Search Results - "Rayan, Nirmala Arul"

DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data by Ranjan, Bobby, Sun, Wenjie, Park, Jinyu, Mishra, Kunal, Schmidt, Florian, Xie, Ronald, Alipour, Fatemeh, Singhal, Vipul, Joanito, Ignasius, Honardoost, Mohammad Amin, Yong, Jacy Mei Yun, Koh, Ee Tzun, Leong, Khai Pang, Rayan, Nirmala Arul, Lim, Michelle Gek Liang, Prabhakar, Shyam

“…Feature selection (marker gene selection) is widely believed to improve clustering accuracy, and is thus a key component of single cell clustering pipelines…”
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Systematic immune cell dysregulation and molecular subtypes revealed by single-cell RNA-seq of subjects with type 1 diabetes by Honardoost, Mohammad Amin, Adinatha, Andreas, Schmidt, Florian, Ranjan, Bobby, Ghaeidamini, Maryam, Arul Rayan, Nirmala, Gek Liang Lim, Michelle, Joanito, Ignasius, Xiao Xuan Lin, Quy, Rajagopalan, Deepa, Qi Mok, Shi, Hwang, You Yi, Larbi, Anis, Khor, Chiea Chuen, Foo, Roger, Boehm, Bernhard Otto, Prabhakar, Shyam

“…Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting…”
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Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas by Ohka, Fumiharu, Shinjo, Keiko, Deguchi, Shoichi, Matsui, Yusuke, Okuno, Yusuke, Katsushima, Keisuke, Suzuki, Miho, Kato, Akira, Ogiso, Noboru, Yamamichi, Akane, Aoki, Kosuke, Suzuki, Hiromichi, Sato, Shinya, Arul Rayan, Nirmala, Prabhakar, Shyam, Göke, Jonathan, Shimamura, Teppei, Maruyama, Reo, Takahashi, Satoru, Suzumura, Akio, Kimura, Hiroshi, Wakabayashi, Toshihiko, Zong, Hui, Natsume, Atsushi, Kondo, Yutaka

“…Gliomas are classified by combining histopathologic and molecular features, including isocitrate dehydrogenase ( ) status. Although -wild-type diffuse…”
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Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development by Utz, Sebastian G., See, Peter, Mildenberger, Wiebke, Thion, Morgane Sonia, Silvin, Aymeric, Lutz, Mirjam, Ingelfinger, Florian, Rayan, Nirmala Arul, Lelios, Iva, Buttgereit, Anne, Asano, Kenichi, Prabhakar, Shyam, Garel, Sonia, Becher, Burkhard, Ginhoux, Florent, Greter, Melanie

“…Central nervous system (CNS) macrophages comprise microglia and border-associated macrophages (BAMs) residing in the meninges, the choroid plexus, and the…”
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Uniform, optimal signal processing of mapped deep-sequencing data by Kumar, Vibhor, Muratani, Masafumi, Rayan, Nirmala Arul, Kraus, Petra, Lufkin, Thomas, Ng, Huck Hui, Prabhakar, Shyam

“…Optimized algorithms from the field of electrical-signal processing improve the identification of genomic signals from diverse high-throughput sequencing…”
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scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data by Ranjan, Bobby, Schmidt, Florian, Sun, Wenjie, Park, Jinyu, Honardoost, Mohammad Amin, Tan, Joanna, Arul Rayan, Nirmala, Prabhakar, Shyam

“…Clustering is a crucial step in the analysis of single-cell data. Clusters identified in an unsupervised manner are typically annotated to cell types based on…”
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RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data by Schmidt, Florian, Ranjan, Bobby, Lin, Quy Xiao Xuan, Krishnan, Vaidehi, Joanito, Ignasius, Honardoost, Mohammad Amin, Nawaz, Zahid, Venkatesh, Prasanna Nori, Tan, Joanna, Rayan, Nirmala Arul, Ong, Sin Tiong, Prabhakar, Shyam

“…Abstract The transcriptomic diversity of cell types in the human body can be analysed in unprecedented detail using single cell (SC) technologies. Unsupervised…”
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Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters by Kumar, Vibhor, Rayan, Nirmala Arul, Muratani, Masafumi, Lim, Stefan, Elanggovan, Bavani, Xin, Lixia, Lu, Tess, Makhija, Harshyaa, Poschmann, Jeremie, Lufkin, Thomas, Ng, Huck Hui, Prabhakar, Shyam

“…Although over 35 different histone acetylation marks have been described, the overwhelming majority of regulatory genomics studies focus exclusively on H3K27ac…”
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Noncoding origins of anthropoid traits and a new null model of transposon functionalization by del Rosario, Ricardo C H, Rayan, Nirmala Arul, Prabhakar, Shyam

“…Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify…”
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Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease by Bardile, Costanza Ferrari, Garcia-Miralles, Marta, Caron, Nicholas S., Rayan, Nirmala Arul, Langley, Sarah R., Harmston, Nathan, Rondelli, Ana Maria, Teo, Roy Tang Yi, Waltl, Sabine, Anderson, Lisa M., Bae, Han-Gyu, Jung, Sangyong, Williams, Anna, Prabhakar, Shyam, Petretto, Enrico, Hayden, Michael R., Pouladi, Mahmoud A.

“…Whitematter abnormalities are a nearly universal pathological feature of neurodegenerative disorders including Huntington disease (HD). A long-held assumption…”
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A single-cell atlas identifies pretreatment features of primary imatinib resistance in chronic myeloid leukemia by Krishnan, Vaidehi, Schmidt, Florian, Nawaz, Zahid, Venkatesh, Prasanna Nori, Lee, Kian Leong, Ren, Xi, Chan, Zhu En, Yu, Mengge, Makheja, Meera, Rayan, Nirmala Arul, Lim, Michelle Gek Liang, Cheung, Alice Man Sze, Bari, Sudipto, Chng, Wee Joo, Than, Hein, Ouyang, John, Rackham, Owen, Tan, Tuan Zea, Hwang, William Ying Khee, Chuah, Charles, Prabhakar, Shyam, Ong, S. Tiong

“…•A high-resolution single-cell map of diagnostic CML bone marrow to annotate features of TKI resistance.•Gene expression signatures within the LSCs and NK…”
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The common marmoset genome provides insight into primate biology and evolution by Worley, Kim C, Warren, Wesley C, Rogers, Jeffrey, Locke, Devin, Muzny, Donna M, Mardis, Elaine R, Weinstock, George M, Tardif, Suzette D, Aagaard, Kjersti M, Archidiacono, Nicoletta, Wang, Qing, Warner, Crystal M, Wildman, Derek E, Witherspoon, David J, Wright, Rita A, Wu, Yuanqing, Xiao, Weimin, Xing, Jinchuan, Zhu, Baoli, Rayan, Nirmala Arul, Gibbs, Richard A, Wilson, Richard K, Batzer, Mark A, Beal, Kathryn, Brejova, Brona, Capozzi, Oronzo, Capuano, Saverio B, Casola, Claudio, Chandrabose, Mimi M, Dao, Marvin Diep, de Jong, Pieter J, del Rosario, Ricardo Cruz-Herrera, Delehaunty, Kkim D, Dinh, Huyen H, Eichler, Evan E, Fitzgerald, Stephen, Flicek, Paul, Fowler, R Gerald, Fronick, Catrina, Fulton, Lucinda A, Fulton, Robert S, Gabisi, Ramatu Ayiesha, Gerlach, Daniel, Graves, Tina A, Gunaratne, Preethi H, Hahn, Matthew W, Haig, David, Han, Yi, Harris, R Alan, Herrero, Javier, Hillier, LaDdeana W, Hubley, Robert, Jhangiani, Shalini N, Jorde, Lynn B, Joshi, Vandita, Karakor, Emre, Konkel, Miriam K, Kovar, Christie L, Kriventseva, Evgenia V, Lee, Sandra L, Liu, Yih-shin, Lopez, John, Lopez-Otin, Carlos, Mansfield, Keith G, Marques-Bonet, Tomas, Minx, Patrick, Misceo, Doriana, Moncrieff, J Scott, Morgan, Margaret B, Nazareth, Lynne V, Newsham, Irene, Nguyen, Ngoc Bich, Okwuonu, Geoffrey O, Prabhakar, Shyam, Pu, Ling-Ling, Quesada, Victor, Ranck, Megan C, Raney, Brian J, Deiros, David Rio, Rocchi, Mariano, Rodriguez, David, Ross, Corinna, Ruffier, Magali, Ruiz, San Juana, Sajjadian, Saba, Santibanez, Jireh, Schrider, Daniel R, Searle, Steve, Skaletsky, Helen, Soibam, Benjamin, Smit, Arian F A, Tennakoon, Jayantha B, Tomaska, Lubomir, Ullmer, Brygg, Vejnar, Charles E, Ventura, Mario, Vilella, Albert J, Vinar, Tomas, Vogel, Jan-Hinnerk, Walker, Jerilyn A

“…Kim Worley and colleagues report the whole-genome sequence of the common marmoset, Callithrix jacchus , the first New World monkey to be sequenced. We report…”
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Shared and unique transcriptomic signatures of antidepressant and probiotics action in the mammalian brain by Rayan, Nirmala Arul, Aow, Jonathan, Lim, Michelle Gek Liang, Arcego, Danusa Mar, Ryan, Richard, Nourbakhsh, Nooshin, de Lima, Randriely Merscher Sobreira, Craig, Kelly, Zhang, Tie Yuan, Goh, Yeek Teck, Sun, Alfred Xuyang, Tompkins, Thomas, Bronner, Stéphane, Binda, Sylvie, Diorio, Josie, Parent, Carine, Meaney, Michael J., Prabhakar, Shyam

“…Understanding the shared and divergent mechanisms across antidepressant (AD) classes and probiotics is critical for improving treatment for mood disorders…”
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Integrative multi-omics landscape of fluoxetine action across 27 brain regions reveals global increase in energy metabolism and region-specific chromatin remodelling by Rayan, Nirmala Arul, Kumar, Vibhor, Aow, Jonathan, Rastegar, Naghmeh, Lim, Michelle Gek Liang, O’Toole, Nicholas, Aliwarga, Edita, Arcego, Danusa Mar, Yeo, Hui Ting Grace, Wong, Jen Yi, Lee, May Yin, Schmidt, Florian, Haja, Hajira Shreen, Tam, Wai Leong, Zhang, Tie-Yuan, Diorio, Josie, Anacker, Christoph, Hen, Rene, Parent, Carine, Meaney, Michael J, Prabhakar, Shyam

“…Depression and anxiety are major global health burdens. Although SSRIs targeting the serotonergic system are prescribed over 200 million times annually, they…”
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A glucocorticoid-sensitive hippocampal gene network moderates the impact of early life adversity on mental health outcomes by Arcego, Danusa Mar, Buschdorf, Jan-Paul, O’Toole, Nicholas, Wang, Zihan, Barth, Barbara, Pokhvisneva, Irina, Rayan, Nirmala Arul, Patel, Sachin, José de Mendonça Filho, Euclides, Lee, Patrick, Tan, Jennifer, Koh, Ming Xuan, Sim, Chu Ming, Parent, Carine, Sobreira de Lima, Randriely Merscher, Clappison, Andrew, O’Donnel, Kieran, Dalmaz, Carla, Arloth, Janine, Provençal, Nadine, Binder, Elisabeth B., Diorio, Josie, Silveira, Patrícia Pelufo, Meaney, Michael J.

“…Early stress increases the risk for psychiatric disorders. Glucocorticoids are stress mediators that regulate transcriptional activity and morphology in the…”
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A Single-Cell Atlas Identifies Pretreatment Features of Primary Imatinib Resistance in Chronic Myeloid Leukemia by Krishnan, Vaidehi, Schmidt, Florian, Nawaz, Zahid, Lee, Kian Leong, Nori Venkatesh, Prasanna, Makheja, Meera, Chan, Zhu En, Yu, Mengge, Arul Rayan, Nirmala, Gek Liang Lim, Michelle, Cheung, Alice, Bari, Sudipto, Ouyang, John, Rackham, Owen, Tan, Tuan Zea, Hwang, William YK, Chuah, Charles, Prabhakar, Shyam, Ong, Sin Tiong

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Massive contribution of transposable elements to mammalian regulatory sequences by Rayan, Nirmala Arul, del Rosario, Ricardo C.H., Prabhakar, Shyam

“…Barbara McClintock discovered the existence of transposable elements (TEs) in the late 1940s and initially proposed that they contributed to the gene…”
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Sex and cell-specific gene expression in corticolimbic brain regions associated with psychiatric disorders revealed by bulk and single-nuclei RNA sequencing by Fitzgerald, Eamon, Arcego, Danusa Mar, Shen, Mo Jun, O'Toole, Nicholas, Wen, Xianglan, Nagy, Corina, Mostafavi, Sara, Craig, Kelly, Silveira, Patricia Pelufo, Rayan, Nirmala Arul, Diorio, Josie, Meaney, Michael J., Zhang, Tie-Yuan

“…There are sex-specific differences in the prevalence, symptomology and course of psychiatric disorders. However, preclinical models have primarily used males,…”
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Sex and cell-specific gene expression in corticolimbic brain regions associated with psychiatric disorders revealed by bulk and single-nuclei RNA sequencingResearch in context by Eamon Fitzgerald, Danusa Mar Arcego, Mo Jun Shen, Nicholas O'Toole, Xianglan Wen, Corina Nagy, Sara Mostafavi, Kelly Craig, Patricia Pelufo Silveira, Nirmala Arul Rayan, Josie Diorio, Michael J. Meaney, Tie-Yuan Zhang

“…Background: There are sex-specific differences in the prevalence, symptomology and course of psychiatric disorders. However, preclinical models have primarily…”
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Histone acetylome-wide associations in immune cells from individuals with active Mycobacterium tuberculosis infection by del Rosario, Ricardo C. H., Poschmann, Jeremie, Lim, Carey, Cheng, Catherine Y., Kumar, Pavanish, Riou, Catherine, Ong, Seow Theng, Gerges, Sherif, Hajan, Hajira Shreen, Kumar, Dilip, Marzuki, Mardiana, Lu, Xiaohua, Lee, Andrea, Wijaya, Giovani Claresta, Rayan, Nirmala Arul, Zhuang, Zhong, Du Bruyn, Elsa, Chee, Cynthia Bin Eng, Lee, Bernett, Lum, Josephine, Zolezzi, Francesca, Poidinger, Michael, Rotzschke, Olaf, Khor, Chiea Chuen, Wilkinson, Robert J., Wang, Yee T., Chandy, George K, De Libero, Gennaro, Singhal, Amit, Prabhakar, Shyam

“…Host cell chromatin changes are thought to play an important role in the pathogenesis of infectious diseases. Here we describe a histone acetylome-wide…”
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