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TIRE-seq simplifies transcriptomics via integrated RNA capture and library preparation O'Keeffe, Piper; Nouri, Yasmin; Saw, Hui Shi; Moore, Zachery; Baldwin, Tracey M.; Olechnowicz, Sam W. Z.; Jabbari, Jafar S.; Squire, David McG; Leslie, Stephen; Wang, Changqing; You, Yupei; Ritchie, Matthew E.; Cross, Ryan S.; Jenkins, Misty R.; Audiger, Cindy; Naik, Shalin H.; Whittle, James R.; Freytag, Saskia; Best, Sarah A.; Hickey, Peter F.; Amann-Zalcenstein, Daniela; Bowden, Rory; Brown, Daniel V. Share Save
Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset Du, Mei R. M.; Wang, Changqing; Law, Charity W.; Amann-Zalcenstein, Daniela; Anttila, Casey J. A.; Ling, Ling; Hickey, Peter F.; Sargeant, Callum J.; Chen, Yunshun; Ioannidis, Lisa J.; Rajasekhar, Pradeep; Yip, Raymond K. H.; Rogers, Kelly L.; Hansen, Diana S.; Bowden, Rory; Ritchie, Matthew E. Share Save
An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing Zeglinski, Kathleen; Montellese, Christian; Ritchie, Matthew E.; Alhamdoosh, Monther; Vonarburg, Cedric; Bowden, Rory; Jordi, Monika; Gouil, Quentin; Aeschimann, Florian; Hsu, Arthur Share Save
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing Gocuk, Sena A.; Lancaster, James; Su, Shian; Jolly, Jasleen K.; Edwards, Thomas L.; Hickey, Doron G.; Ritchie, Matthew E.; Blewitt, Marnie E.; Ayton, Lauren N.; Gouil, Quentin Share Save
Establishment of single-cell transcriptional states during seed germination Liew, Lim Chee; You, Yue; Auroux, Lucas; Oliva, Marina; Peirats-Llobet, Marta; Ng, Sophia; Tamiru-Oli, Muluneh; Berkowitz, Oliver; Hong, Uyen Vu Thuy; Haslem, Asha; Stuart, Tim; Ritchie, Matthew E.; Bassel, George W.; Lister, Ryan; Whelan, James; Gouil, Quentin; Lewsey, Mathew G. Share Save
Systematic comparison of sequencing-based spatial transcriptomic methods You, Yue; Fu, Yuting; Li, Lanxiang; Zhang, Zhongmin; Jia, Shikai; Lu, Shihong; Ren, Wenle; Liu, Yifang; Xu, Yang; Liu, Xiaojing; Jiang, Fuqing; Peng, Guangdun; Sampath Kumar, Abhishek; Ritchie, Matthew E.; Liu, Xiaodong; Tian, Luyi Share Save
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Pardo-Palacios, Francisco J.; Wang, Dingjie; Reese, Fairlie; Diekhans, Mark; Carbonell-Sala, Silvia; Williams, Brian; Loveland, Jane E.; De Maria, Maite; Adams, Matthew S.; Balderrama-Gutierrez, Gabriela; Behera, Amit K.; Gonzalez Martinez, Jose M.; Hunt, Toby; Lagarde, Julien; Liang, Cindy E.; Li, Haoran; Meade, Marcus Jerryd; Moraga Amador, David A.; Prjibelski, Andrey D.; Birol, Inanc; Bostan, Hamed; Brooks, Ashley M.; Celik, Muhammed Hasan; Chen, Ying; Du, Mei R. M.; Felton, Colette; Goeke, Jonathan; Hafezqorani, Saber; Herwig, Ralf; Kawaji, Hideya; Lee, Joseph; Li, Jian-Liang; Lienhard, Matthias; Mikheenko, Alla; Mulligan, Dennis; Nip, Ka Ming; Pertea, Mihaela; Ritchie, Matthew E.; Sim, Andre D.; Tang, Alison D.; Wan, Yuk Kei; Wang, Changqing; Wong, Brandon Y.; Yang, Chen; Barnes, If; Berry, Andrew E.; Capella-Gutierrez, Salvador; Cousineau, Alyssa; Dhillon, Namrita; Fernandez-Gonzalez, Jose M.; Ferrandez-Peral, Luis; Garcia-Reyero, Natalia; Goetz, Stefan; Hernandez-Ferrer, Carles; Kondratova, Liudmyla; Liu, Tianyuan; Martinez-Martin, Alessandra; Menor, Carlos; Mestre-Tomas, Jorge; Mudge, Jonathan M.; Panayotova, Nedka G.; Paniagua, Alejandro; Repchevsky, Dmitry; Ren, Xingjie; Rouchka, Eric; Saint-John, Brandon; Sapena, Enrique; Sheynkman, Leon; Smith, Melissa Laird; Suner, Marie-Marthe; Takahashi, Hazuki; Youngworth, Ingrid A.; Carninci, Piero; Denslow, Nancy D.; Guigo, Roderic; Hunter, Margaret E.; Maehr, Rene; Shen, Yin; Tilgner, Hagen U.; Wold, Barbara J.; Vollmers, Christopher; Frankish, Adam; Au, Kin Fai; Sheynkman, Gloria M.; Mortazavi, Ali; Conesa, Ana; Brooks, Angela N. Share Save
An immunohistochemical atlas of necroptotic pathway expression Chiou, Shene; Al-Ani, Aysha H.; Pan, Yi; Patel, Komal M.; Kong, Isabella Y.; Whitehead, Lachlan W.; Light, Amanda; Young, Samuel N.; Barrios, Marilou; Sargeant, Callum; Rajasekhar, Pradeep; Zhu, Leah; Hempel, Anne; Lin, Ann; Rickard, James A.; Hall, Cathrine; Gangatirkar, Pradnya; Yip, Raymond K. H.; Cawthorne, Wayne; Jacobsen, Annette, V; Horne, Christopher R.; Martin, Katherine R.; Ioannidis, Lisa J.; Hansen, Diana S.; Day, Jessica; Wicks, Ian P.; Law, Charity; Ritchie, Matthew E.; Bowden, Rory; Hildebrand, Joanne M.; O'Reilly, Lorraine A.; Silke, John; Giulino-Roth, Lisa; Tsui, Ellen; Rogers, Kelly L.; Hawkins, Edwin D.; Christensen, Britt; Murphy, James M.; Samson, Andre L. Share Save
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scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor Amarasinghe, Shanika L.; Yang, Phil; Voogd, Oliver; Yang, Haoyu; Du, Mei R. M.; Su, Shian; Brown, Daniel, V; Jabbari, Jafar S.; Bowden, Rory; Ritchie, Matthew E. Share Save
Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures Dong, Xueyi; Du, Mei R. M.; Gouil, Quentin; Tian, Luyi; Jabbari, Jafar S.; Bowden, Rory; Baldoni, Pedro L.; Chen, Yunshun; Smyth, Gordon K.; Amarasinghe, Shanika L.; Law, Charity W.; Ritchie, Matthew E. Share Save
SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease Tapia del Fierro, Andres; den Hamer, Bianca; Benetti, Natalia; Jansz, Natasha; Chen, Kelan; Beck, Tamara; Vanyai, Hannah; Gurzau, Alexandra D.; Daxinger, Lucia; Xue, Shifeng; Ly, Thanh Thao Nguyen; Wanigasuriya, Iromi; Iminitoff, Megan; Breslin, Kelsey; Oey, Harald; Krom, Yvonne D.; van der Hoorn, Dinja; Bouwman, Linde F.; Johanson, Timothy M.; Ritchie, Matthew E.; Gouil, Quentin A.; Reversade, Bruno; Prin, Fabrice; Mohun, Timothy; van der Maarel, Silvere M.; Mcglinn, Edwina; Murphy, James M.; Keniry, Andrew; de Greef, Jessica C.; Blewitt, Marnie E. Share Save
Venetoclax treatment in patients with cancer has limited impact on circulating T and NK cells Teh, Charis E.; Peng, Hongke; Luo, Meng-Xiao; Tan, Tania; Trussart, Marie; Howson, Lauren J.; Chua, Chong Chyn; Muttiah, Christine; Brown, Fiona; Ritchie, Matthew E.; Wei, Andrew H.; Roberts, Andrew W.; Bryant, Vanessa L.; Anderson, Mary Ann; Lindeman, Geoffrey J.; Huang, David C. S.; Thijssen, Rachel; Gray, Daniel H. D. Share Save
Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data (vol 24, pg 107, 2023) You, Yue; Dong, Xueyi; Wee, Yong Kiat; Maxwell, Mhairi J.; Alhamdoosh, Monther; Smyth, Gordon K.; Hickey, Peter F.; Ritchie, Matthew E.; Law, Charity W. Share Save
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