44 Works

Additional file 7 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Lipei Shao, Rongye Shi, Yingdong Zhao, Hui Liu, Alexander Lu, Jinxia Ma, Yihua Cai, Tatyana Fuksenko, Alejandra Pelayo, Nirali N. Shah, James N. Kochenderfer, Scott M. Norberg, Christian Hinrichs, Steven L. Highfill, Robert P Somerville, Sandhya R. Panch, Ping Jin & David F. Stroncek
Additional file 7: Table S2. Differentially expressed genes in non-transduced and transduced CAR T-cell products.

Additional file 2 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Jie Zhou, Jiahui Guo, Qingsheng Chen, Baosong Wang, Xudong He, Qiang Zhuge & Pu Wang
Additional file 2: TableS6. The metabolites identified in positive ion mode.

Additional file 2 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Jie Zhou, Jiahui Guo, Qingsheng Chen, Baosong Wang, Xudong He, Qiang Zhuge & Pu Wang
Additional file 2: TableS6. The metabolites identified in positive ion mode.

Additional file 3 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Jie Zhou, Jiahui Guo, Qingsheng Chen, Baosong Wang, Xudong He, Qiang Zhuge & Pu Wang
Additional file 3: Table S7. The metabolites identified in negative ionmode.

Additional file 4 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Jie Zhou, Jiahui Guo, Qingsheng Chen, Baosong Wang, Xudong He, Qiang Zhuge & Pu Wang
Additional file 4: Table S8. The differential expressed genes identified inwillow barks.

A novel role for nucleolin in splice site selection

Kinneret Shefer, Ayub Boulos, Valer Gotea, Maram Arafat, Yair Ben Chaim, Aya Muharram, Sara Isaac, Amir Eden, Joseph Sperling, Laura Elnitski & Ruth Sperling
Latent 5ʹ splice sites, not normally used, are highly abundant in human introns, but are activated under stress and in cancer, generating thousands of nonsense mRNAs. A previously proposed mechanism to suppress latent splicing was shown to be independent of NMD, with a pivotal role for initiator-tRNA independent of protein translation. To further elucidate this mechanism, we searched for nuclear proteins directly bound to initiator-tRNA. Starting with UV-crosslinking, we identified nucleolin (NCL) interacting directly and...

Datasets for: The HIV-1 viral protease is activated during assembly and budding prior to particle release

Caroline Tabler, Sarah Wegman, Jiji Chen, Hari Shroff, John Tilton & Najwa Alhusaini
HIV-1 encodes a viral protease that is essential for the maturation of infectious viral particles. While protease inhibitors are effective antiretroviral agents, recent studies have shown that prematurely activating – rather than inhibiting – protease function leads to the pyroptotic death of infected cells, with exciting implications for efforts to eradicate viral reservoirs. Despite 40 years of research into the kinetics of protease activation, it remains unclear exactly when protease becomes activated. Recent reports have...

A B cell actomyosin arc network couples integrin co-stimulation to mechanical force-dependent immune synapse formation

Jia Wang
B-cell activation and immune synapse (IS) formation with membrane-bound antigens are actin-dependent processes that scale positively with the strength of antigen-induced signals. Importantly, ligating the B-cell integrin, LFA-1, with ICAM-1 promotes IS formation when antigen is limiting. Whether the actin cytoskeleton plays a specific role in integrin-dependent IS formation is unknown. Here we show using super-resolution imaging of mouse primary B cells that LFA-1: ICAM-1 interactions promote the formation of an actomyosin network that dominates...

A novel role for nucleolin in splice site selection

Kinneret Shefer, Ayub Boulos, Valer Gotea, Maram Arafat, Yair Ben Chaim, Aya Muharram, Sara Isaac, Amir Eden, Joseph Sperling, Laura Elnitski & Ruth Sperling
Latent 5ʹ splice sites, not normally used, are highly abundant in human introns, but are activated under stress and in cancer, generating thousands of nonsense mRNAs. A previously proposed mechanism to suppress latent splicing was shown to be independent of NMD, with a pivotal role for initiator-tRNA independent of protein translation. To further elucidate this mechanism, we searched for nuclear proteins directly bound to initiator-tRNA. Starting with UV-crosslinking, we identified nucleolin (NCL) interacting directly and...

Epigenome-wide association studies of occupational exposure to benzene and formaldehyde

Rachael V. Phillips, Linqing Wei, Andres Cardenas, Alan E. Hubbard, Cliona M. McHale, Roel Vermeulen, Hu Wei, Martyn T. Smith, Luoping Zhang, Qing Lan & Nathaniel Rothman
Sufficient evidence supports a relationship between certain myeloid neoplasms and exposure to benzene or formaldehyde. DNA methylation could underlie benzene- and formaldehyde-induced health outcomes, but data in exposed human populations are limited. We conducted two cross-sectional epigenome-wide association studies (EWAS), one in workers exposed to benzene and another in workers exposed to formaldehyde. Using HumanMethylation450 BeadChips, we investigated differences in blood cell DNA methylation among 50 benzene-exposed subjects and 48 controls, and among 31 formaldehyde-exposed...

Supplemental Material for md_harmonize

Hunter Moseley & Huan Jin
Supplemental Material for:
md_harmonize: a Python package for atom-level harmonization of public metabolic data-bases

iCite Database Snapshot 2022-09

iCite, B. Ian Hutchins, George Santangelo & Ehsanul Haque
This is a database snapshot of the iCite web service (provided here as a single zipped CSV file, or compressed, tarred JSON files). In addition, citation links in the NIH Open Citation Collection are provided as a two-column CSV table in open_citation_collection.zip. iCite provides bibliometrics and metadata on publications indexed in PubMed, organized into three modules:
Influence: Delivers metrics of scientific influence, field-adjusted and benchmarked to NIH publications as the baseline.
Translation: Measures...

Additional file 3 of The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Hiba Mohammed Taha, Reza Aalizadeh, Nikiforos Alygizakis, Jean-Philippe Antignac, Hans Peter H. Arp, Richard Bade, Nancy Baker, Lidia Belova, Lubertus Bijlsma, Evan E. Bolton, Werner Brack, Alberto Celma, Wen-Ling Chen, Tiejun Cheng, Parviel Chirsir, Ľuboš Čirka, Lisa A. D’Agostino, Yannick Djoumbou Feunang, Valeria Dulio, Stellan Fischer, Pablo Gago-Ferrero, Aikaterini Galani, Birgit Geueke, Natalia Głowacka, Juliane Glüge … & Emma L. Schymanski
Additional file 3: Summary of Zenodo view and download statistics, plus citations (CSV format) as of 28 April 2022 [235].

Additional file 5 of The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Hiba Mohammed Taha, Reza Aalizadeh, Nikiforos Alygizakis, Jean-Philippe Antignac, Hans Peter H. Arp, Richard Bade, Nancy Baker, Lidia Belova, Lubertus Bijlsma, Evan E. Bolton, Werner Brack, Alberto Celma, Wen-Ling Chen, Tiejun Cheng, Parviel Chirsir, Ľuboš Čirka, Lisa A. D’Agostino, Yannick Djoumbou Feunang, Valeria Dulio, Stellan Fischer, Pablo Gago-Ferrero, Aikaterini Galani, Birgit Geueke, Natalia Głowacka, Juliane Glüge … & Emma L. Schymanski
Additional file 5: Authorship contributions and acknowledgements mapped to NORMAN-SLE lists (XLSX format).

A telltale sign of irreversibility in transcriptional regulation

Robert Shelansky, Sara Abrahamsson, Michael Doody, Christopher R. Brown, Heta P. Patel, Tineke L. Lenstra, Daniel R. Larson & Hinrich Boeger
Transcription occurs in stochastic bursts, i.e., transcription events are temporally clustered. The clustering does not ensue from environmental fluctuations but springs from the intrinsically stochastic behavior of the regulatory process that controls transcription. Based on microscopic observations of transcription at a single gene copy of yeast, we show that the regulatory process is cyclic and irreversible, i.e., the process violates the detailed balance conditions for thermodynamic equilibrium. The theoretical significance of this finding is discussed.

Additional file 7 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Lipei Shao, Rongye Shi, Yingdong Zhao, Hui Liu, Alexander Lu, Jinxia Ma, Yihua Cai, Tatyana Fuksenko, Alejandra Pelayo, Nirali N. Shah, James N. Kochenderfer, Scott M. Norberg, Christian Hinrichs, Steven L. Highfill, Robert P Somerville, Sandhya R. Panch, Ping Jin & David F. Stroncek
Additional file 7: Table S2. Differentially expressed genes in non-transduced and transduced CAR T-cell products.

Additional file 8 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Lipei Shao, Rongye Shi, Yingdong Zhao, Hui Liu, Alexander Lu, Jinxia Ma, Yihua Cai, Tatyana Fuksenko, Alejandra Pelayo, Nirali N. Shah, James N. Kochenderfer, Scott M. Norberg, Christian Hinrichs, Steven L. Highfill, Robert P Somerville, Sandhya R. Panch, Ping Jin & David F. Stroncek
Additional file 8: Table S3. Differential alternative splicing transcripts with viral integration.

Additional file 3 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Jie Zhou, Jiahui Guo, Qingsheng Chen, Baosong Wang, Xudong He, Qiang Zhuge & Pu Wang
Additional file 3: Table S7. The metabolites identified in negative ionmode.

Supplemental Material for md_harmonize

Hunter Moseley & Huan Jin
Supplemental Material for:
md_harmonize: a Python package for atom-level harmonization of public metabolic data-bases

Registration Year

  • 2022
    44

Resource Types

  • Dataset
    44

Affiliations

  • National Institutes of Health
    44
  • Southern Medical University
    15
  • Tianjin Medical University
    15
  • Chinese Academy of Sciences
    15
  • Guangzhou Medical University
    13
  • Huazhong University of Science and Technology
    11
  • National Human Genome Research Institute
    10
  • Shanghai Jiao Tong University
    9
  • National Center for AIDS/STD Control and Prevention,China CDC
    9
  • Sichuan Agricultural University
    9