Search Results - "Jabbari, Jafar S"

Benchmarking UMI-based single-cell RNA-seq preprocessing workflows by You, Yue, Tian, Luyi, Su, Shian, Dong, Xueyi, Jabbari, Jafar S, Hickey, Peter F, Ritchie, Matthew E

“…Single-cell RNA-sequencing (scRNA-seq) technologies and associated analysis methods have rapidly developed in recent years. This includes preprocessing…”
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Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions by Nahar, Nusrat, Tram, Greg, Jen, Freda E-C, Phillips, Zachary N, Weinert, Lucy A, Bossé, Janine T, Jabbari, Jafar S, Gouil, Quentin, Du, Mei R M, Ritchie, Matthew E, Bowden, Rory, Langford, Paul R, Tucker, Alexander W, Jennings, Michael P, Turni, Conny, Blackall, Patrick J, Atack, John M

“…Abstract Actinobacillus pleuropneumoniae is the cause of porcine pleuropneumonia, a severe respiratory tract infection that is responsible for major economic…”
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Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence by Huerlimann, Roger, Cowley, Jeff A, Wade, Nicholas M, Wang, Yinan, Kasinadhuni, Naga, Chan, Chon-Kit Kenneth, Jabbari, Jafar S, Siemering, Kirby, Gordon, Lavinia, Tinning, Matthew, Montenegro, Juan D, Maes, Gregory E, Sellars, Melony J, Coman, Greg J, McWilliam, Sean, Zenger, Kyall R, Khatkar, Mehar S, Raadsma, Herman W, Donovan, Dallas, Krishna, Gopala, Jerry, Dean R

“…Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms…”
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scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor by 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

“…Abstract scPipe is a flexible R/Bioconductor package originally developed to analyse platform-independent single-cell RNA-Seq data. To expand its preprocessing…”
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The First Genetic Map for a Psoraleoid Legume (Bituminaria bituminosa) Reveals Highly Conserved Synteny with Phaseoloid Legumes by Nelson, Matthew N., Jabbari, Jafar S., Turakulov, Rust, Pradhan, Aneeta, Pazos-Navarro, Maria, Stai, Jacob S., Cannon, Steven B., Real, Daniel

“…We present the first genetic map of tedera (Bituminaria bituminosa (L.) C.H. Stirton), a drought-tolerant forage legume from the Canary Islands with useful…”
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Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments by Tian, Luyi, Dong, Xueyi, Freytag, Saskia, Lê Cao, Kim-Anh, Su, Shian, JalalAbadi, Abolfazl, Amann-Zalcenstein, Daniela, Weber, Tom S., Seidi, Azadeh, Jabbari, Jafar S., Naik, Shalin H., Ritchie, Matthew E.

“…Single cell RNA-sequencing (scRNA-seq) technology has undergone rapid development in recent years, leading to an explosion in the number of tailored data…”
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High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS) by Yin, Danqing, Ritchie, Matthew E., Jabbari, Jafar S., Beck, Tamara, Blewitt, Marnie E., Keniry, Andrew

“…Reduced representation bisulfite sequencing (RRBS) provides an efficient method for measuring DNA methylation at single base resolution in regions of high CpG…”
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A single‐cell transcriptome atlas of the adult human retina by Lukowski, Samuel W, Lo, Camden Y, Sharov, Alexei A, Nguyen, Quan, Fang, Lyujie, Hung, Sandy SC, Zhu, Ling, Zhang, Ting, Grünert, Ulrike, Nguyen, Tu, Senabouth, Anne, Jabbari, Jafar S, Welby, Emily, Sowden, Jane C, Waugh, Hayley S, Mackey, Adrienne, Pollock, Graeme, Lamb, Trevor D, Wang, Peng‐Yuan, Hewitt, Alex W, Gillies, Mark C, Powell, Joseph E, Wong, Raymond CB

“…The retina is a specialized neural tissue that senses light and initiates image processing. Although the functional organization of specific retina cells has…”
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Single-cell multiomics reveal the scale of multilayered adaptations enabling CLL relapse during venetoclax therapy by Thijssen, Rachel, Tian, Luyi, Anderson, Mary Ann, Flensburg, Christoffer, Jarratt, Andrew, Garnham, Alexandra L., Jabbari, Jafar S., Peng, Hongke, Lew, Thomas E., Teh, Charis E., Gouil, Quentin, Georgiou, Angela, Tan, Tania, Djajawi, Tirta M., Tam, Constantine S., Seymour, John F., Blombery, Piers, Gray, Daniel H.D., Majewski, Ian J., Ritchie, Matthew E., Roberts, Andrew W., Huang, David C.S.

“…•Multiple independent but recurring genetic and epigenetic changes drive venetoclax resistance, with marked NF-κB activation ubiquitous.•NF-κB activation is…”
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Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures by 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.

“…The lack of benchmark data sets with inbuilt ground-truth makes it challenging to compare the performance of existing long-read isoform detection and…”
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Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing by Tian, Luyi, Jabbari, Jafar S, Thijssen, Rachel, Gouil, Quentin, Amarasinghe, Shanika L, Voogd, Oliver, Kariyawasam, Hasaru, Du, Mei R M, Schuster, Jakob, Wang, Changqing, Su, Shian, Dong, Xueyi, Law, Charity W, Lucattini, Alexis, Prawer, Yair David Joseph, Collar-Fernández, Coralina, Chung, Jin D, Naim, Timur, Chan, Audrey, Ly, Chi Hai, Lynch, Gordon S, Ryall, James G, Anttila, Casey J A, Peng, Hongke, Anderson, Mary Ann, Flensburg, Christoffer, Majewski, Ian, Roberts, Andrew W, Huang, David C S, Clark, Michael B, Ritchie, Matthew E

“…A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational…”
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Single cell RNA sequencing of stem cell-derived retinal ganglion cells by Daniszewski, Maciej, Senabouth, Anne, Nguyen, Quan H., Crombie, Duncan E., Lukowski, Samuel W., Kulkarni, Tejal, Sluch, Valentin M., Jabbari, Jafar S., Chamling, Xitiz, Zack, Donald J., Pébay, Alice, Powell, Joseph E., Hewitt, Alex W.

“…We used single cell sequencing technology to characterize the transcriptomes of 1,174 human embryonic stem cell-derived retinal ganglion cells (RGCs) at the…”
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Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition by Hogg, Simon J., Motorna, Olga, Cluse, Leonie A., Johanson, Timothy M., Coughlan, Hannah D., Raviram, Ramya, Myers, Robert M., Costacurta, Matteo, Todorovski, Izabela, Pijpers, Lizzy, Bjelosevic, Stefan, Williams, Tobias, Huskins, Shannon N., Kearney, Conor J., Devlin, Jennifer R., Fan, Zheng, Jabbari, Jafar S., Martin, Ben P., Fareh, Mohamed, Kelly, Madison J., Dupéré-Richer, Daphné, Sandow, Jarrod J., Feran, Breon, Knight, Deborah, Khong, Tiffany, Spencer, Andrew, Harrison, Simon J., Gregory, Gareth, Wickramasinghe, Vihandha O., Webb, Andrew I., Taberlay, Phillippa C., Bromberg, Kenneth D., Lai, Albert, Papenfuss, Anthony T., Smyth, Gordon K., Allan, Rhys S., Licht, Jonathan D., Landau, Dan A., Abdel-Wahab, Omar, Shortt, Jake, Vervoort, Stephin J., Johnstone, Ricky W.

“…To separate causal effects of histone acetylation on chromatin accessibility and transcriptional output, we used integrated epigenomic and transcriptomic…”
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Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus by Frazier, Ann E, Compton, Alison G, Kishita, Yoshihito, Hock, Daniella H, Welch, AnneMarie E, Amarasekera, Sumudu S C, Rius, Rocio, Formosa, Luke E, Imai-Okazaki, Atsuko, Francis, David, Wang, Min, Lake, Nicole J, Tregoning, Simone, Jabbari, Jafar S, Lucattini, Alexis, Nitta, Kazuhiro R, Ohtake, Akira, Murayama, Kei, Amor, David J, McGillivray, George, Wong, Flora Y, van der Knaap, Marjo S, Jeroen Vermeulen, R, Wiltshire, Esko J, Fletcher, Janice M, Lewis, Barry, Baynam, Gareth, Ellaway, Carolyn, Balasubramaniam, Shanti, Bhattacharya, Kaustuv, Freckmann, Mary-Louise, Arbuckle, Susan, Rodriguez, Michael, Taft, Ryan J, Sadedin, Simon, Cowley, Mark J, Minoche, André E, Calvo, Sarah E, Mootha, Vamsi K, Ryan, Michael T, Okazaki, Yasushi, Stroud, David A, Simons, Cas, Christodoulou, John, Thorburn, David R

“…In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the…”
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