Streaming fragment assignment for real-time analysis of sequencing experiments

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

Cited by (1,000)

Items 401–500 of 1,000

  1. Identification of NRAS isoform 2 overexpression as a mechanism facilitating BRAF inhibitor resistance in malignant melanoma
    Megan Christina Duggan, Andrew R. Stiff, Maryam A. Bainazar, Kelly Regan, Gonzalo N. Olaverria Salavaggione, Sophia E. Maharry, James Stewart Blachly, Madison K. Krischak, Christopher James Walker, Nicholas Latchana et al. · 2017 · Proceedings of the National Academy of Sciences
  2. Comprehensive multi-omics and biochemical analysis to elucidate the molecular response mechanisms of gill and kidney tissues under acute salinity stress in Pseudobagras ussuriensis
    Yu Liu, Libo Gu, Jun Zhao, Mengzhu Liu, Ke Wang, Qingbo Zhou, Yang Cao, Ruyi Hu, Weiwei Wang, Qing Liu · 2025 · BMC Genomics
  3. The transcriptional response of skin to fluorescent light exposure in viviparous (Xiphophorus) and oviparous (Danio, Oryzias) fishes
    Mikki Boswell, William T. Boswell, Yuan Lü, Markita G. Savage, Zachary Mazurek, Jordan T. Chang, Jeanot Muster, Ronald B. Walter · 2017 · Comparative Biochemistry and Physiology Part C Toxicology & Pharmacology
  4. RNA-Seq Transcriptome Analysis of the Liver and Brain of the Black Carp (Mylopharyngodon piceus) During Fasting
    Yafan Dai, Yubang Shen, Shentong Wang, Jia-Hua Zhang, Yuhong Su, Sheng-cheng Bao, Xiaoyan Xu, Jiale Li · 2021 · Marine Biotechnology
  5. Long-Term Cultivation and Meta-Omics Reveal Methylotrophic Methanogenesis in Hydrocarbon-Impacted Habitats
    Yi‐Fan Liu, Jing Chen, Zhonglin Liu, Zhaowei Hou, Bo Liang, Li-Ying Wang, Lei Zhou, Li-Bin Shou, Dandan Lin, Shi‐Zhong Yang et al. · 2022 · Engineering
  6. Exposure of Larvae to Sublethal Thiacloprid Delays Bee Development and Affects Transcriptional Responses of Newly Emerged Honey Bees
    Bin Li, Ke Li, Ai-Rui Li, Qingyun Diao, Qiang Wang, Yong‐Jun Liu · 2022 · Frontiers in Insect Science
  7. Transcriptomic analysis of adaptive mechanisms in response to inland saline-alkaline water in the mud crab, Scylla paramamosain
    Guoling Liang, Kangxiang Qin, Yuhao Chen, Mingming Niu, Huan Wang, Chunlin Wang, Changkao Mu, Lizhi Chen, Fangfang Wang, Qiong Su et al. · 2022 · Frontiers in Marine Science
  8. Integrative analysis of many RNA-seq datasets to study alternative splicing
    Wenyuan Li, Chao Dai, Shuli Kang, Xianghong Jasmine Zhou · 2014 · Methods
  9. Improving read mapping using additional prefix grams
    Jongik Kim, Chen Li, Xiaohui S. Xie · 2014 · BMC Bioinformatics
  10. Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants
    Nicholas J. B. Brereton, Emmanuel Gonzalez, J. Marleau, Werther Guidi Nissim, Michel Labrecque, Simon Joly, Frédéric Emmanuel Pitre · 2016 · PLANT PHYSIOLOGY
  11. Hobbes3: Dynamic generation of variable-length signatures for efficient approximate subsequence mappings
    Jongik Kim, Chen Li, Xiaohui S. Xie · 2016 · IEEE International Conference on Data Engineering (ICDE)
  12. De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water
    Peter A. Bain, Adrienne L. Gregg, Anupama Kumar · 2016 · BMC Genomics
  13. Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans
    Sabrina Simon, Sven Sagasser, Edoardo Saccenti, Mercer R. Brugler, M. Eric Schranz, Heike Hadrys, George Amato, Rob DeSalle · 2017 · Scientific Reports
  14. Physiological and Transcriptomic Analyses Elucidate That Exogenous Calcium Can Relieve Injuries to Potato Plants (Solanum tuberosum L.) under Weak Light
    Jinfeng Hou, Jie Li, Yang Yang, Zixin Wang, Bowen Chang, Xiaowei Yu, Lingyun Yuan, Chenggang Wang, Guohu Chen, Xiaoyan Tang et al. · 2019 · International Journal of Molecular Sciences
  15. Conserved Proteins Are Fragile
    Raquel Assis, Alexey S. Kondrashov · 2013 · Molecular Biology and Evolution
  16. An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq
    Yongxian Yuan, Huaiqian Xu, Ross Ka‐Kit Leung · 2016 · BMC Genomics
  17. A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
    Charlotte Soneson, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D. Robinson · 2019 · Life Science Alliance
  18. A time-resolved dual transcriptome analysis reveals the molecular regulating network underlying the compatible/incompatible interactions between cabbage (Brassica oleracea) and Fusarium oxysporum f. sp. conglutinans
    Xing Liu, Cunbao Zhao, Limei Yang, Mu Zhuang, Yangyong Zhang, Yong Wang, Zhiyuan Fang, Honghao Lv · 2020 · Plant and Soil
  19. Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle
    Chao Yuan, Ke Zhang, Yaojing Yue, Tingting Guo, Jianbin Liu, Chune Niu, Xiaoping Sun, Ruilin Feng, Xiaolong Wang, Bohui Yang · 2020 · PeerJ
  20. Transcriptome analysis reveals the underlying mechanism of nanocomposite packaging in delaying quality deterioration of Flammulina velutipes
    Changzhou Zuo, Qiuhui Hu, Anxiang Su, Fei Pei, Gaoxing Ma, Hui Xu, Minhao Xie, Jianhui Liu, Alfred Mugambi Mariga, Wenjian Yang · 2021 · Postharvest Biology and Technology
  21. Candidate Effectors of Plasmodiophora brassicae Pathotype 5X During Infection of Two Brassica napus Genotypes
    Leonardo Galindo‐González, Sheau‐Fang Hwang, Stephen E. Strelkov · 2021 · Frontiers in Microbiology
  22. Integrative analysis of the transcriptome and metabolome reveals the mechanism of saline–alkali stress tolerance in Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge.) Hsiao
    Jie Liu, Xiongjie Zhang, Jinhua Sheng · 2022 · Food Quality and Safety
  23. A scoping review on deep learning for next-generation RNA-Seq. data analysis
    Diksha Pandey, P. O. Perumal · 2023 · Functional & Integrative Genomics
  24. Thermal stress and predation risk trigger distinct transcriptomic responses in the intertidal snail Nucella lapillus
    Nathaniel D. Chu, Luke P. Miller, Stefan T. Kaluziak, Geoffrey C. Trussell, Steven V. Vollmer · 2014 · Molecular Ecology
  25. Expression of Antisense Long Noncoding RNAs as Potential Regulators in Rainbow Trout with Different Tolerance to Plant-Based Diets
    Jason W. Abernathy, Ken Overturf · 2018 · Animal Biotechnology
  26. Population‐specific transcriptional differences associated with freeze tolerance in a terrestrial worm
    Tjalf E. de Boer, Dick Roelofs, Riet Vooijs, Martin Holmstrup, Mónica J.B. Amorim · 2018 · Ecology and Evolution
  27. The transcriptome of the veiled chameleon ( Chamaeleo calyptratus ): A resource for studying the evolution and development of vertebrates
    Brendan J. Pinto, Daren C. Card, Todd A. Castoe, Raúl E. Díaz, Stuart V. Nielsen, Paul A. Trainor, Tony Gamble · 2019 · Developmental Dynamics
  28. Tick Gené’s organ engagement in lipid metabolism revealed by a combined transcriptomic and proteomic approach
    Marina Amaral Xavier, Lucas Tirloni, Antônio F. M. Pinto, Jolene K. Diedrich, John R. Yates, Sergio A. Gonzales, Marisa Diana Farber, Itabajara da Silva Vaz, Carlos Termignoni · 2019 · Ticks and Tick-borne Diseases
  29. Surface coating and particle size are main factors explaining the transcriptome-wide responses of the earthworm Lumbricus rubellus to silver nanoparticles
    Dick Roelofs, Sunday Makama, Tjalf E. de Boer, Riet Vooijs, Cornelis A.M. van Gestel, N.W. van den Brink · 2020 · Environmental Science Nano
  30. A large-scale comparative study of isoform expressions measured on four platforms
    Wei Zhang, Raphael Petegrosso, Jae-Woong Chang, Jiao Sun, Jeongsik Yong, JEREMY R. CHIEN, Rui Kuang · 2020 · BMC Genomics
  31. Whole-transcriptome sequencing–based concomitant detection of viral and human genetic determinants of cutaneous lesions
    Amir Hossein Saeidian, Leila Youssefian, Charles Huang, Fahimeh Palizban, Mahtab Naji, Zahra Saffarian, Hamidreza Mahmoudi, Azadeh Goodarzi, Soheila Sotoudeh, Fatemeh Vahidnezhad et al. · 2022 · JCI Insight
  32. No evidence for Fabaceae Gametophytic self-incompatibility being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes
    Bruno Aguiar, Jorge Vieira, Ana E Cunha, Cristina P. Vieira · 2015 · BMC Plant Biology
  33. Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño
    María Rocío Aguilar-Rangel, Ricardo A. Chávez Montes, Eric Gerardo González Segovia, Jeffrey Ross‐Ibarra, June Kilpatrick Simpson, Ruairidh J. H. Sawers · 2017 · PeerJ
  34. Transcriptome Analysis
    Anuj Srivastava, Joshy George, Radha Krishna Murthy Karuturi · 2018 · Elsevier eBooks
  35. Multi-omics analysis reveals the attenuation of the interferon pathway as a driver of chemo-refractory ovarian cancer
    Daria Afenteva, Rong Yu, Anna Rajavuori, Marina Salvadores, Inga-Maria P. Launonen, Kari Lavikka, Kaiyang Zhang, Anna Pirttikoski, Giovanni Marchi, Sanaz Jamalzadeh et al. · 2025 · Cell Reports Medicine
  36. Regulation of cellular sterol homeostasis by the oxygen responsive noncoding RNA lincNORS
    Xue Wu, Cristina Mariana Niculite, Mihai Bogdan Preda, Annalisa Rossi, Toma Tebaldi, Elena Dragomir Butoi, Mattie K. White, Oana Mihaela Tudoran, Daniela Nicoleta Petrusca, Amber S. Hopf Jannasch et al. · 2020 · Nature Communications
  37. Zucchini Plants Alter Gene Expression and Emission of (E)-β-Caryophyllene Following Aphis gossypii Infestation
    Alessia Vitiello, Donata Molisso, Maria Cristina Digilio, Massimo Giorgini, Giandomenico Corrado, Toby J. A. Bruce, Nunzio D’Agostino, Rosa Rao · 2021 · Frontiers in Plant Science
  38. Phylogenomic approach reveals strong signatures of introgression in the rapid diversification of neotropical true fruit flies (Anastrepha: Tephritidae)
    Carlos Congrains, Roberto Antonio Zucchi, Reinaldo Alves de Brito · 2021 · Molecular Phylogenetics and Evolution
  39. Transcriptome and Metabolome Analyses Provide Insights into the Stomium Degeneration Mechanism in Lily
    Ling He, Xinyue Liu, Ze Wu, Nianjun Teng · 2021 · International Journal of Molecular Sciences
  40. Metatranscriptomic Analysis of Corals Inoculated With Tolerant and Non-Tolerant Symbiont Exposed to High Temperature and Light Stress
    Ikuko Yuyama, Tomihiko Higuchi, Takuma Mezaki, Hisako Tashiro, Kazuho Ikeo · 2022 · Frontiers in Physiology
  41. Resistance to dinotefuran in Bemisia tabaci in China: status and characteristics
    Kaixin Li, Jiantao Liu, Ziqiong Geng, Wei Xu, Zhuang Zhang, Dong Chu, Lei Guo · 2022 · Pest Management Science
  42. Whole transcriptome–based skin virome profiling in typical epidermodysplasia verruciformis reveals α-, β-, and γ-HPV infections
    Amir Hossein Saeidian, Leila Youssefian, Mahtab Naji, Hamidreza Mahmoudi, Samantha M. Barnada, Charles Huang, Karim Naghipoor, Amir Hozhabrpour, Jason S. Park, Flavia Manzo Margiotta et al. · 2023 · JCI Insight
  43. Host Transcriptome Analysis of Spodoptera frugiperda Larvae Parasitized by Microplitis manilae
    Ahamaijiang Gulinuer, Binglin Xing, Lei Yang · 2023 · Insects
  44. De novo Sequencing and Comparative Transcriptomics of Floral Development of the Distylous Species Lithospermum multiflorum
    James I. Cohen · 2016 · Frontiers in Plant Science
  45. Inflammatory responses induce an identity crisis of alveolar macrophages, leading to pulmonary alveolar proteinosis
    Risa Ebina‐Shibuya, Mitsuyo Matsumoto, Makoto Kuwahara, Kyoung‐Jin Jang, Manabu Sugai, Yoshiaki Ito, Ryo Funayama, Keiko Nakayama, Yuki Sato, Naoto Ishii et al. · 2017 · Journal of Biological Chemistry
  46. Transcriptomic response to decreased pH in adult, larval and juvenile red king crab, Paralithodes camtschaticus , and interactive effects of pH and temperature on juveniles
    Jonathon H. Stillman, Scott A. Fay, Syed Mudasir Ahmad, Katherine M. Swiney, Robert J. Foy · 2020 · Journal of the Marine Biological Association of the United Kingdom
  47. Analysis of Allelic Imbalance in Rice Hybrids Under Water Stress and Association of Asymmetrically Expressed Genes with Drought-Response QTLs
    Nelzo C. Ereful, Li-Yu Daisy Liu, Eric Tsai, Shu‐Min Kao, Shalabh Dixit, Ramil Mauleon, Katrina Malabanan, Michael J. Thomson, Antonio C. Laurena, David Lee et al. · 2016 · Rice
  48. A direct comparison of genome alignment and transcriptome pseudoalignment
    Lynn Yi, Lauren Liu, Páll Melsted, Lior S. Pachter · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  49. Conservation and lineage-specific rearrangements in the GOBP/PBP gene complex of distantly related ditrysian Lepidoptera
    Yuji Yasukochi, Bin Yang, Toshiaki Fujimoto, Ken Sahara, Takashi Matsuo, Yukio Ishikawa · 2018 · PLoS ONE
  50. Enhanced migration and adhesion of peripheral blood neutrophils from SAPHO patients revealed by RNA-Seq
    Yuxiu Sun, Chen Li, Mengmeng Zhu, Shen Zhang, Yihan Cao, Qiao Yang, Pengfei Zhao, Guangrui Huang, Anlong Xu · 2019 · Orphanet Journal of Rare Diseases
  51. Transcriptome analysis of immune-related gene expression in Yellow River carp (Cyprinus carpio var.) after challenge with Flavobacterium columnare
    Yongfang Jia, Zhishuai Li, Qiyan Du, Zhongjie Chang · 2021 · Microbial Pathogenesis
  52. Demonstration of an aggregated biomarker response approach to assess the impact of point and diffuse contaminant sources in feral fish in a small river case study
    Markus Schmitz, Björn Deutschmann, Nele Markert, Thomas Backhaus, Werner Brack, Mario Brauns, Markus Brinkmann, Thomas‐Benjamin Seiler, Patrick Fink, Song Tang et al. · 2021 · The Science of The Total Environment
  53. Significance of phosphorus deficiency for the mitigation of mercury toxicity in the Robinia pseudoacacia L.– rhizobia symbiotic association
    Rui Liu, Bin Hu, Michael Dannenmann, Anette Giesemann, Christoph‐Martin Geilfus, Canbo Li, Lan Gao, Emmanouil Flemetakis, Robert Hänsch, Dingyong Wang et al. · 2024 · Journal of Hazardous Materials
  54. EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering
    Soohyun Lee, Chae Hwa Seo, B. Alver, Sanghyuk Lee, Peter J. Park · 2015 · BMC Bioinformatics
  55. Transcriptome characterization of male accessory glands in ants to identify molecules involved in their reproductive success
    Ayako Gotoh, Shuji Shigenobu, Katsushi Yamaguchi, Satoru Kobayashi, Fuminori Ito, Kazuki Tsuji · 2017 · Insect Molecular Biology
  56. Investigating the NAD-ME biochemical pathway within C4 grasses using transcript and amino acid variation in C4 photosynthetic genes
    Alexander Watson‐Lazowski, Alexie Papanicolaou, Robert Edward Sharwood, Oula Ghannoum · 2018 · Photosynthesis Research
  57. Modularity Facilitates Flexible Tuning of Plastic and Evolutionary Gene Expression Responses during Early Divergence
    H. Mäkinen, Tiina Sävilammi, S. Papakostas, E. Leder, L. A. Vøllestad, C. Primmer · 2017 · bioRxiv
  58. Functional shell matrix proteins tentatively identified by asymmetric snail shell morphology
    Akito Ishikawa, Keisuke Shimizu, Yukinobu Isowa, Takeshi Takeuchi, Ran Zhao, Keiji Kito, Manabu Fujie, Noriyuki Satoh, Kazuyoshi Endo · 2020 · Scientific Reports
  59. Transcriptomic analysis of the bagworm moth silk gland reveals a number of silk genes conserved within Lepidoptera
    Takuya Tsubota, Taiyo Yoshioka, Akiya Jouraku, Takao K. Suzuki, Naoyuki Yonemura, Kenji Yukuhiro, Tsunenori Kameda, Hideki Sezutsu · 2020 · Insect Science
  60. Transcriptome Analysis Reveals the Symbiotic Mechanism of Ustilago esculenta -Induced Gall Formation of Zizania latifolia
    Jie Li, Zhiyuan Lǚ, Yang Yang, Yuanlin Guan, Jinfeng Hou, Lingyun Yuan, Guohu Chen, Chenggang Wang, Shaoke Jia, Feng Xuming et al. · 2021 · Molecular Plant-Microbe Interactions
  61. Aggressive and recurrent ovarian cancers upregulate ephrinA5, a non-canonical effector of EphA2 signaling duality
    Joonas Jukonen, Lidia Moyano‐Galceran, Katrin Höpfner, Elina A. Pietilä, Laura Lehtinen, Kaisa Huhtinen, Erika Gucciardo, Johanna Hynninen, Sakari Hietanen, Seija Grénman et al. · 2021 · Scientific Reports
  62. Discovery of new genetic loci for male sexual orientation in Han population
    Shaohua Hu, Haimei Li, Hao Yu, Yan Liu, Chen-Xing Liu, Xian-bo Zuo, Jing Lü, Jiajun Jiang, Cai-Xi Xi, Bochao Huang et al. · 2021 · Cell Discovery
  63. RETRACTED: Molecular mechanism of inhibitory effects of melatonin on prostate cancer cell proliferation, migration and invasion
    Altannavch Nyamsambuu, Md. Asaduzzaman Khan, Xi Zhou, Hanchun Chen · 2022 · PLoS ONE · Retracted
  64. Comparative transcriptome analysis provides insights into the molecular mechanisms of high-frequency hearing differences between the sexes of Odorrana tormota
    Zhuo Chen, Yao Liu, Rui Liang, Chong Cui, Yanjun Zhu, Fang Zhang, Jie Zhang, Xiaohong Chen · 2022 · BMC Genomics
  65. how_are_we_stranded_here: quick determination of RNA-Seq strandedness
    Bethany Signal, Tim Kahlke · 2022 · BMC Bioinformatics
  66. LncRNA-mRNA integrated profiling analysis in response to white spot syndrome virus in hepatopancreas in Penaeus japonicus
    Yaqun Zhang, Na Yao, Chuantao Zhang, Xiangshan Sun, Jingxian Huang, Bingran Zhao, Hengde Li · 2022 · Fish & Shellfish Immunology
  67. Relationships of <i>APOE</i> Genotypes With Small RNA and Protein Cargo of Brain Tissue Extracellular Vesicles From Patients With Late-Stage AD
    Huang, Yiyao, Driedonks, Tom A.P., Cheng, Lesley, Rajapaksha, Harinda, Turchinovich, Andrey, Routenberg, David A., Nagaraj, Rajini, Redding-Ochoa, Javier, Arab, Tanina, Powell, Bonita H. et al. · 2022 · Neurology Genetics
  68. Genome-wide quantification of copy-number aberration impact on gene expression in ovarian high-grade serous carcinoma
    Sanaz Jamalzadeh, Jun Dai, Kari Lavikka, Yilin Li, Jing Jiang, Kaisa Huhtinen, Anni Virtanen, Jaana Oikkonen, Sakari Hietanen, Johanna Hynninen et al. · 2024 · BMC Cancer
  69. Transcriptomic and Proteomic Research To Explore Bruchid-Resistant Genes in Mungbean Isogenic Lines
    Wu-Jui Lin, Chia-Yun Ko, Mao‐Sen Liu, Chien-Yen Kuo, Dung-Chi Wu, Chien‐Yu Chen, Roland Schafleitner, Long‐Fang O. Chen, Hsiao-Feng Lo · 2016 · Journal of Agricultural and Food Chemistry
  70. Host genetic modifiers of nonproductive angiogenesis inhibit breast cancer
    Michael J. Flister, Shirng‐Wern Tsaih, Alexander Stoddard, Cody Plasterer, Jaidip Manikrao M. Jagtap, Abdul Kareem Parchur, Gayatri Sharma, Anthony R. Prisco, Angela Lemke, Dana Murphy et al. · 2017 · Breast Cancer Research and Treatment
  71. Computer Analysis of Glioma Transcriptome Profiling: Alternative Splicing Events
    Vladimir N. Babenko, Н. В. Губанова, А. О. Брагин, И. В. Чадаева, Gennady V. Vasiliev, Irina V. Medvedeva, Alekey S. Gaytan, А. Л. Кривошапкин, Yuriy Lvovich Orlov · 2017 · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
  72. Characterization of candidate genes involved in halotolerance using high-throughput omics in the halotolerant bacterium Virgibacillus chiguensis
    Yan-Huey Chen, Yuan‐Tay Shyu, Shih‐Shun Lin · 2018 · PLoS ONE
  73. Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis
    Shaowei Qin, Jiang Ren-jun, Na Zhang, Zhan-Wen Liu, Cai-Lin Li, Zhongzhong Guo, Lianghong Bao, Lifeng Zhao · 2018 · Scientific Reports
  74. Transcriptomic landscape of prophase I sunflower male meiocytes
    Nathalia M. V. Florez-Zapata, Manuel Humberto Reyes-Valdés, Fernando Hernández-Godínez, Octavio Martínez · 2014 · Frontiers in Plant Science
  75. Transcriptomic response in Acropora muricata under acute temperature stress follows preconditioned seasonal temperature fluctuations
    Sonny T. M. Lee, Shashank Keshavmurthy, Silvia Fontana, Takuma Mezaki, Wen-Hua Chou, Chaolun Allen Chen · 2018 · BMC Research Notes
  76. Ambiguous fragment assignment for high-throughput sequencing experiments
    Adam Roberts · 2013 · eScholarship (California Digital Library)
  77. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays
    Li, Bo, Tambe, Akshay, Aviran, Sharon, Pachter, Lior · 2017 · Cell Systems
  78. ZFP207 sustains pluripotency by coordinating OCT4 stability, alternative splicing and RNA export
    Sandhya Malla, Devi Prasad Bhattarai, Paula Groza, Dario Melguizo‐Sanchis, Ionut Atanasoai, Carlos Martinez‐Gamero, Ángel‐Carlos Román, Dandan Zhu, Dung‐Fang Lee, Claudia Kutter et al. · 2022 · EMBO Reports
  79. Integrative Investigation of Root-Related mRNAs, lncRNAs and circRNAs of “Muscat Hamburg” (Vitis vinifera L.) Grapevine in Response to Root Restriction through Transcriptomic Analyses
    Jingjing Liu, Hui Li, Lipeng Zhang, Yue Qin Song, Juan He, Wenping Xu, Chao Ma, Yi Ren, Huaifeng Liu · 2022 · Genes
  80. Characterization of the molecular, cellular, and behavioral changes caused by exposure to a saline-alkali environment in the Chinese mitten crab, Eriocheir sinensis
    Meiyao Wang, Pao Xu, Jun Zhou, Jiachun Ge, Gangchun Xu · 2024 · Environmental Research
  81. Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools
    Dena Leshkowitz, Ester Feldmesser, Gilgi Friedlander, Ghil Jona, Elena Ainbinder, Yisrael Parmet, Shirley Horn‐Saban · 2016 · PLoS ONE
  82. RNA-Seq Data Analysis, Applications and Challenges
    Anna Esteve‐Codina · 2018 · Comprehensive analytical chemistry
  83. Transcriptomic analysis reveals differences in the regulation of amino acid metabolism in asexual and sexual planarians
    Kiyono Sekii, Shunta Yorimoto, Hikaru Okamoto, Nanna Nagao, Takanobu Maezawa, Yasuhisa Matsui, Katsushi Yamaguchi, Ryohei Furukawa, Shuji Shigenobu, Kazuya Kobayashi · 2019 · Scientific Reports
  84. Out of the testis, into the ovary: biased outcomes of gene duplication and deletion in Drosophila
    Raquel Assis · 2019 · Evolution
  85. Telomeric TART elements target the piRNA machinery in Drosophila
    Christopher E. Ellison, Meenakshi S. Kagda, Weihuan Cao · 2020 · PLoS Biology
  86. Whole-Genome Duplication Facilitated the Evolution of C4 Photosynthesis in Gynandropsis gynandra
    Chi-Fa Huang, Wen-Yu Liu, Mei‐Yeh Jade Lu, Yi-Hua Chen, Maurice S. B. Ku, Wen‐Hsiung Li · 2021 · Molecular Biology and Evolution
  87. Integrated transcriptomic and metabolic analysis response in gills, hepatopancreas, and muscle metabolism in oriental river prawn Macrobrachium nipponense in response to acute high salinity stress
    Yaoran Fan, Jianbin Feng, Zefei Wang, Feiyue Ling, Keyi Ma, Xueming Hua, Juan‐Ying Li, Jiale Li · 2022 · Aquaculture Reports
  88. SmgGDS is a transient nucleolar protein that protects cells from nucleolar stress and promotes the cell cycle by regulating DREAM complex gene expression
    Patrick Gonyo, Carmen R. Bergom, Anthony C. Brandt, S-W Tsaih, Yunguang Sun, Tarin M. Bigley, Ellen Lorimer, Scott S. Terhune, Hallgeir Rui, Michael J. Flister et al. · 2017 · Oncogene
  89. Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data
    Jeremy R. B. Newman, PATRICK J. CONCANNON, Manuel Tardáguila, Ana Conesa, Lauren M. McIntyre · 2018 · G3 Genes Genomes Genetics
  90. Genomic and Transcriptomic Analyses Reveals ZNF124 as a Critical Regulator in Highly Aggressive Medulloblastomas
    Zaili Luo, Xinran Dong, Jianzhong Yu, Yong Xia, Kalen Berry, Rohit Rao, Lingli Xu, Ping Xue, Tong Chen, Yifeng Lin et al. · 2021 · Frontiers in Cell and Developmental Biology
  91. Emu: Species-Level Microbial Community Profiling for Full-Length Nanopore 16S Reads
    Kristen D. Curry, Qi Wang, Michael Nute, Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Enid Graeber, Patrick Finzer, Werner Mendling, Qinglong Wu et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  92. NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data
    Ma, Xinyun, Zhang, Xuegong · 2013 · BMC Bioinformatics
  93. miR-210 Expression Is Strongly Hypoxia-Induced in Anaplastic Thyroid Cancer Cell Lines and Is Associated with Extracellular Vesicles and Argonaute-2
    Bonita H. Powell, Andrey A. Turchinovich, Yongchun Wang, Olesia A. Gololobova, Dominik Buschmann, Martha A. Zeiger, Christopher B. Umbricht, Kenneth Whitaker Witwer · 2023 · International Journal of Molecular Sciences
  94. Emodin‐Induced Necroptosis in Prostate Cancer Cells via the Mitochondrial Fission HSP90/MLKL/PGAM Pathway
    Xi Zhou, Farjana Yeasmin Khusbu, Yang Xie, Peng Hui Yang · 2023 · Chemistry & Biodiversity
  95. The Nuclear Cap-Binding Complex Mediates Meiotic Silencing by Unpaired DNA
    Logan M Decker, Hua Xiao, Erin C. Boone, Michael M Vierling, Benjamin S Shanker, Shanika L Kingston, Shannon F Boone, Jackson B Haynes, Patrick Shiu · 2017 · G3 Genes Genomes Genetics
  96. Molecular insights into the sex-differential regulation of signal transduction in the cerebral ganglion and metabolism in the hepatopancreas of Eriocheir sinensis during reproduction
    Meiyao Wang, Yongkai Tang, Juhua Yu, Shengyan Su, Jianlin Li, Fan Dong Yu, Hongxia Li, Changyou Song, Fukuan Du, Pao Xu · 2019 · Genomics
  97. Changes in long non-coding RNA transcriptomic profiles after ischemia-reperfusion injury in rat spinal cord
    Zhibin Zhou, Bin Han, Hai Jin, Aimin Chen, Lei Zhu · 2020 · PeerJ
  98. Plasma membrane phylloquinone biosynthesis in nonphotosynthetic parasitic plants
    Xi Gu, Ing-Gin Chen, Scott A. Harding, Batbayar Nyamdari, Maria Andrea Ortega, Kristen Clermont, James H. Westwood, Chung‐Jui Tsai · 2021 · PLANT PHYSIOLOGY
  99. Genome-wide and comparative phylogenetic analysis of senescence-associated NAC transcription factors in sunflower (Helianthus annuus)
    Sofia A. Bengoa Luoni, Alberto Cenci, Sebastián Moschen, Salvador Nicosia, Laura Mabel Radonic, Julia Sabio y García, Nicolas Langlade, Denis Vile, Cecilia Vazquez-Rovere, Paula del Carmen Fernández · 2021 · BMC Genomics
  100. Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression
    Carol A Soderlund, William M. Nelson, Stephen A. Goff · 2014 · PLoS ONE