19 Works

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...

Additional file 2 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 2: Supplementary Table 1. TOGA status of 18430 ancestral placental mammal genes in muroid rodent genome assemblies. Supplementary Table 2. Positively selected genes and their mutation tolerance in humans according to gnomAD.

Research on infrared dim and small target detection algorithm based on local contrast and gradient

Weihong Lin, Leihong Zhang, Zimin Shen, Dawei Zhang, Jian Chen, Jie Zhou, Wei Peng & Fengshou Wu
The rapid development of infrared technology makes it widely applicable in such fields as military, medical, testing and communications.This paper proposes an algorithm based on local contrast and gradient (LCG). Specifically, the algorithm uses the difference of gaussian and threshold segmentation to preprocess to obtain the position of possible target points. Then, local contrast processing is conducted for the possible target points. Finally, the global is processed using an improved directional gradient. According to the...

Research on infrared dim and small target detection algorithm based on local contrast and gradient

Weihong Lin, Leihong Zhang, Zimin Shen, Dawei Zhang, Jian Chen, Jie Zhou, Wei Peng & Fengshou Wu
The rapid development of infrared technology makes it widely applicable in such fields as military, medical, testing and communications.This paper proposes an algorithm based on local contrast and gradient (LCG). Specifically, the algorithm uses the difference of gaussian and threshold segmentation to preprocess to obtain the position of possible target points. Then, local contrast processing is conducted for the possible target points. Finally, the global is processed using an improved directional gradient. According to the...

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.

Scheduling method for pairing night-shift and morning-shift duties on metro lines with complex structure

Zixuan Zhu, Ruihua Xu, Fangsheng Wang & Pieter Vansteenwegen
Scheduling the night-shift and morning-shift duties pairing plan (NMDPP) is a common process in Chinese metro crew management. Since metro crews work in a special working environment, sufficient rest is essential for them. NMDPP will affect the rest time of crews on metro lines with multiple depots and handover points. To improve the rest time of crews, this paper proposes a binary programming model to optimise the NMDPP. Moreover, a hybrid algorithm combining General Variable...

The effects of age, sex, weight, and breed on canid methylomes

Liudmilla Rubbi, Haoxuan Zhang, Junxi Feng, Christopher He, Patrick Kurnia, Prashansa Ratan, Aakash Tammana, Sabina House, Michael Thompson, Colin Farrell, Sagi Snir, Daniel Stahler, Elaine A. Ostrander, Bridgett M. vonHoldt & Matteo Pellegrini
Unlike genomes, which are static throughout the lifespan of an organism, DNA methylomes are dynamic. To study these dynamics, we developed quantitative models that measure the effect of multiple factors on DNA methylomes including, age, sex, weight, and genetics. We conducted our study in canids, which prove to be an ideal species to assess epigenetic moderators due to their extreme variability in size and well-characterized genetic structure. We collected buccal swabs from 217 canids (207...

Scheduling method for pairing night-shift and morning-shift duties on metro lines with complex structure

Zixuan Zhu, Ruihua Xu, Fangsheng Wang & Pieter Vansteenwegen
Scheduling the night-shift and morning-shift duties pairing plan (NMDPP) is a common process in Chinese metro crew management. Since metro crews work in a special working environment, sufficient rest is essential for them. NMDPP will affect the rest time of crews on metro lines with multiple depots and handover points. To improve the rest time of crews, this paper proposes a binary programming model to optimise the NMDPP. Moreover, a hybrid algorithm combining General Variable...

Additional file 4 of A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng … & Barry Smith
Additional file 4: Supplemental Table 3. Protein Ontology representation of SARS-CoV-2 proteins. Comparative information in RefSeq and UniProtKB is also provided.

Additional file 2 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 2: Supplementary Table 1. TOGA status of 18430 ancestral placental mammal genes in muroid rodent genome assemblies. Supplementary Table 2. Positively selected genes and their mutation tolerance in humans according to gnomAD.

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...

The effects of age, sex, weight, and breed on canid methylomes

Liudmilla Rubbi, Haoxuan Zhang, Junxi Feng, Christopher He, Patrick Kurnia, Prashansa Ratan, Aakash Tammana, Sabina House, Michael Thompson, Colin Farrell, Sagi Snir, Daniel Stahler, Elaine A. Ostrander, Bridgett M. vonHoldt & Matteo Pellegrini
Unlike genomes, which are static throughout the lifespan of an organism, DNA methylomes are dynamic. To study these dynamics, we developed quantitative models that measure the effect of multiple factors on DNA methylomes including, age, sex, weight, and genetics. We conducted our study in canids, which prove to be an ideal species to assess epigenetic moderators due to their extreme variability in size and well-characterized genetic structure. We collected buccal swabs from 217 canids (207...

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...

Additional file 4 of A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng … & Barry Smith
Additional file 4: Supplemental Table 3. Protein Ontology representation of SARS-CoV-2 proteins. Comparative information in RefSeq and UniProtKB is also provided.

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.

Registration Year

  • 2022
    19

Resource Types

  • Dataset
    19

Affiliations

  • National Human Genome Research Institute
    19
  • Chinese Academy of Sciences
    12
  • National Institutes of Health
    11
  • Southern Medical University
    9
  • Shanghai Jiao Tong University
    9
  • Nantong University
    9
  • Wuhan University
    9
  • Sichuan Agricultural University
    9
  • Tongji University
    9
  • Nanjing Tech University
    9