Challenges and recommendations to improve the installability and archival stability of omics computational tools
Mangul, Serghei, Mosqueiro, Thiago, Abdill, Richard J, Duong, Dat, Mitchell, Keith, Sarwal, Varuni, Hill, Brian, Brito, Jaqueline, Littman, Russell Jared, Statz, Benjamin, Lam, Angela Ka-Mei, Dayama, Gargi, Grieneisen, Laura, Martin, Lana S, Flint, Jonathan, Eskin, Eleazar, Blekhman, Ran
Published in PLoS biology (20.06.2019)
Published in PLoS biology (20.06.2019)
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Journal Article
Single‐cell transcriptomic profiling of satellite glial cells in stellate ganglia reveals developmental and functional axial dynamics
Weperen, Valerie Y. H., Littman, Russell J., Arneson, Douglas V., Contreras, Jaime, Yang, Xia, Ajijola, Olujimi A.
Published in Glia (01.05.2021)
Published in Glia (01.05.2021)
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Journal Article
SCING: Inference of robust, interpretable gene regulatory networks from single cell and spatial transcriptomics
Littman, Russell, Cheng, Michael, Wang, Ning, Peng, Chao, Yang, Xia
Published in iScience (21.07.2023)
Published in iScience (21.07.2023)
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Journal Article
Benchmarking of computational error-correction methods for next-generation sequencing data
Mitchell, Keith, Brito, Jaqueline J, Mandric, Igor, Wu, Qiaozhen, Knyazev, Sergey, Chang, Sei, Martin, Lana S, Karlsberg, Aaron, Gerasimov, Ekaterina, Littman, Russell, Hill, Brian L, Wu, Nicholas C, Yang, Harry Taegyun, Hsieh, Kevin, Chen, Linus, Littman, Eli, Shabani, Taylor, Enik, German, Yao, Douglas, Sun, Ren, Schroeder, Jan, Eskin, Eleazar, Zelikovsky, Alex, Skums, Pavel, Pop, Mihai, Mangul, Serghei
Published in Genome Biology (17.03.2020)
Published in Genome Biology (17.03.2020)
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Journal Article
Tiered sympathetic control of cardiac function revealed by viral tracing and single cell transcriptome profiling
Sharma, Sachin, Littman, Russell, Tompkins, John D, Arneson, Douglas, Contreras, Jaime, Dajani, Al-Hassan, Ang, Kaitlyn, Tsanhani, Amit, Sun, Xin, Jay, Patrick Y, Herzog, Herbert, Yang, Xia, Ajijola, Olujimi A
Published in eLife (10.05.2023)
Published in eLife (10.05.2023)
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Journal Article
q-Diffusion leverages the full dimensionality of gene coexpression in single-cell transcriptomics
Marmarelis, Myrl G., Littman, Russell, Battaglin, Francesca, Niedzwiecki, Donna, Venook, Alan, Ambite, Jose-Luis, Galstyan, Aram, Lenz, Heinz-Josef, Ver Steeg, Greg
Published in Communications biology (02.04.2024)
Published in Communications biology (02.04.2024)
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Journal Article
Glial-Neuronal Crosstalk in the Ageing Murine Nodose Ganglion
Van Weperen, Valerie, Devarajan, Asokan, Littman, Russell, Wang, Kerry, Shannon, Kassandra, Yang, Xia, Vaseghi, Marmar
Published in Physiology (Bethesda, Md.) (01.05.2024)
Published in Physiology (Bethesda, Md.) (01.05.2024)
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Journal Article
Aging shifts the transcriptomic profile of satellite glial cells in murine nodose ganglia towards a pro-inflammatory phenotype
van Weperen, Valerie, Devarajan, Asokan, Littman, Russell, Wang, Ke, Shannon, Kassandra, Yang, Xia, Vaseghi, Marmar
Published in Physiology (Bethesda, Md.) (01.05.2023)
Published in Physiology (Bethesda, Md.) (01.05.2023)
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Journal Article
A comprehensive benchmarking of WGS-based deletion structural variant callers
Sarwal, Varuni, Niehus, Sebastian, Ayyala, Ram, Kim, Minyoung, Sarkar, Aditya, Chang, Sei, Lu, Angela, Rajkumar, Neha, Darfci-Maher, Nicholas, Littman, Russell, Chhugani, Karishma, Soylev, Arda, Comarova, Zoia, Wesel, Emily, Castellanos, Jacqueline, Chikka, Rahul, Distler, Margaret G, Eskin, Eleazar, Flint, Jonathan, Mangul, Serghei
Published in Briefings in bioinformatics (18.07.2022)
Published in Briefings in bioinformatics (18.07.2022)
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Journal Article
Tiered Sympathetic Control of Cardiac Function Revealed by Viral Tracing and Single Cell Transcriptome Profiling
Sharma, Sachin, Littman, Russell, Tompkins, John, Arneson, Douglas, Contreras, Jaime, Dajani, Al-Hassan, Ang, Kaitlyn, Tsanhani, Amit, Sun, Xin, Jay, Patrick Y, Herzog, Herbert, Yang, Xia, Ajijola, Olujimi A
Published in bioRxiv : the preprint server for biology (19.01.2023)
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Published in bioRxiv : the preprint server for biology (19.01.2023)
Journal Article
A comprehensive benchmarking of WGS-based structural variant callers
Sarwal, Varuni, Niehus, Sebastian, Ayyala, Ram, Chang, Sei, Lu, Angela, Darci-Maher, Nicholas, Littman, Russell, Chhugani, Karishma, Soylev, Arda, Comarova, Zoia, Wesel, Emily, Castellanos, Jacqueline, Chikka, Rahul, Distler, Margaret G, Eskin, Eleazar, Flint, Jonathan, Serghei Mangul
Published in bioRxiv (17.09.2020)
Published in bioRxiv (17.09.2020)
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Paper
Challenges and recommendations to improve the installability and archival stability of omics computational tools
Serghei Mangul, Mosqueiro, Thiago, Abdill, Richard J, Duong, Dat, Mitchell, Keith, Sarwal, Varuni, Hill, Brian, Brito, Jaqueline, Littman, Russell, Statz, Benjamin, Lam, Angela, Dayama, Gargi, Grieneisen, Laura, Martin, Lana, Flint, Jonathan, Eskin, Eleazar, Blekhman, Ran
Published in bioRxiv (14.05.2019)
Published in bioRxiv (14.05.2019)
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Paper
Benchmarking of computational error-correction methods for next-generation sequencing data
Mitchell, Keith, Brito, Jaqueline, Mandric, Igor, Wu, Qiaozhen, Knyazev, Sergey, Chang, Sei, Martin, Lana S, Karlsberg, Aaron, Gerasimov, Ekaterina, Littman, Russell, Hill, Brian L, Wu, Nicholas C, Yang, Harry, Hsieh, Kevin, Chen, Linus, Littman, Eli, Taylor Shabani, Shabanets, German, Yao, Douglas, Sun, Ren, Schroeder, Jan, Eskin, Eleazar, Zelikovsky, Alex, Skums, Pavel, Pop, Mihai, Serghei Mangul
Published in bioRxiv (06.03.2020)
Published in bioRxiv (06.03.2020)
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Paper