Article
Biochemical Research Methods
Ziad Al Bkhetan, Gursharan Chana, Cheng Soon Ong, Benjamin Goudey, Kotagiri Ramamohanarao
Summary: The study introduces a novel method, eQTLHap, for eQTL analysis which significantly outperforms traditional SNP-based methods in causal genetic architectures involving multiple SNPs. Phase-aware eQTL analysis demonstrates robustness to phase errors and detects numerous novel eQTLs in real datasets, highlighting its utility.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Plant Sciences
Yoichi Hashida, Ayumi Tezuka, Yasuyuki Nomura, Mari Kamitani, Makoto Kashima, Yuko Kurita, Atsushi J. Nagano
Summary: This study reveals the differences in transcriptome expression between plants grown in field and controlled environments. The SmartGC growth chamber is capable of reproducing the fluctuating conditions of field environments. The analysis shows that fluctuation of irradiance and temperature affects transcriptome dynamics, while some environmental factors cannot be mimicked by SmartGC.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Ramon E. Rivera-Vicens, Catalina A. Garcia-Escudero, Nicola Conci, Michael Eitel, Gert Woerheide
Summary: The use of RNA sequencing and de novo transcriptome assembly is crucial for ecological and evolutionary studies, especially for nonmodel organisms lacking genome information. A multi-assembler approach, followed by a reduction step, is often employed to improve the assembly quality. TransPi is a comprehensive pipeline for de novo transcriptome assembly that achieves higher completeness percentages and reduces duplication rates compared to single assembler approaches. It is easy to configure and can be seamlessly deployed using Conda, Docker, and Singularity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biotechnology & Applied Microbiology
Yue Li, Yufei Lu, Yun Zhou, Xiaoli Wei, Yonggang Peng, Yan Dai, Lei Zhang, Zhen Zhu
Summary: The study compared the dynamic transcriptional profiles of a super-hybrid rice and its parents, identifying 1552 rhythmic differentially expressed genes (RDGs) associated with photosynthesis and stress response during day and night phases. Regulatory network analysis revealed that circadian-related RDGs are core components regulating downstream genes involved in various pathways. Additionally, a majority of RDGs mapped onto quantitative trait loci were significantly enriched in yield, vigor, and anatomy categories, offering valuable information for understanding heterosis mechanisms and informing breeding practices.
Article
Chemistry, Applied
Qing-Hua Liu, Zi-Yi Wang, Jia-Wei Tang, Jing-Yi Mou, Zhang-Wen Ma, Bin Deng, Zhao Liu, Liang Wang
Summary: The study re-examined the diurnal alterations of liver glycogen structure using liver tissue transcriptome analysis, confirming the structural changes between fragile and stable glycogen particles during different times of the day. Differential expression of the gene ppp1r3g, encoding PPP1R3G with glycogen binding domain, was identified as a key factor in the structural alterations of glycogen alpha particles.
CARBOHYDRATE POLYMERS
(2022)
Article
Gastroenterology & Hepatology
Leonardo Vinicius Monteiro de Assis, Muenevver Demir, Henrik Oster
Summary: Circadian profiling improves the detection of target genes and characterization of pathways in mouse models of nonalcoholic steatohepatitis. Fatty livers show a 3-hour advance in metabolic and clock gene transcript rhythms. Circadian profiling reveals temporal changes in lipid, carbohydrate, and cholesterol metabolic transcripts.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Biodiversity Conservation
Chen-Yang Tang, Meng-Huan Song, Zhong-Liang Peng, Wei Wu, Changjun Peng, Kong Yang, Jia-Tang Li
Summary: The visual characteristics and gene expression patterns in the eyes of snakes with different circadian habits, such as diurnal Ahaetulla prasina and nocturnal Lycodon flavozonatum, show significant variations. Gene expression analysis revealed different functional pathways enriched in the eyes of these two snake species, indicating distinct biological functions and adaptive evolution in response to their circadian activities.
Article
Biochemistry & Molecular Biology
So Young Park, Dong-Hoon Jeong
Summary: This study used RNA-seq analysis to examine the gene expression patterns in rice seedling shoots during dehydration and rehydration. It revealed that drought-responsive genes were dynamically regulated during rehydration. The study also highlighted the potential role of nitrogen metabolism and jasmonic acid signaling in the drought stress response. The transcriptome data in this study could be a valuable resource for understanding drought stress responses in rice and developing drought-resistant crop plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Plant Sciences
Zhixin Liu, Xiaole Yu, Aizhi Qin, Zihao Zhao, Yumeng Liu, Susu Sun, Hao Liu, Chenxi Guo, Rui Wu, Jincheng Yang, Mengke Hu, George Bawa, Xuwu Sun
Summary: This article reviews the progress and challenges of plant single-cell transcriptome research and provides a speculative outlook for future developments.
Article
Biochemistry & Molecular Biology
Long Zhang, Zhengmin Tang, Hao Zheng, Caihong Zhong, Qiong Zhang
Summary: In this study, the differences in metabolite profiles between kiwifruit roots and fruits were compared, and several differentially expressed metabolites were identified. Among them, three flavonols and one dihydrochalcone showed the greatest differences in content between the two tissues. Transcriptome analysis revealed that genes related to flavonols and dihydrochalcones were highly expressed in roots. Furthermore, two transcription factors were highly expressed in roots, while one transcription factor showed extremely low expression, indicating their potential roles in regulating flavonoid accumulation in kiwifruit.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Entomology
Kohei Kakino, Hiroaki Mon, Takeru Ebihara, Masato Hino, Akitsu Masuda, Jae Man Lee, Takahiro Kusakabe
Summary: This study characterizes the gene expression patterns and function in the testis of Bombyx mori, revealing peculiar features in spermatogenesis. The transcriptome analysis identifies widespread gene expression and testis-specific genes in B. mori, and compares it with Drosophila melanogaster for a better understanding. The study fills a knowledge gap and provides a basis for future research in spermatogenesis.
Article
Biotechnology & Applied Microbiology
Roman Jaksik, Monika Drobna-Sledzinska, Malgorzata Dawidowska
Summary: RNA-seq allows comprehensive transcriptome analysis of cancer cells with long reads and high coverage, but optimal library length is crucial to avoid data loss. TruSeq Stranded library preparation with poly(A) enrichment outperforms rRNA depletion for gene expression and structural analysis of acute lymphoblastic leukemia cells. Reduced RNA fragmentation time positively affects detection of structural RNA changes.
Article
Biochemistry & Molecular Biology
Jessica Marie Perez, Stefano Berto, Kelly Gleason, Subroto Ghose, Chunfeng Tan, Tae-Kyung Kim, Genevieve Konopka, Carol A. Tamminga
Summary: The study demonstrates unique molecular changes in hippocampal subfields of individuals with schizophrenia, suggesting different biological functions in each subfield which may help identify potential hippocampal-based therapeutic targets for schizophrenia.
MOLECULAR PSYCHIATRY
(2021)
Article
Biochemistry & Molecular Biology
Yuanpeng Fang, Bingqian Zhou, Yushan Guo, Junmei Jiang, Xiangyang Li, Xin Xie
Summary: This study aimed to investigate the key factors influencing plant disease resistance and identify the core molecular network in Sorghum bicolor. The type of PAMP was found to have a stronger influence on the PTI network than the sorghum cultivar. PAMP treatment altered the expression of genes related to resistance, signaling, salt sensitivity, heavy metal response, and transportation.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Physiology
Huiquan Shan, Ke Ren, Jiasheng Liu, Saif ur Rehman, Xiuying Yan, Xiaocong Ma, Yalin Zheng, Tong Feng, Xiaobo Wang, Zhipeng Li, Weiguan Zhou, Chen Chuang, Mingkun Liang, Jinghui Zheng, Qingyou Liu
Summary: This study used transcriptome analysis to compare the gene expression in different growth stages of Hirudinaria manillensis, revealing differential gene expression patterns between larval, young, and adult stages. The results showed that adult leeches had higher protein expression, especially in the Hirudin-HM (HIRM2) genes, along with a variety of other genes associated with muscle development. Additionally, the comparative transcriptome profiling identified a large number of differentially expressed genes and long non-coding RNAs, suggesting potential associations with the growth and development of H. manillensis.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Biochemical Research Methods
Oleg Suslov, Daniel J. Silver, Florian A. Siebzehnrubl, Arturo Orjalo, Andrey Ptitsyn, Dennis A. Steindler
Article
Multidisciplinary Sciences
Mohammed El Anbari, Abeer Fadda, Andrey Ptitsyn
Article
Genetics & Heredity
Abeer Fadda, Mohammed El Anbari, Andrey Ptitsyn
BMC MEDICAL GENOMICS
(2018)
Article
Geriatrics & Gerontology
Gregory M. Sutton, Andrey A. Ptitsyn, Z. Elizabeth Floyd, Gang Yu, Xiying Wu, Katie Hamel, Forum S. Shah, Armand Centanni, Kenneth Eilertsen, Indu Kheterpal, Susan Newman, Claudia Leonardi, Michael A. Freitas, Bruce A. Bunnell, Jeffrey M. Gimble
Review
Medicine, General & Internal
Andrey A. Ptitsyn, Jeffrey M. Gimble
ANNALS OF MEDICINE
(2011)
Article
Biochemical Research Methods
Andrey Ptitsyn, Leonid L. Moroz
BMC BIOINFORMATICS
(2012)
Article
Biochemistry & Molecular Biology
Luke A. Wittenburg, Andrey A. Ptitsyn, Douglas H. Thamm
JOURNAL OF CELLULAR BIOCHEMISTRY
(2012)
Article
Biochemical Research Methods
Indu Kheterpal, Ginger Ku, Liana Coleman, Gang Yu, Andrey A. Ptitsyn, Z. Elizabeth Floyd, Jeffrey M. Gimble
JOURNAL OF PROTEOME RESEARCH
(2011)
Article
Multidisciplinary Sciences
Leonid L. Moroz, Kevin M. Kocot, Mathew R. Citarella, Sohn Dosung, Tigran P. Norekian, Inna S. Povolotskaya, Anastasia P. Grigorenko, Christopher Dailey, Eugene Berezikov, Katherine M. Buckley, Andrey Ptitsyn, Denis Reshetov, Krishanu Mukherjee, Tatiana P. Moroz, Yelena Bobkova, Fahong Yu, Vladimir V. Kapitonov, Jerzy Jurka, Yuri V. Bobkov, Joshua J. Swore, David O. Girardo, Alexander Fodor, Fedor Gusev, Rachel Sanford, Rebecca Bruders, Ellen Kittler, Claudia E. Mills, Jonathan P. Rast, Romain Derelle, Victor V. Solovyev, Fyodor A. Kondrashov, Billie J. Swalla, Jonathan V. Sweedler, Evgeny I. Rogaev, Kenneth M. Halanych, Andrea B. Kohn
Review
Endocrinology & Metabolism
Jeffrey M. Gimble, Gregory M. Sutton, Bruce A. Bunnell, Andrey A. Ptitsyn, Z. Elizabeth Floyd
NATURE REVIEWS ENDOCRINOLOGY
(2011)
Article
Multidisciplinary Sciences
Andrey Ptitsyn, Ramzi Temanni, Christelle Bouchard, Peter A. V. Anderson
Article
Biochemical Research Methods
Jairam Vanamala, Sridhar Radhakrishnan, Lavanya Reddivari, Vadiraja B. Bhat, Andrey Ptitsyn
Article
Multidisciplinary Sciences
Jennifer M. Polinski, Aleksey V. Zimin, K. Fraser Clark, Andrea B. Kohn, Norah Sadowski, Winston Timp, Andrey Ptitsyn, Prarthana Khanna, Daria Y. Romanova, Peter Williams, Spencer J. Greenwood, Leonid L. Moroz, David R. Walt, Andrea G. Bodnar
Summary: The American lobster plays a crucial role in marine ecosystems and supports commercial fishing. It serves as a valuable model for studying neural networks and olfaction, with complex chemosensory and defense mechanisms contributing to its longevity and ecological success in the marine environment.
Article
Biotechnology & Applied Microbiology
Natalia Ptitsyna, Sabri Boughorbel, Mohammed El Anbari, Andrey Ptitsyn
Proceedings Paper
Engineering, Biomedical
Andrey Ptitsyn, Natalia Ptitsyna, Emad Elsebakhi, Francesco Marincola, Rashid Al-Ali, M. -Ramzi Temanni, Rawan AlSaad, Ena Wang
2014 MIDDLE EAST CONFERENCE ON BIOMEDICAL ENGINEERING (MECBME)
(2014)
