Streaming fragment assignment for real-time analysis of sequencing experiments

Roberts, Adam, Pachter, Lior·2013·Nature Methods

Cited by (1,000)

Items 501–600 of 1,000

  1. Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping
    Xin Wu Zeng, Bo Li, Rene Welch, Constanza Rojo, Ye Zheng, Colin N. Dewey, Sündüz Keleş · 2015 · PLoS Computational Biology
  2. Bayesian nonparametric discovery of isoforms and individual specific quantification
    Derek Aguiar, Lifang Cheng, Bianca Dumitrascu, Fantine Mordelet, Athma A. Pai, Barbara Elizabeth Engelhardt · 2018 · Nature Communications
  3. De novo transcriptome sequencing reveals candidate genes involved in orange shell coloration of bay scallop Argopecten irradians
    Wen Teng, Rihao Cong, Huayong Que, Guofan Zhang · 2018 · Journal of Oceanology and Limnology
  4. Transcriptome-wide effect of DE-ETIOLATED1 (DET1) suppression in embryogenic callus of Carica papaya
    Nur Diyana Jamaluddin, Emelda Rosseleena Rohani, Normah Mohd Noor, Hoe‐Han Goh · 2019 · Journal of Plant Research
  5. Native and introduced Argentine ant populations are characterised by distinct transcriptomic signatures associated with behaviour and immunity
    Antoine Felden, Carolina Paris, David G. Chapple, Andrew V. Suarez, Neil Durie Tsutsui, Philip John Lester, Monica A. M. Gruber · 2019 · NeoBiota
  6. Keep Me Around: Intron Retention Detection and Analysis
    Harold Pimentel, John G. Conboy, Lior S. Pachter · 2015 · arXiv (Cornell University)
  7. Genome concentration limits cell growth and modulates proteome composition in Escherichia coli
    Jarno Mäkelä, Alexandros Papagiannakis, Wei-Hsiang Lin, Michael Charles Lanz, Skye Glenn, Matthew P. Swaffer, Georgi K. Marinov, Jan Marcel Skotheim, Christine Jacobs · 2024 · eLife
  8. Effects of berberine hydrochloride on immune response in the crab Charybdis japonica
    Tianheng Gao, Mingming Han, Hui Ren Zhou, Chenxi Zhu, Ying Yang, Zuraini Zakaria, Yanxia Guo, Qichen Jiang · 2022 · BMC Genomics
  9. Integrative transcriptomic and metabolomic analyses unveil tanshinone biosynthesis in Salvia miltiorrhiza root under N starvation stress
    Lilan Lu, Yuxiu Zhang, Yanfang Yang · 2022 · PLoS ONE
  10. The role of cis -zeatin in enhancing high-temperature resistance and fucoxanthin biosynthesis in Phaeodactylum tricornutum
    Sizhe Fan, Yixuan Li, Qi Wang, Mengjie Jin, Mange Yu, Hejing Zhao, Chengxu Zhou, Jilin Xu, Bing Li, Xiaohui Li · 2024 · Applied and Environmental Microbiology
  11. Faucet: streaming de novo assembly graph construction
    Roye Rozov, Gil Goldshlager, Eran Halperin, Ron Shamir A · 2017 · Bioinformatics
  12. NGScloud2: optimized bioinformatic analysis using Amazon Web Services
    Fernando Mora‐Márquez, José Luis Vázquez‐Poletti, Unai López de Heredia · 2021 · PeerJ
  13. Comprehensive Transcriptome Analysis of Gonadal and Somatic Tissues for Identification of Sex-Related Genes in the Largemouth Bass Micropterus salmoides
    Wenzhi Guan, Kai Jiang, Xing-Lin Lai, Yao-Ting Dong, Gao‐Feng Qiu · 2022 · Marine Biotechnology
  14. Dnmt3l -knockout donor cells improve somatic cell nuclear transfer reprogramming efficiency
    Hung‐Fu Liao, Chu-Fan Mo, Shinn‐Chih Wu, Dai-Han Cheng, Chih-Yun Yu, Kai‐Wei Chang, Tzu-Hao Kao, Chia‐Wei Lu, Marina Pinskaya, Antonin Morillon et al. · 2015 · Reproduction
  15. Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity
    Shannon L. Hateley, Ravikumar Hosamani, Shilpa R. Bhardwaj, Lior S. Pachter, Sharmila Bhattacharya · 2016 · Genomics
  16. Transcriptome sequencing and estimation of DNA methylation level in the subsocial wood-feeding cockroach Cryptocercus punctulatus (Blattodea: Cryptocercidae)
    Yoshinobu Hayashi, Kiyoto Maekawa, Christine A. Nalepa, Toru Miura, Shuji Shigenobu · 2017 · Applied Entomology and Zoology
  17. Transcripts immunoprecipitated with Sxl protein in primordial germ cells of Drosophila embryos
    Ryoma Ota, Shumpei Morita, Masanao Sato, Shuji Shigenobu, Makoto Hayashi, Satoru Kobayashi · 2017 · Development Growth & Differentiation
  18. AMBRA1-mediated autophagy and apoptosis associated with an epithelial-mesenchymal transition in the development of cleft palate induced by all-trans retinoic acid
    Xuan Shu, Zejun Dong, Shenyou Shu · 2019 · Annals of Translational Medicine
  19. DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data
    Hongfei Cui, Hailin Hu, Jianyang Zeng, Ting Chen · 2019 · BMC Bioinformatics
  20. VSG mRNA levels are regulated by the production of functional VSG protein
    Isabella E. Maudlin, Steven L. Kelly, Angela Schwede, Mark Carrington · 2020 · Molecular and Biochemical Parasitology
  21. Regulation Networks of Non-Coding RNA-Associated ceRNAs in Cisplatin-Induced Acute Kidney Injury
    Yun Ding, Shengfeng Wan, Wenna Liu, Yanfang Lu, Qin Xu, Yujin Gan, Lei Yan, Yue Gu, Ziyang Liu, Yifeng Hu et al. · 2022 · Cells
  22. Dioscin Ameliorates Experimental Autoimmune Thyroiditis via the mTOR and TLR4/NF-κB Signaling
    Chengfei Zhang, Qiue Zhang, Lingling Qin, Zhiyi Yan, Lili Wu, Tonghua Liu · 2023 · Drug Design Development and Therapy
  23. Impact of Heat Stress on Transposable Element Expression and Derived Small RNAs in Drosophila subobscura
    Alejandra Bodelόn, Marie Fablet, Daniel Siqueira de Oliveira, Cristina P Vieira, Maria Pilar García Guerreiro · 2023 · Genome Biology and Evolution
  24. Improving gene isoform quantification with miniQuant
    Haoran Li, Dingjie Wang, Qi Gao, Puwen Tan, Yunhao Wang, Xiaoyu Cai, Aifu Li, Yue Zhao, Andrew L. Thurman, Seyed Amir Malekpour et al. · 2025 · Nature Biotechnology
  25. Evolution of the RH gene family in vertebrates revealed by brown hagfish (Eptatretus atami) genome sequences
    Akinori Suzuki, Hidero Komata, Shogo Iwashita, Shotaro Seto, Hironobu Ikeya, Mitsutoshi Tabata, Takashi Kitano · 2016 · Molecular Phylogenetics and Evolution
  26. Seasonal differences in the testicular transcriptome profile of free-living European beavers (Castor fiber L.) determined by the RNA-Seq method
    Iwona Bogacka, Łukasz Paukszto, J Jastrzebski, Joanna Czerwińśka, Katarzyna Chojnowska, Barbara Kamińska, Aleksandra Kurzyńska, Nina Smolińska, Zygmunt Giżejewski, Tadeusz Kamiński · 2017 · PLoS ONE
  27. Superantigen SpeA attenuates the biofilm forming capacity of Streptococcus pyogenes
    Anshu Babbar, Israel Barrantes, Dietmar Helmut Pieper, Andreas Itzek · 2019 · The Journal of Microbiology
  28. Differential gene expression during substrate probing in larvae of the Caribbean coral Porites astreoides
    Nia Walker, Rosa Fernández, Jennifer M. Sneed, Valerie Jean Paul, Gonzalo Giribet, David J. Combosch · 2019 · Molecular Ecology
  29. Transcriptome analysis of the brain provides insights into the regulatory mechanism for Coilia nasus migration
    Meiyao Wang, Gangchun Xu, Yongkai Tang, Pao Xu · 2020 · BMC Genomics
  30. Transcriptome analysis of the effect of diosgenin on autoimmune thyroiditis in a rat model
    Chengfei Zhang, Lingling Qin, Boju Sun, You Wu, Fengying Zhong, Lili Wu, Tonghua Liu · 2021 · Scientific Reports
  31. Identification of microRNA and analysis of target genes in Panax ginseng
    Yingfang Wang, Yanlin Chen, Mengyuan Peng, Chang Yang, Ze‐Min Yang, Mengjuan Gong, Yong-Qin Yin, Yu Zeng · 2022 · Chinese Herbal Medicines
  32. Transcriptomic insights into the immune response of the intestine to Aeromonas veronii infection in northern snakehead (Channa argus)
    Peng Gang Sun, Di Zhang, Na Li, Xiaofei Li, Yi-Han Ma, Hui Li, Ye Tian, Tao Wang, Shahrood Ahmed Siddiquid, Wuwen Sun et al. · 2023 · Ecotoxicology and Environmental Safety
  33. Tissue-Specific Transcriptome for Poeciliopsis prolifica Reveals Evidence for Genetic Adaptation Related to the Evolution of a Placental Fish
    Nathaniel K. Jue, Robert J. Foley, David N. Reznick, Rachel J. Waugh O'Neill, Michael J. O’Neill · 2018 · G3 Genes Genomes Genetics
  34. Temperature-induced embryonic diapause in blue-breasted quail (Coturnix chinensis) correlates with decreased mitochondrial-respiratory network and increased stress-response network
    Jia-Huei Cai, Ting‐Feng Yeh, Hen‐Wei Wei, I‐Hsuan Liu · 2019 · Poultry Science
  35. Viral and fungal pathogens associated with Pneumolaelaps niutirani (Acari: Laelapidae): a mite found in diseased nests of Vespula wasps
    Antoine Felden, James W. Baty, Mariana Bulgarella, Robert L. Brown, Jana Dobelmann, Monica A. M. Gruber, Oliver Quinn, Philip John Lester · 2019 · Insectes Sociaux
  36. Effects of cold stress and starvation on the liver of yellow drum Nibea albiflora: histological alterations and transcriptomic analysis
    Qihui Zhu, Hongbin Song, Y Zhang, R Chen, L Tian, Dongdong Xu · 2020 · Aquaculture Environment Interactions
  37. Transcriptomic Profiling of Cryptomeria fortunei Hooibrenk Vascular Cambium Identifies Candidate Genes Involved in Phenylpropanoid Metabolism
    Junjie Yang, Zhenhao Guo, Yingting Zhang, Jiaxing Mo, Jiebing Cui, Hailiang Hu, Yunya He, Jin Xu · 2020 · Forests
  38. Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data
    Michael DeGiorgio, Raquel Assis · 2020 · Molecular Biology and Evolution
  39. Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern
    Jingwen Lin, Adam James Reid, Deirdre Cunningham, Ulrike Böhme, Irene Tumwine, Sara Keller-Mclaughlin, Mandy J Sanders, Matthew Berriman, Jean Langhorne · 2018 · Wellcome Open Research
  40. High temperature in the root zone repressed flowering in Lilium × formolongi by disturbing the photoperiodic pathway and reconfiguring hormones and primary metabolism
    Yuqian Zhao, Qian Zhang, Jiewen Li, Xiao Yan, Hengbin He, Xue Gao, Guixia Jia · 2021 · Environmental and Experimental Botany
  41. Bioinformatics Tools for RNA-seq Gene and Isoform Quantification
    Chi Zhang, Baohong Zhang, Michael S. Vincent, Shanrong Zhao · 2016 · Journal of Next Generation Sequencing & Applications
  42. Leveraging transcript quantification for fast computation of alternative splicing profiles
    Gael P. Alamancos, Amadís Pagès, Juan L. Trincado, Nicolás Bellora, Eduardo Eyras · 2014 · bioRxiv (Cold Spring Harbor Laboratory)
  43. Heterologous vvdreb2c expression improves heat tolerance in arabidopsis by inducing photoprotective responses
    Zha, Qian, Yin, Xiangjing, Xi, Xiaojun, Jiang, Aili · 2023 · International Journal of Molecular Sciences
  44. Sexually biased expression of odorant-binding proteins and chemosensory proteins in Asian corn borer Ostrinia furnacalis (Lepidoptera: Crambidae)
    Bin Yang, Katsuhisa Ozaki, Yukio Ishikawa, Takashi Matsuo · 2016 · Applied Entomology and Zoology
  45. Whole-Transcriptome Sequencing of Ovary Reveals the ceRNA Regulation Network in Egg Production of Gaoyou Duck
    Lei Zhang, Rui Zhu, Guobo Sun, Jian Wang, Qisheng Zuo, Shanyuan Zhu · 2023 · Genes
  46. Antibiotic synergistic effect surge bioenergy potential and pathogen resistance of Chlorella variabilis biofilm
    Adamu Yunusa Ugya, Diya’uddeen Basheer Hasan, Hadiza Abdullahi Ari, Yangyang Sheng, Hui Chen, Qiang Wang · 2024 · Environmental Research
  47. Risk Assessment of Fenpropathrin: Cause Hepatotoxicity and Nephrotoxicity in Common Carp (Cyprinus carpio L.)
    Gongming Zhu, Zhihui Liu, Hao Eric Wang, Shaoyu Mou, Yuanyuan Li, Junguo Ma, Xiaoyu Li · 2024 · International Journal of Molecular Sciences
  48. De novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in Drosophila miranda
    Vera B. Kaiser, Doris Bachtrog · 2014 · BMC Genomics
  49. Pushing the annotation of cellular activities to a higher resolution: Predicting functions at the isoform level
    Wenyuan Li, Chun-Chi Liu, Shuli Kang, Jianrong Li, Yu‐Ting Tseng, Xianghong Jasmine Zhou · 2015 · Methods
  50. Non‐canonical expression patterns and evolutionary rates of sex‐biased genes in a seasonal fish
    Miguel P. Machado, I. Matos, Ana Rita Grosso, Manfred Schartl, Maria M. Coelho · 2016 · Molecular Reproduction and Development
  51. The Dm-Myb Oncoprotein Contributes to Insulator Function and Stabilizes Repressive H3K27me3 PcG Domains
    Juan F. Santana, Mrutyunjaya Parida, Abby Long, Joshua Wankum, Anthony J. Lilienthal, Krishna Madhav Nukala, John Robert Manak · 2020 · Cell Reports
  52. Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation
    Kunjing Wu, Xiaojing Duan, Zhonglong Zhu, Ziyang Sang, Jie Duan, Zhongkui Jia, Lüyi Ma · 2021 · BMC Plant Biology
  53. De novo transcriptome analysis of gonads reveals the sex-associated genes in Chinese hook snout carp Opsariichthys bidens
    Rongkang Tang, Yefei Zhu, Wu Gan, Yu Zhang, Ziliang Yao, Jianfeng Ren, Mingyou Li · 2022 · Aquaculture Reports
  54. Toxic effects of triphenyltin on the silkworm Bombyx mori as a lepidopterous insect model
    Xuedong Chen, Xing Zhang, Aihong Ye, Xuehui Wu, Jinru Cao, Wenlin Zhou · 2022 · Ecotoxicology and Environmental Safety
  55. Combined transcriptomics and metabolomics analysis reveals the molecular mechanism of heat tolerance of Le023M, a mutant in Lentinula edodes
    Qin Zhang, Rencai Feng, Renyun Miao, Junbin Lin, Luping Cao, Yanqing Ni, Wensheng Li, Xu Zhao · 2023 · Heliyon
  56. The gene expression and enzymatic activity of pinoresinol-lariciresinol reductase during wood formation in Taiwania cryptomerioides Hayata
    Nien-Ting Chiang, Li‐Ting Ma, Yi-Ru Lee, Nai‐Wen Tsao, Chih-Kai Yang, Sheng‐Yang Wang, Fang‐Hua Chu · 2018 · Holzforschung
  57. Structural and functional analyses of calcium ion response factors in the mantle of Pinctada fucata
    Akihiro Matsuura, Ko Yoshimura, Hiroyuki Kintsu, Takashi Atsumi, Yasushi Tsuchihashi, Takeshi Takeuchi, Noriyuki Satoh, Lumi Negishi, Shohei Sakuda, Tomiko Asakura et al. · 2018 · Journal of Structural Biology
  58. High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report
    Craig P. Hersh, Ian Michael Adcock, Juan Carlos Celedon, Michael H. Cho, David C. Christiani, Blanca E. Himes, Naftali Kaminski, Rasika A. Mathias, Deborah A. Meyers, John F Quackenbush et al. · 2018 · Annals of the American Thoracic Society
  59. Temporal Profile of Brain Gene Expression After Prey Catching Conditioning in an Anuran Amphibian
    Vern Lewis, Frédéric Laberge, Andreas Heyland · 2020 · Frontiers in Neuroscience
  60. WGS and WTS in leukaemia: A tool for diagnostics?
    Manja Meggendorfer, Wencke Walter, Torsten Haferlach · 2020 · Best Practice & Research Clinical Haematology
  61. Preliminary Identification of Candidate Genes Related to Survival of Gynogenetic Rainbow Trout (Oncorhynchus mykiss) Based on Comparative Transcriptome Analysis
    Konrad Ocalewicz, Artur Gurgul, Marcin Polonis, Stefan Dobosz · 2020 · Animals
  62. Multi-omics analysis revealed crucial genes and pathways associated with black carp antiviral innate immunity
    Ji Liu, Yujie Yan, Jun Yan, Junting Wang, Jing Wei, Jun Xiao, Yong Zeng, Hao Feng · 2020 · Fish & Shellfish Immunology
  63. Comparative Transcriptomic Analysis of Differentially Expressed Transcripts Associated with Flowering Time of Loquat (Eriobotya japonica Lindl.)
    Haishan An, Shuang Jiang, Jiaying Zhang, Fangjie Xu, Xueying Zhang · 2021 · Horticulturae
  64. Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells
    Yixin Zhao, Noah Dukler, Gilad Barshad, Shushan Toneyan, Charles G. Danko, Adam C. Siepel · 2021 · Bioinformatics
  65. Comprehensive molecular profiling of UV-induced metastatic melanoma in Nme1/Nme2-deficient mice reveals novel markers of survival in human patients
    M. Kathryn Leonard, Gemma S. Puts, Nidhi Pamidimukkala, Gautam Adhikary, Yili Xu, Eric Kwok, Yuxin Jin, Devin E. Snyder, Nicolette Matsangos, Marián Novak et al. · 2021 · Oncogene
  66. Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data
    Francisca Rojas, Shounak Chakraborty, Caroline Vissers, Derek J. Reiman, Akshay M. Patel, Ki-Heon Lee, Ari Hong, Chan-Woo Park, Tim Reska, Julien Gagneur et al. · 2022 · Nature Biotechnology
  67. Recalcitrant Cutaneous Warts in a Family with Inherited ICOS Deficiency
    Leila Youssefian, Amir Hossein Saeidian, Ali Reza Tavasoli, Elnaz Kalamati, Karim Naghipoor, Amir Hozhabrpour, Mehrnaz Mesdaghi, Zahra Saffarian, Hamidreza Mahmoudi, Mohammad Nabavi et al. · 2022 · Journal of Investigative Dermatology
  68. Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling
    Pieter Spealman, Hao Wang, Gemma E. May, Carl Kingsford, C. Joel McManus · 2015 · Methods in molecular biology
  69. Detecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification
    Cong Ma, Carl Kingsford · 2019 · Cell Systems
  70. Alternative RNA Splicing in the Retina: Insights and Perspectives
    Casey J. Keuthan, Sadik Karma, Donald J. Zack · 2023 · Cold Spring Harbor Perspectives in Medicine
  71. Molecular Response of the Mediterranean Fruit Fly (Diptera: Tephritidae) to Heat
    Kay Anantanawat, Alexie Papanicolaou, Kelly Hill, Wei Xu · 2020 · Journal of Economic Entomology
  72. Co-expression network analyses of anthocyanin biosynthesis genes in Ruellia (Wild Petunias; Acanthaceae)
    Yongbin Zhuang, Erin A. Tripp · 2022 · BMC Ecology and Evolution
  73. Genome-wide analysis of long noncoding RNAs and their association in regulating the metamorphosis of the Sarcophaga peregrina (Diptera: Sarcophagidae)
    Yanjie Shang, Yakai Feng, Lipin Ren, Xiangyan Zhang, Fengqin Yang, Changquan Zhang, Yadong Guo · 2023 · PLoS neglected tropical diseases
  74. The E3-ligase AoUBR1 in N-end rule pathway is involved in the vegetative growth, secretome, and trap formation in Arthrobotrys oligospora
    Weiwei Zhang, Jiezuo Chen, Yani Fan, Muzammil Hussain, Xingzhong Liu, Meichun Xiang · 2021 · Fungal Biology
  75. Transcriptomic response of the intertidal limpet Patella vulgata to temperature extremes
    Catarina Moreira, Jonathon H. Stillman, Fernando Pádua Lima, Raquel Xavier, Rui Seabra, Filipa Gomes, Ana Veríssimo, Sofia Marques Silva · 2021 · Journal of Thermal Biology
  76. The Neoantigen Landscape of the Coding and Noncoding Cancer Genome Space
    Tammy Lau, Zahra J. Sefid Dashti, Emma Titmuss, Alexandra Pender, James Thomas Topham, Joshua Bridgers, Jonathan M. Loree, Xiaolan Feng, Erin Pleasance, Daniel John Renouf et al. · 2022 · Journal of Molecular Diagnostics
  77. Transcriptome profiling of two Moringa species and insights into their antihyperglycemic activity
    K. Mohamed Shafi, Radha Sivarajan Sajeevan, Sania Kouser, Chethala N. Vishnuprasad, Ramanathan Sowdhamini · 2022 · BMC Plant Biology
  78. Gene Co-Expression Network Analysis for the Selection of Candidate Early Warning Indicators of Heat and Nutrient Stress in Posidonia Oceanica
    Alex Santillán‐Sarmiento, Jessica Pazzaglia, Miriam Ruocco, Emanuela Dattolo, Luca Ambrosino, Gidon Winters, Lázaro Marín‐Guirao, Gabriele Procaccini · 2022 · The Science of The Total Environment
  79. Comparative Venom Multiomics Reveal the Molecular Mechanisms Driving Adaptation to Diverse Predator–Prey Ecosystems in Closely Related Sea Snakes
    Hao Zheng, Junjie Wang, Hairong Fan, Shuocun Wang, Ruiwei Ye, Linxue Li, Sheng Wang, An Li, Yiming Lu · 2023 · Molecular Biology and Evolution
  80. Small RNA Profiles of Brain Tissue-Derived Extracellular Vesicles in Alzheimer’s Disease
    Yiyao Huang, Tom A. P. Driedonks, Lesley Cheng, Andrey A. Turchinovich, Olga Pletniková, Javier Redding‐Ochoa, Juan Carlos Troncoso, Andrew Francis Hill, Vasiliki Mahairaki, Lei Zheng et al. · 2023 · Journal of Alzheimer s Disease
  81. EPI-X4, a CXCR4 antagonist inhibits tumor growth in pancreatic cancer and lymphoma models
    Micah N. Sagini, Michael Zepp, Ergül Eyol, Doaa M. Ali, Svetlana Gromova, Mathias Dahlmann, Diana Behrens, Christian Groeschel, Linus Tischmeier, Jens Hoffmann et al. · 2023 · Peptides
  82. Cognitive specialization for learning faces is associated with shifts in the brain transcriptome of a social wasp
    Ali J. Berens, Elizabeth A. Tibbetts, Amy L. Toth · 2017 · Journal of Experimental Biology
  83. Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data
    Yasunobu Okamura, Kengo Kinoshita · 2018 · BMC Bioinformatics
  84. Induced androgenetic development in rainbow trout and transcriptome analysis of irradiated eggs
    Konrad Ocalewicz, Artur Gurgul, Klaudia Pawlina‐Tyszko, Tomasz Szmatoła, Igor Jasielczuk, Monika Bugno‐Poniewierska, Stefan Dobosz · 2019 · Scientific Reports
  85. Integration analysis of a miRNA-mRNA expression in A549 cells infected with a novel H3N2 swine influenza virus and the 2009 H1N1 pandemic influenza virus
    Lingxi Gao, Jie Gao, Ying Liang, Rui Li, Qing Xiao, Zengfeng Zhang, Xiaohui Fan · 2019 · Infection Genetics and Evolution
  86. Regulatory networks of circRNAs related to transcription factors in Populus euphratica Oliv. heteromorphic leaves
    Lianghong Bao, Shaowei Qin, Cai-Lin Li, Zhongzhong Guo, Lifeng Zhao · 2019 · Bioscience Reports
  87. Insecticidal and synergistic activity of dsRNAs targeting buprofezin‐specific genes against the small brown planthopper, Laodelphax striatellus
    Ying Fang, Min Gu Park, Jae Young Choi, Dong H Park, Minghui Wang, Hyun Joo Kim, Woo J. Kim, Yeon Ho Je · 2020 · Archives of Insect Biochemistry and Physiology
  88. Analysis of the Glyphodes pyloalis larvae immune transcriptome in response to parasitization by its endoparasitoid, Aulacococentrum confusum
    Sheng Sheng, Jiao Wang, Jie Chu, Jianhao Ding, Zhixiang Liu, De‐Lei Jiang, Xinhao Liang, Zuo-min Shao, Jun Wang, Fu‐An Wu · 2021 · Comparative Biochemistry and Physiology Part D Genomics and Proteomics
  89. High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts
    Žana Kapustina, Justina Medžiūnė, Gediminas Alzbutas, Irmantas Rokaitis, Karolis Matjošaitis, Gytis Mackevičius, Simona Žeimytė, Laurynas Karpus, Arvydas Lubys · 2021 · Microbial Genomics
  90. Investigation of P1/HC-Pro-Mediated ABA/Calcium Signaling Responses via Gene Silencing through High- and Low-Throughput RNA-seq Approaches
    Yen-Hsin Chiu, Yu‐Ling Hung, Hsin-Ping Wang, Wei-Lun Wei, Qian-Wen Shang, Thanh Ha Pham, Chien‐Kang Huang, Zhao‐Jun Pan, Shih‐Shun Lin · 2021 · Viruses
  91. Searching for non‐transposable targets of planarian nuclear PIWI in pluripotent stem cells and differentiated cells
    Makoto Kashima, Kiyokazu Agata, Norito Shibata · 2018 · Development Growth & Differentiation
  92. Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister-species complex
    Clément Rougeux, Pierre‐Alexandre Gagnaire, Kim Præbel, Ole Seehausen C D, Louis Bernatchez · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  93. Outcomes of Low-Temperature Stress on Biological Alterations within Pothos (Epipremnum aureum) Leaves
    Wu, Yanqing, Cai, Xiang, Tang, Yuhan · 2022 · Life
  94. The utilization of photophosphorylation uncoupler to improve lipid production of Chlorella, a case study using transcriptome and functional gene expression analysis to reveal its mechanism
    Zhangzhang Xie, Fangyan Wu, Weitie Lin, Jianfei Luo · 2021 · Biochemical Engineering Journal
  95. Differential LRRK2 Signalling and Gene Expression in WT-LRRK2 and G2019S-LRRK2 Mouse Microglia Treated with Zymosan and MLi2
    Iqra Nazish, Adamantios Mamais, Anna Mallach, Conceição Bettencourt, Alice Kaganovich, Thomas T. Warner, John Hardy, Patrick Alfryn Lewis, Jennifer M. Pocock, Mark Cookson et al. · 2023 · Cells
  96. Microbiome changes and characteristics under nutrient injection for enhanced oil production at Daqing oilfield
    Zi-Yue Fu, Wentao Chen, Gui-Na Qi, Zhao-wei Hou, Yi‐Fan Liu, Li-Bin Shou, Lei Zhou, Shi‐Zhong Yang, Xiao‐Lin Wu, Ji‐Dong Gu et al. · 2024 · International Biodeterioration & Biodegradation
  97. Decoding the Genomic and Functional Landscape of Emerging Subtypes in Ovarian Cancer
    Giulia Micoli, Kari Lavikka, Yilin Li, Anna Pirttikoski, Daria Afenteva, Wojciech Senkowski, Giovanni Marchi, Anna Vähärautio, Taru Muranen, Titta Joutsiniemi et al. · 2025 · Cancer Discovery
  98. Trichoderma koningiopsis Induced Changes in Root Exudates of Masson Pine Seedlings Alter Rhizosphere Microbiome to Enhance Damping‐Off Disease Resistance
    Xuewen Wang, Hongjin Wei, Jiaojiao Lei, Zhibing Rui, Cun Yu · 2025 · Plant Cell & Environment
  99. UDP-glycosyltransferase confers anthranilic diamide resistance in Bemisia tabaci
    Huiwen Tan, Xichao Hu, Jinghao Hu, Wei Xu, Qianwen Wang, Xiaolan Liu, Lei Guo · 2025 · Journal of Advanced Research
  100. Integrating long noncoding RNAs and mRNAs expression profiles of response to Plasmodiophora brassicae infection in Pakchoi (Brassica campestris ssp. chinensis Makino)
    Hanji Zhu, Xiaofeng Li, Dandan Xi, Wen Zhai, Zhaohui Zhang, Yuying Zhu · 2019 · PLoS ONE