given this small number of signaling pathways, the existence of multiple related ligands for many of these pathways... Mujeeb Qadiri, Ying Liu, Ah-Ram Kim, Myeonghoon Han, Eric Zhou, Austin Veal, Tzu-Chiao Lu, Hongjie Li, Yanhui Hu, and Norbert Perrimon. 2025. “[FlyPhoneDB2: A Computational Framework for Analyzing Cell-Cell Communication in ScRNA-Seq Data Integrating AlphaFold-Multimer Predictions.](/publication/flyphonedb2-computational-framework-analyzing-cell-cell-communication-scrna-seq-data)”. Computational and Structural Biotechnology Journal, 27, Pp. 2814-22. doi:10.1016/j.csbj.2025.06.032 Mujeeb Qadiri, Ying Liu, Ah-Ram Kim, Myeonghoon Han, Eric Zhou, Austin Veal, Tzu-Chiao Lu, Hongjie Li, Yanhui Hu, and Norbert Perrimon. 2025. “[FlyPhoneDB2: A Computational Framework for Analyzing Cell-Cell Communication in ScRNA-Seq Data Integrating AlphaFold-Multimer Predictions.](/publication/flyphonedb2-computational-framework-analyzing-cell-cell-communication-scrna-seq-data)”. Computational and Structural Biotechnology Journal, 27, Pp. 2814-22. doi:10.1016/j.csbj.2025.06.032 - add\_circle do\_not\_disturb\_on Abstract Cell-cell communication (CCC) plays a critical role in the physiological regulation of organisms and has been implicated in numerous diseases. Previously, we introduced FlyPhoneDB, a tool designed to explore CCC in single-cell RNA-sequencing datasets... Yanhui Hu, Aram Comjean, Jonathan Rodiger, Weihang Chen, Ah-Ram Kim, Mujeeb Qadiri, Chenxi Gao, Jonathan Zirin, Stephanie E Mohr, and Norbert Perrimon. 2025. “[FlyRNAi.Org 2025 Update-Expanded Resources for New Technologies and Species.](/publication/flyrnaiorg-2025-update-expanded-resources-new-technologies-and-species-0)”. Nucleic Acids Research, 53, D1, Pp. D958-D965. doi:10.1093/nar/gkae917 Yanhui Hu, Aram Comjean, Jonathan Rodiger, Weihang Chen, Ah-Ram Kim, Mujeeb Qadiri, Chenxi Gao, Jonathan Zirin, Stephanie E Mohr, and Norbert Perrimon. 2025. “[FlyRNAi.Org 2025 Update-Expanded Resources for New Technologies and Species.](/publication/flyrnaiorg-2025-update-expanded-resources-new-technologies-and-species-0)”. Nucleic Acids Research, 53, D1, Pp. D958-D965. doi:10.1093/nar/gkae917 - add\_circle do\_not\_disturb\_on Abstract The design, analysis and mining of large-scale 'omics studies with the goal of advancing biological and biomedical understanding require use of a range of bioinformatics tools, including approaches tailored to needs specific to a given species and/or... ### 2024 Yanhui Hu, Aram Comjean, Jonathan Rodiger, Weihang Chen, Ah-Ram Kim, Mujeeb Qadiri, Chenxi Gao, Jonathan Zirin, Stephanie E Mohr, and Norbert Perrimon. 2024. “[FlyRNAi.Org 2025 Update-Expanded Resources for New Technologies and Species.](/publication/flyrnaiorg-2025-update-expanded-resources-new-technologies-and-species)”. Nucleic Acids Research. doi:10.1093/nar/gkae917 Yanhui Hu, Aram Comjean, Jonathan Rodiger, Weihang Chen, Ah-Ram Kim, Mujeeb Qadiri, Chenxi Gao, Jonathan Zirin, Stephanie E Mohr, and Norbert Perrimon. 2024. “[FlyRNAi.Org 2025 Update-Expanded Resources for New Technologies and Species.](/publication/flyrnaiorg-2025-update-expanded-resources-new-technologies-and-species)”. Nucleic Acids Research. doi:10.1093/nar/gkae917 - add\_circle do\_not\_disturb\_on Abstract The design, analysis and mining of large-scale 'omics studies with the goal of advancing biological and biomedical understanding require use of a range of bioinformatics tools, including approaches tailored to needs specific to a given species and/or... Enzo Mameli, George-Rafael Samantsidis, Raghuvir Viswanatha, Hyeogsun Kwon, David R Hall, Matthew Butnaru, Yanhui Hu, Stephanie E Mohr, Norbert Perrimon, and Ryan C Smith. 2024. “[A Genome-Wide CRISPR Screen in Mosquito Cells Identifies Essential Genes and Required Components of Clodronate Liposome Function.](/publication/genome-wide-crispr-screen-mosquito-cells-identifies-essential-genes-and-required)”. BioRxiv : The Preprint Server for Biology. doi:10.1101/2024.09.24.614595 Enzo Mameli, George-Rafael Samantsidis, Raghuvir Viswanatha, Hyeogsun Kwon, David R Hall, Matthew Butnaru, Yanhui Hu, Stephanie E Mohr, Norbert Perrimon, and Ryan C Smith. 2024. “[A Genome-Wide CRISPR Screen in Mosquito Cells Identifies Essential Genes and Required Components of Clodronate Liposome Function.](/publication/genome-wide-crispr-screen-mosquito-cells-identifies-essential-genes-and-required)”. BioRxiv : The Preprint Server for Biology. doi:10.1101/2024.09.24.614595 - add\_circle do\_not\_disturb\_on Abstract mosquitoes are the sole vector of human malaria, the most burdensome vector-borne disease worldwide. Strategies aimed at reducing mosquito populations and limiting their ability to transmit disease show the most promise for disease control. Therefore... - Previous page chevron\_left - [1](?page=0 "Current page") - [2](?page=1 "Go to page 2") - [3](?page=2 "Go to page 3") - [ Last page 19 ](?page=18 "Go to last page") - [ Next page chevron\_right ](?page=1 "Go to next page")