A Novel Approach for Pancreas Transcriptomics Reveals the Cellular Landscape in Homeostasis and Acute Pancreatitis, Katherine J Aney, Woo-Jeong Jeong, Andres F Vallejo, Cassandra Burdziak, Ethan Chen, Austin Wang, Pal Koak, Kellie Wise, Kirk Jensen, Dana Pe’er, Stephanie K Dougan, Luciano Martelotto, Sahar Nissim, Gastroenterology, https://doi.org/10.1053/j.gastro.2024.01.043

HAMSAB diet ameliorates dysfunctional signaling in pancreatic islets in autoimmune diabetes, Valerie Vandenbempt, Sema Elif Eski, Manoja K Brahma, Ao Li, Javier Negueruela, Ylke Bruggeman, Stéphane Demine, Peng Xiao, Alessandra K Cardozo, Nicolas Baeyens, Luciano G Martelotto, Sumeet Pal Singh, Eliana Mariño, Conny Gysemans, Esteban N Gurzov, Iscience, https://doi.org/10.1016/j.isci.2023.108694

A machine learning one-class logistic regression model to predict stemness for single cell transcriptomics and spatial omics, Felipe Segato Dezem, Maycon Marção, Bassem Ben-Cheikh, Nadya Nikulina, Ayodele Omotoso, Destiny Burnett, Priscila Coelho, Judith Hurley, Carmen Gomez, Tien Phan-Everson, Giang Ong, Luciano Martelotto, Zachary R Lewis, Sophia George, Oliver Braubach, Tathiane M Malta, Jasmine Plummer, BMC genomics, https://doi.org/10.1186/s12864-023-09722-6

Koverage: Read-coverage analysis for massive (meta) genomics datasets, Michael J Roach, Bradley J Hart, Sarah J Beecroft, Bhavya Papudeshi, Laura K Inglis, Susanna R Grigson, Vijini Mallawaarachchi, George Bouras, Robert A Edwards, Journal of Open Source Software, https://doi.org/10.21105/joss.06235

Ligand-dependent hedgehog signaling maintains an undifferentiated, malignant osteosarcoma phenotype, Vijesh G Vaghjiani, Catherine R Cochrane, W Samantha N Jayasekara, Wai Chin Chong, Anette Szczepny, Beena Kumar, Luciano G Martelotto, Andrew McCaw, Kirstyn Carey, Maya Kansara, David M Thomas, Carl Walkley, Stuart Mudge, Daniel J Gough, Peter A Downie, Craig D Peacock, William Matsui, D Neil Watkins, Jason E Cain, Oncogene, https://doi.org/10.1038/s41388-023-02864-7

Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals, Vanessa Tsui, Ruqian Lyu, Stevan Novakovic, Jessica M Stringer, Jessica EM Dunleavy, Elissah Granger, Tim Semple, Anna Leichter, Luciano G Martelotto, D Jo Merriner, Ruijie Liu, Lucy McNeill, Nadeen Zerafa, Eva R Hoffmann, Moira K O’Bryan, Karla Hutt, Andrew J Deans, Jörg Heierhorst, Davis J McCarthy, Wayne Crismani, Cell Genomics, https://doi.org/10.1016/j.xgen.2023.100349

Systematic benchmarking of single-cell ATAC-sequencing protocols, Florian V De Rop, Gert Hulselmans, Chris Flerin, Paula Soler-Vila, Albert Rafels, Valerie Christiaens, Carmen Bravo González-Blas, Domenica Marchese, Ginevra Caratù, Suresh Poovathingal, Orit Rozenblatt-Rosen, Michael Slyper, Wendy Luo, Christoph Muus, Fabiana Duarte, Rojesh Shrestha, S Tansu Bagdatli, M Ryan Corces, Lira Mamanova, Andrew Knights, Kerstin B Meyer, Ryan Mulqueen, Akram Taherinasab, Patrick Maschmeyer, Jörn Pezoldt, Camille Lucie Germaine Lambert, Marta Iglesias, Sebastián R Najle, Zain Y Dossani, Luciano G Martelotto, Zach Burkett, Ronald Lebofsky, José Ignacio Martin-Subero, Satish Pillai, Arnau Sebé-Pedrós, Bart Deplancke, Sarah A Teichmann, Leif S Ludwig, Theodore P Braun, Andrew C Adey, William J Greenleaf, Jason D Buenrostro, Aviv Regev, Stein Aerts, Holger Heyn, Nature biotechnology, https://doi.org/10.1038/s41587-023-01881-x

Type I interferon dynamics determines memory B cell epigenetic identity in chronic viral infection, Lucy Cooper, Hui Xu, Jack Polmear, Christopher Szeto, Ee Shan Pang, Mansi Gupta, Justin J Taylor, Katherine JL Jackson, Angela Nguyen, Nicole La Gruta, Luciano Martelotto, Ian A Parish, Meredith O’Keeffe, Christopher D Scharer, Stephanie Gras, Kim L Good-Jacobson, BioRxiv, https://doi.org/10.1101/2023.03.02.530850

Single-cell gene expression links SARS-CoV-2 infection and gut serotonin, Alyce M Martin, Michael Roach, Lauren A Jones, Daniel Thorpe, Rosemary A Coleman, Caitlin Allman, Robert Edwards, Damien J Keating, Gut, https://doi.org/10.1136/gutjnl-2022-328262

Non-genetic determinants of malignant clonal fitness at single-cell resolution, Katie A Fennell, Dane Vassiliadis, Enid YN Lam, Luciano G Martelotto, Jesse J Balic, Sebastian Hollizeck, Tom S Weber, Timothy Semple, Qing Wang, Denise C Miles, Laura MacPherson, Yih-Chih Chan, Andrew A Guirguis, Lev M Kats, Emily S Wong, Sarah-Jane Dawson, Shalin H Naik, Mark A Dawson, Nature, https://doi.org/10.1038/s41586-021-04206-7

RNA-chromatin interactions: Biology, mechanism, disease and therapeutics, Prabhu Mathiyalagan, Luciano G Martelotto, Samir Ounzain, Assam El-Osta, Shizuka Uchida, Frontiers in Genetics, https://doi.org/10.3389/fgene.2022.1069427

STOmics-GenX: CRISPR based approach to improve cell identity specific gene detection from spatially resolved transcriptomics, Jennifer Currenti, Liang Qiao, Rhea Pai, Saurabh Gupta, Costerwell Khyriem, Kellie Wise, Xiaohuan Sun, Jon Armstrong, Jordan Crane, Smita Pathak, Bicheng Yang, Jacob George, Jasmine Plummer, Luciano Martelotto, Ankur Sharma, bioRxiv, https://doi.org/10.1101/2022.12.08.519589

Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution, Charles A Herring, Rebecca K Simmons, Saskia Freytag, Daniel Poppe, Joel JD Moffet, Jahnvi Pflueger, Sam Buckberry, Dulce B Vargas-Landin, Olivier Clément, Enrique Goñi Echeverría, Gavin J Sutton, Alba Alvarez-Franco, Rui Hou, Christian Pflueger, Kerrie McDonald, Jose M Polo, Alistair RR Forrest, Anna K Nowak, Irina Voineagu, Luciano Martelotto, Ryan Lister, Cell, https://doi.org/10.1016/j.cell.2022.09.039

Paraspeckle subnuclear bodies depend on dynamic heterodimerisation of DBHS RNA-binding proteins via their structured domains, Pei Wen Lee, Andrew C Marshall, Gavin J Knott, Simon Kobelke, Luciano Martelotto, Ellie Cho, Paul J McMillan, Mihwa Lee, Charles S Bond, Archa H Fox, Journal of Biological Chemistry, https://doi.org/10.1016/j.jbc.2022.102563

Single-nuclei and bulk-tissue gene-expression analysis of pheochromocytoma and paraganglioma links disease subtypes with tumor microenvironment, Magnus Zethoven, Luciano Martelotto, Andrew Pattison, Blake Bowen, Shiva Balachander, Aidan Flynn, Fernando J Rossello, Annette Hogg, Julie A Miller, Zdenek Frysak, Sean Grimmond, Lauren Fishbein, Arthur S Tischler, Anthony J Gill, Rodney J Hicks, Patricia LM Dahia, Roderick Clifton-Bligh, Karel Pacak, Richard W Tothill, Nature Communications, https://doi.org/10.1038/s41467-022-34011-3

SSNIP-seq: A simple and rapid method for isolation of single-sperm nucleic acid for high-throughput sequencing, Stevan Novakovic, Vanessa Tsui, Tim Semple, Luciano Martelotto, Davis J McCarthy, Wayne Crismani, Plos one, https://doi.org/10.1371/journal.pone.0275168

Inhibition of mutant IDH1 promotes cycling of acute myeloid leukemia stem cells, Emily Gruber, Joan So, Alexander C Lewis, Rheana Franich, Rachel Cole, Luciano G Martelotto, Amy J Rogers, Eva Vidacs, Peter Fraser, Kym Stanley, Lisa Jones, Anna Trigos, Niko Thio, Jason Li, Brandon Nicolay, Scott Daigle, Adriana E Tron, Marc L Hyer, Jake Shortt, Ricky W Johnstone, Lev M Kats, Cell Reports, https://doi.org/10.1016/j.celrep.2022.111182

Epigenetic activation of plasmacytoid DCs drives IFNAR-dependent therapeutic differentiation of AML, Jessica M Salmon, Izabela Todorovski, Kym L Stanley, Claudia Bruedigam, Conor J Kearney, Luciano G Martelotto, Fernando Rossello, Timothy Semple, Gisela Mir Arnau, Magnus Zethoven, Michael Bots, Stefan Bjelosevic, Leonie A Cluse, Peter J Fraser, Veronique Litalien, Eva Vidacs, Kate McArthur, Antony Y Matthews, Elise Gressier, Nicole A De Weerd, Jens Lichte, Madison J Kelly, Simon J Hogg, Paul J Hertzog, Lev M Kats, Stephin J Vervoort, Daniel D De Carvalho, Stefanie Scheu, Sammy Bedoui, Benjamin T Kile, Steven W Lane, Andrew C Perkins, Andrew H Wei, Pilar M Dominguez, Ricky W Johnstone, Cancer Discovery, https://doi.org/10.1158/2159-8290.CD-20-1145

Discovery of embryonically derived bipotent endothelial-macrophage progenitor cells in postnatal aorta, Anna E Williamson, Sanuri Liyanage, Mohammadhossein Hassanshahi, Malathi SI Dona, Toledo-Flores Deborah, Dang XA Tran, Catherine Dimasi, Nisha Schwarz, Sanuja Fernando, Thalia Salagaras, Long Aaron, Jan Kazenwadel, Natasha L Harvey, Grant R Drummond, Antony Vinh, Vashe Chandrakanthan, Ashish Misra, Zoltan Neufeld, Joanne TM Tan, Luciano Martelotto, Jose M Polo, Claudine S Bonder, Alexander R Pinto, Shiwani Sharma, Stephen J Nicholls, Christina A Bursill, Peter J Psaltis, bioRxiv, https://doi.org/10.1101/2021.10.18.464001

CDK4/6 inhibition promotes antitumor immunity through the induction of T-cell memory, Emily J Lelliott, Isabella Y Kong, Magnus Zethoven, Kelly M Ramsbottom, Luciano G Martelotto, Deborah Meyran, Joe Jiang Zhu, Matteo Costacurta, Laura Kirby, Jarrod J Sandow, Lydia Lim, Pilar M Dominguez, Izabela Todorovski, Nicole M Haynes, Paul A Beavis, Paul J Neeson, Edwin D Hawkins, Grant A McArthur, Ian A Parish, Ricky W Johnstone, Jane Oliaro, Karen E Sheppard, Conor J Kearney, Stephin J Vervoort, Cancer discovery, https://doi.org/10.1158/2159-8290.CD-20-1554

γδ T cells in merkel cell carcinomas have a proinflammatory profile prognostic of patient survival, Nicholas A Gherardin, Kelly Waldeck, Alex Caneborg, Luciano G Martelotto, Shiva Balachander, Magnus Zethoven, Pasquale M Petrone, Andrew Pattison, James S Wilmott, Sergio M Quiñones-Parra, Fernando Rossello, Atara Posner, Annie Wong, Alison M Weppler, Kerwin F Shannon, Angela Hong, Peter M Ferguson, Valerie Jakrot, Jeanette Raleigh, Athena Hatzimihalis, Paul J Neeson, Paolo Deleso, Meredith Johnston, Margaret Chua, Juergen C Becker, Shahneen Sandhu, Grant A McArthur, Anthony J Gill, Richard A Scolyer, Rodney J Hicks, Dale I Godfrey, Richard W Tothill, Cancer immunology research, https://doi.org/10.1158/2326-6066.CIR-20-0817

Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance, Mayura V Wagle, Stephin J Vervoort, Madison J Kelly, Willem Van Der Byl, Timothy J Peters, Ben P Martin, Luciano G Martelotto, Simone Nüssing, Kelly M Ramsbottom, James R Torpy, Deborah Knight, Sinead Reading, Kevin Thia, Lisa A Miosge, Debbie R Howard, Renee Gloury, Sarah S Gabriel, Daniel T Utzschneider, Jane Oliaro, Jonathan D Powell, Fabio Luciani, Joseph A Trapani, Ricky W Johnstone, Axel Kallies, Christopher C Goodnow, Ian A Parish, Nature communications, https://doi.org/10.1038/s41467-021-23044-9

Prevalence and potential biological role of TERT amplifications in ALK translocated adenocarcinoma of the lung, Christina Alidousty, Nicolai Duerbaum, Svenja Wagener‐Ryczek, Till Baar, Luciano G Martelotto, Carina Heydt, Janna Siemanowski, Barbara Holz, Elke Binot, Jana Fassunke, Sabine Merkelbach‐Bruse, Jürgen Wolf, Anna Kron, Reinhard Buettner, Anne M Schultheis, Histopathology, https://doi.org/10.1111/his.14256

SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells, Conor J Kearney, Stephin J Vervoort, Kelly M Ramsbottom, Izabela Todorovski, Emily J Lelliott, Magnus Zethoven, Lizzy Pijpers, Ben P Martin, Timothy Semple, Luciano Martelotto, Joseph A Trapani, Ian A Parish, Nichollas E Scott, Jane Oliaro, Ricky W Johnstone, Science advances, https://doi.org/10.1126/sciadv.abe3610

Combined BRAF, MEK, and CDK4/6 inhibition depletes intratumoral immune-potentiating myeloid populations in melanoma, Emily J Lelliott, Stefano Mangiola, Kelly M Ramsbottom, Magnus Zethoven, Lydia Lim, Peter KH Lau, Amanda J Oliver, Luciano G Martelotto, Laura Kirby, Claire Martin, Riyaben P Patel, Alison Slater, Carleen Cullinane, Anthony T Papenfuss, Nicole M Haynes, Grant A McArthur, Jane Oliaro, Karen E Sheppard, Cancer Immunology Research, https://doi.org/10.1158/2326-6066.CIR-20-0401