pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1155/2015/862130

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library
Cited by: 29
Author(s): Yan Guo, Shilin Zhao, Quanhu Sheng, Mingsheng Guo, Brian D. Lehmann, Jennifer A. Pietenpol, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: almost 10 years ago

10.3390/ijms21228749

Dysregulation of Transcription Factor Activity during Formation of Cancer-Associated Fibroblasts
Cited by: 6
Author(s): Przemysław Kapusta, Joanna Dulińska-Litewka, Justyna Totoń‐Żurańska, A. Borys, Paweł Konieczny, Paweł Wołkow, Michał Seweryn
Software Mentions: 4
Published: about 4 years ago

10.3390/ijms20051100

Folate Repletion after Deficiency Induces Irreversible Genomic and Transcriptional Changes in Human Papillomavirus Type 16 (HPV16)-Immortalized Human Keratinocytes
Cited by: 6
Author(s): Claudia Savini, Ruwen Yang, Larisa Savelyeva, Elke Göckel-Krzikalla, Agnes Hotz‐Wagenblatt, Frank Westermann, Frank Rösl
Software Mentions: 4
Published: over 5 years ago

10.1155/2019/2725192

In Silico Integration Approach Reveals Key MicroRNAs and Their Target Genes in Follicular Thyroid Carcinoma
Cited by: 10
Author(s): Shengqing Hu, Yunfei Liao, Juan Zheng, Luoning Gou, Anita Regmi, Mohammad Ishraq Zafar, Lulu Chen
Software Mentions: 4
Published: over 5 years ago

10.3390/ani10010002

Atmospheric Ammonia Affects Myofiber Development and Lipid Metabolism in Growing Pig Muscle
Cited by: 10
Author(s): Shouwei Tang, Jingjing Xie, Sheng Zhang, Weida Wu, Bao Yi, Hongfu Zhang
Software Mentions: 4
Published: almost 5 years ago

10.3390/v12080817

Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain
Cited by: 6
Author(s): Jayeshbhai Chaudhari, Chia-Sin Liew, Aspen M. Workman, Jean-Jack M. Riethoven, David Steffen, Sarah Sillman, Hiep L.X. Vu
Software Mentions: 4
Published: over 4 years ago

10.1523/JNEUROSCI.2979-20.2021

Changes in Presynaptic Gene Expression during Homeostatic Compensation at a Central Synapse
Cited by: 10
Author(s): Evan R. Harrell, Diogo Pimentel, Gero Miesenböck
Software Mentions: 4
Published: almost 4 years ago

10.1084/jem.20200137

PDGFA-associated protein 1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification
Cited by: 6
Author(s): Verónica Delgado-Benito, Maria Berruezo-Llacuna, Robert Altwasser, Wiebke Winkler, Devakumar Sundaravinayagam, Sandhya Balasubramanian, Marieta Caganova, Robin Graf, Ali Rahjouei, Marie-Thérèse Henke, Madlen Driesner, Lisa Keller, Alessandro Prigione, Martin Janz, Altuna Akalin, Michela Di Virgilio
Software Mentions: 4
Published: over 4 years ago

10.1186/s12915-020-00779-3

Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
Cited by: 15
Author(s): Helen Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony Adamson, Craig Taylor, Julia Ding, Vasanthi Priyadarshini Gaddi, Yao Fu, Patrick M. Gaffney, Gisela Orozco, Richard B Warren, Steve Eyre
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-016-2403-1

RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations
Cited by: 20
Author(s): Edin Hamzić, Rikke Brødsgaard Kjærup, Núria Mach, Guilietta Minozzi, Francesco Strozzi, V. Gualdi, J. L. Williams, Jun Chen, Eva Wattrang, Bart Buitenhuis, Helle R. Juul‐Madsen, Tina Sørensen Dalgaard
Software Mentions: 4
Published: almost 9 years ago

10.1084/jem.20181276

Contrasting requirements during disease evolution identify EZH2 as a therapeutic target in AML
Cited by: 78
Author(s): Faisal Basheer, George Giotopoulos, Eshwar Meduri, Haiyang Yun, Milena Mazan, Daniel Sasca, Paolo Gallipoli, Ludovica Marando, Malgorzata Gozdecka, Ryan Asby, Olivia Sheppard, Monika Dudek, Lars Bullinger, Hartmut Döhner, Richard Dillon, Sylvie Freeman, Oliver G. Ottmann, Alan Kenneth Burnett, Nigel H. Russell, Elli Papaemmanuil, Robert Kerrin Hills, Peter J. Campbell, George S. Vassiliou, Brian J. P. Huntly
Software Mentions: 4
Published: over 5 years ago

10.1084/jem.20170412

A multidimensional blood stimulation assay reveals immune alterations underlying systemic juvenile idiopathic arthritis
Cited by: 43
Author(s): Alma-Martina Cepika, Romain Banchereau, Élodie Segura, Marina Ohouo, Brandi L. Cantarel, Kristina Goller, V. Ashley Cantrell, Emily Ruchaud, Elizabeth Gatewood, Phuong Nguyen, Jin Gu, Esperanza Anguiano, Sandra Zurawski, Jeanine Baisch, Marilynn Punaro, Nicole Baldwin, Gerlinde Obermoser, Karolina Palucka, Jacques Banchereau, Sebastián Amigorena, Virginia Pascual
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.35786

Human axial progenitors generate trunk neural crest cells in vitro
Cited by: 70
Author(s): Thomas J.R. Frith, Ilaria Granata, Matthew Wind, Erin Stout, Oliver Thompson, Katrin Neumann, Dylan Stavish, Paul R. Heath, Daniel Ortmann, James Hackland, Konstantinos Anastassiadis, Mina Gouti, James Briscoe, Valerie Wilson, Stuart L. Johnson, Marysia Placzek, Mario Rosario Guarracino, Peter W. Andrews, Anestis Tsakiridis
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-015-2114-z

Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis
Cited by: 9
Author(s): Gareth D. Weedall, Helen Irving, Margaret Hughes, Charles S. Wondji
Software Mentions: 4
Published: about 9 years ago

10.1038/s41418-019-0285-x

CBP and SRF co-regulate dendritic growth and synaptic maturation
Cited by: 25
Author(s): Beatriz del Blanco, Deisy Guiretti, Romana Tomasoni, María T. Lopez-Cascales, Rafael Muñoz‐Viana, Michał Lipiński, Marilyn Scandaglia, Yaiza Coca, Román Olivares, Luis M. Valor, Eloı́sa Herrera, Ángel Barco
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-4362-6

Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii
Cited by: 20
Author(s): Musa A. Hassan, Juan J. Vasquez, Guo-Liang Chew, Markus Meissner, T. Nicolai Siegel
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12917-020-02373-9

Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility
Cited by: 5
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Dag Inge Våge, Teklu Tewoldebrhan Zeremichael, Frøydis Deinboll Myromslien, Eli Grindflek
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-016-3070-y

The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets
Cited by: 27
Author(s): Pablo Ivan Pereira Ramos, Márlon Grégori Flores Custódio, Guadalupe del Rosario Quispe Saji, Thiago Bérgamo Cardoso, Gisele Lucchetti da Silva, Graziela Braun, Willames M. B. S. Martins, Raquel Girardello, Ana Tereza Ribeiro de Vasconcelos, Elmer Fernández, Ana Cristina Gales, Marisa Fabiana Nicolás
Software Mentions: 4
Published: about 8 years ago

10.1038/s41419-019-2040-0

Severe head dysgenesis resulting from imbalance between anterior and posterior ontogenetic programs
Cited by: 2
Author(s): Emmanuelle Grall, Victor Gourain, Asmaa Naïr, Elisabeth Martin, Marie‐Christine Birling, Jean–Noël Freund, Isabelle Duluc
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms20040962

Transcriptional Dynamics of Grain Development in Barley (Hordeum vulgare L.)
Cited by: 29
Author(s): Jianxin Bian, Pingchuan Deng, Haoshuang Zhan, Xiaotong Wu, Mutthanthirige Don Lalith Chandana Nishantha, Zhaogui Yan, Xianghong Du, Xiaojun Nie, Weining Song
Software Mentions: 4
Published: over 5 years ago

10.1186/s12918-018-0582-x

A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test
Cited by: 6
Author(s): Qingyang Zhang
Software Mentions: 4
Published: over 6 years ago

10.1080/19336918.2021.1903684

A role for GLUT3 in glioblastoma cell invasion that is not recapitulated by GLUT1
Cited by: 16
Author(s): Catherine Libby, Sajina Gc, Gloria A. Benavides, Jennifer L. Fisher, Sarah Williford, Sixue Zhang, Anh Tran, Emily R. Gordon, Amber Jones, Kaysaw Tuy, William Flavahan, Juan Gordillo, Ashlee Long, Sara J. Cooper, Brittany N. Lasseigne, Corinne E. Augelli‐Szafran, Victor Darley‐Usmar, Anita B. Hjelmeland
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-017-3755-x

Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults
Cited by: 3
Author(s): Haiwang Yang, Denis Basquin, Daniel Pauli, Brian Oliver
Software Mentions: 4
Published: over 7 years ago

10.1128/mSystems.00607-19

Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer
Cited by: 16
Author(s): Lauren M. Seyler, William J. Brazelton, Craig McLean, Lindsay I. Putman, Alex Hyer, M. D. Kubo, Tori M. Hoehler, D. Cardace, M. O. Schrenk
Software Mentions: 4
Published: over 4 years ago

10.1128/mSystems.00495-20

The Stringent Stress Response Controls Proteases and Global Regulators under Optimal Growth Conditions in Pseudomonas aeruginosa
Cited by: 21
Author(s): Daniel Pletzer, Travis M. Blimkie, Heidi Wolfmeier, Yicong Li, Arjun Baghela, Ahwon Lee, Reza Falsafi, Robert E. W. Hancock
Software Mentions: 4
Published: about 4 years ago

10.1128/mSystems.00024-17

Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing Conditions
Cited by: 11
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, James P. Nataro, David A. Rasko
Software Mentions: 4
Published: about 7 years ago

10.1128/mSphere.00479-21

Rhinovirus Reduces the Severity of Subsequent Respiratory Viral Infections by Interferon-Dependent and -Independent Mechanisms
Cited by: 12
Author(s): James T. Van Leuven, Andrés González, Emmanuel C. Ijezie, Alexander Q. Wixom, John L. Clary, Maricris N. Naranjo, Benjamin J. Ridenhour, Craig R. Miller, Tanya A. Miura
Software Mentions: 4
Published: over 3 years ago

10.1128/mSystems.00205-17

Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer
Cited by: 91
Author(s): Ce Yuan, Michael B. Burns, Subbaya Subramanian, Ran Blekhman
Software Mentions: 4
Published: over 6 years ago

10.1128/mBio.01157-20

Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection
Cited by: 2
Author(s): Emily Speranza, Ignacio Caballero, Anna N. Honko, Joshua C. Johnson, J. Kyle Bohannon, Lisa Evans DeWald, Dawn M. Gerhardt, Jennifer Sword, Lisa E. Hensley, Richard S. Bennett, John H. Connor
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers12092510

RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling
Cited by: 4
Author(s): Dominique Scherer, Marcela Dávila López, Benjamin Goeppert, Sanna Abrahamsson, Rosa González Silos, Igor Nova, Katherine Marcelain, Juan Carlos Roa, David Ibberson, Sinan Uğur Umu, Trine B. Rounge, Stephanie Roessler, Justo Lorenzo Bermejo
Software Mentions: 4
Published: about 4 years ago

10.1128/mBio.00586-21

Intraspecies Transcriptional Profiling Reveals Key Regulators of Candida albicans Pathogenic Traits
Cited by: 13
Author(s): Joshua M. Wang, Andrew L. Woodruff, Matthew J. Dunn, Robert J. Fillinger, Richard J. Bennett, Matthew Anderson
Software Mentions: 4
Published: over 3 years ago

10.1128/mSystems.00596-19

Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics
Cited by: 7
Author(s): Matthew Chung, Laura Teigen, Silvia Libro, Robin E. Bromley, Dustin Olley, Nikhil Kumar, Lisa Sadzewicz, Luke J. Tallon, Anup Mahurkar, Jeremy M. Foster, Michelle L. Michalski, Julie C. Dunning Hotopp
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-14-586

The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions
Cited by: 46
Author(s): Brian R. Johnson, Joel Atallah, David C. Plachetzki
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12870-020-02392-6

Spaceflight induces novel regulatory responses in Arabidopsis seedling as revealed by combined proteomic and transcriptomic analyses
Cited by: 37
Author(s): Colin Kruse, Alexander Meyers, Proma Basu, Sarahann Hutchinson, Darron R. Luesse, Sarah E. Wyatt
Software Mentions: 4
Published: over 4 years ago

10.1038/s41398-019-0426-5

Alcohol-responsive genes identified in human iPSC-derived neural cultures
Cited by: 15
Author(s): Kevin P. Jensen, Richard Lieberman, Henry R. Kranzler, Joel Gelernter, Kaitlin Clinton, Jonathan Covault
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers12102918

Time-Resolved Profiling Reveals ATF3 as a Novel Mediator of Endocrine Resistance in Breast Cancer
Cited by: 8
Author(s): Simone Borgoni, Emre Sofyalı, Maryam Soleimani, Heike Wilhelm, Karin Müller‐Decker, Rainer Will, Ashish Noronha, Lukas Beumers, Pernette J. Verschure, Yosef Yarden, Luca Magnani, Antoine H. C. van Kampen, Perry D. Moerland, Stefan Wiemann
Software Mentions: 4
Published: about 4 years ago

10.1038/s41398-021-01431-6

Mapping the transcriptomics landscape of post-traumatic stress disorder symptom dimensions in World Trade Center responders
Cited by: 3
Author(s): Pei‐Fen Kuan, Xiaohua Yang, Ruwei Xu, Chang Che, Monika A. Waszczuk, Roman Kotov, Sean Clouston, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 4
Published: over 3 years ago

10.1128/mBio.02623-19

Developmentally Regulated Oscillations in the Expression of UV Repair Genes in a Soilborne Plant Pathogen Dictate UV Repair Efficiency and Survival
Cited by: 6
Author(s): Shira Milo-Cochavi, Sheera Adar, Shay Covo
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0187625

RNA-Seq analysis reveals insight into enhanced rice Xa7-mediated bacterial blight resistance at high temperature
Cited by: 46
Author(s): Stephen P. Cohen, Hongxia Liu, Cristiana T. Argueso, Andy Pereira, Casiana Vera Cruz, Valérie Verdier, Jan E. Leach
Software Mentions: 4
Published: about 7 years ago

10.3390/cancers12123839

3′RNA Sequencing Accurately Classifies Formalin-Fixed Paraffin-Embedded Uterine Leiomyomas
Cited by: 9
Author(s): Miika Mehine, Sara Khamaiseh, Terhi Ahvenainen, Tuomas Heikkinen, Anna Äyräväinen, Päivi Pakarinen, Päivi Härkki, Annukka Pasanen, Ralf Bützow, Pia Vahteristo
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12870-017-1037-z

Proanthocyanidin accumulation and transcriptional responses in the seed coat of cranberry beans (Phaseolus vulgaris L.) with different susceptibility to postharvest darkening
Cited by: 30
Author(s): José A. Freixas Coutin, Seth Munholland, Anjali Silva, Sanjeena Subedi, Lewis Lukens, William L. Crosby, K. Peter Pauls, Gale G. Bozzo
Software Mentions: 4
Published: over 7 years ago

10.1186/s12870-018-1293-6

Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch)
Cited by: 20
Author(s): Marco Cirilli, D. Giovannini, Angelo Ciacciulli, Remo Chiozzotto, Stefano Gattolin, Laura Rossini, A. Liverani, D. Bassi
Software Mentions: 4
Published: over 6 years ago

10.3390/cancers13010066

Omics Analysis of Educated Platelets in Cancer and Benign Disease of the Pancreas
Cited by: 18
Author(s): G. Mantini, Laura L. Meijer, Ilias Glogovitis, Sjors G J G In ‘t Veld, Rosita Paleckytė, Mjriam Capula, Tessa Y.S. Le Large, Luca Morelli, Thang V. Pham, Sander R. Piersma, Adam E. Frampton, Connie R. Jiménez, Geert Kazemier, Danijela Koppers-Lalić, Thomas Würdinger, Elisa Giovannetti
Software Mentions: 4
Published: almost 4 years ago

10.1128/mBio.03234-19

RNA-Seq Analysis Illuminates the Early Stages of Plasmodium Liver Infection
Cited by: 24
Author(s): Maria Toro-Moreno, Kayla Sylvester, Tamanna Srivastava, Dora Posfai, Emily R. Derbyshire
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-42570-7

Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle
Cited by: 22
Author(s): Shino Tanaka, Mehmet Dayı, Y. Maeda, Isheng Jason Tsai, Ryusei Tanaka, Mark W. Bligh, Yuko Takeuchi-Kaneko, Kenji Fukuda, Natsumi Kanzaki, Taisei Kikuchi
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-015-2321-7

Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits
Cited by: 16
Author(s): Chiara Biselli, Paolo Bagnaresi, Daniela Cavalluzzo, Simona Urso, Francesca Desiderio, G. Orasen, Alberto Gianinetti, Federico Righettini, M. C. Gennaro, Rosaria Perrini, Manel Ben Hassen, Gian Attilio Sacchi, Luigi Cattivelli, Giampiero Valè
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0256148

RNA-sequencing of AVPV and ARH reveals vastly different temporal and transcriptomic responses to estradiol in the female rat hypothalamus
Cited by: 5
Author(s): Margaret A. Mohr, Angela Wong, Gauthaman Sukumar, Clifton L. Dalgard, Weizhe Hong, Tao Wu, Ye Wu, Paul E. Micevych
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-019-39615-2

Multiple molecular defense strategies in Brachypodium distachyon surmount Hessian fly (Mayetiola destructor) larvae-induced susceptibility for plant survival
Cited by: 9
Author(s): Subhashree Subramanyam, Jill A. Nemacheck, Andrea M. Hargarten, Nagesh Sardesai, Brandon J. Schemerhorn, Christie E. Williams
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0244038

Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation
Cited by: 9
Author(s): Manuel Peter, Dominik F. Aschauer, Renata Rose, Anne Sinning, Florian Grössl, Dominic Kargl, Klaus Kraitsy, Thomas R Burkard, Heiko J. Luhmann, Wulf Haubensak, Simon Rumpel
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-018-35974-4

Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity
Cited by: 29
Author(s): Trine B. Rounge, Sinan Uğur Umu, Andreas Keller, Eckart Meese, Giske Ursin, Steinar Tretli, Robert Lyle, Hilde Langseth
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-018-32904-2

Transcriptomics and co-expression networks reveal tissue-specific responses and regulatory hubs under mild and severe drought in papaya (Carica papaya L.)
Cited by: 33
Author(s): Samuel David Gamboa-Tuz, Alejandro Pereira-Santana, Jesús Alejandro Zamora‐Briseño, Enrique Castaño, Francisco Espadas-Gil, Jorge Tonatiuh Ayala-Sumuano, Miguel A. Keb-Llanes, Lorenzo Felipe Sánchez Teyer, Luis Carlos Rodríguez-Zapata
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-37284-1

A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status
Cited by: 12
Author(s): Harry Clifford, Anna Dulneva, Chris P. Ponting, Wilfried Haerty, Esther B. E. Becker
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0240183

Transcriptome analysis revealed misregulated gene expression in blastoderms of interspecific chicken and Japanese quail F1 hybrids
Cited by: 0
Author(s): Satoshi Ishishita, Shoji Tatsumoto, Keiji Kinoshita, Mitsuo Nunome, Takayuki Suzuki, Yasuhiro Go, Yoichi Matsuda
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0243911

The pharmacodynamic and differential gene expression analysis of PPAR α/δ agonist GFT505 in CDAHFD-induced NASH model
Cited by: 12
Author(s): Linfu Liu, Chuang Liu, Menglong Zhao, Qianru Zhang, Ying Lu, Ping Liu, Hua Yang, Jinliang Yang, Xiaoxin Chen, Yuqin Yao
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-018-29329-2

Determination of system level alterations in host transcriptome due to Zika virus (ZIKV) Infection in retinal pigment epithelium
Cited by: 33
Author(s): Pawan Kumar Singh, Indu Khatri, Alokkumar Jha, Carla D. Pretto, Katherine R. Spindler, Vaithilingaraja Arumugaswami, Shailendra Giri, Ashok Kumar, Manoj Bhasin
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-37033-4

Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow
Cited by: 14
Author(s): Wenli Li, Andrea Edwards, Christina Riehle, Madison S. Cox, Sarah M Raabis, Joseph H. Skarlupka, Andrew J. Steinberger, Jason G. Walling, Derek M. Bickhart, Garret Suen
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13287-019-1323-9

Long noncoding RNA CCDC144NL-AS1 knockdown induces naïve-like state conversion of human pluripotent stem cells
Cited by: 8
Author(s): Yingying Wang, Baosen Guo, Zengrong Xiao, Haijun Lin, Xi Zhang, Yueqiang Song, Yalei Li, Xuehu Gao, Jin-Jun Yu, Zhihua Shao, Xuekun Li, Yuan Luo, Siguang Li
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-23207-7

Comparative High-Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell-Line-Specific Pathway Dysregulation
Cited by: 10
Author(s): Leila Taher, Julia Beck, Wen Li, Catrin Roolf, Jan T. Soller, Barbara C. Rütgen, Sabine E. Hammer, Murali Chodisetti, Sina Sender, Katharina A Sterenczak, Georg Fuellen, Christian Junghanß, Bertram Brenig, Ingo Nolte, Ekkehard Schütz, Hugo Murua Escobar
Software Mentions: 4
Published: over 6 years ago

10.1186/s12868-021-00622-7

Construction of competitive endogenous RNA network reveals regulatory role of long non-coding RNAs in intracranial aneurysm
Cited by: 7
Author(s): Yutong Pan, Jianing Lu, Biao Yang, Cameron Lenahan, Jianmin Zhang, Anwen Shao
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-018-24830-0

Novel analysis of the Harderian gland transcriptome response to Newcastle disease virus in two inbred chicken lines
Cited by: 21
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, David Bunn, T. Ross Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-016-1355-4

SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data
Cited by: 40
Author(s): Sang-Young Chun, Caitlin M. Rodriguez, Peter K. Todd, Ryan E. Mills
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0228933

Transcriptomic analysis to elucidate the response of honeybees (Hymenoptera: Apidae) to amitraz treatment
Cited by: 5
Author(s): Ye Liang, Peng Liu, Tengfei Shi, Wang AnRan, Yujie Zhu, Lai Li, Linsheng Yu
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-017-19072-5

Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs
Cited by: 45
Author(s): Yuliaxis Ramayo-Caldas, María Ballester, Juan Pablo Sánchez, Olga González‐Rodríguez, Manuel Revilla, Henry Reyer, Klaus Wimmers, D. Torrallardona, Raquel Quintanilla
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-018-25110-7

Transcriptional Profiling of Somatostatin Interneurons in the Spinal Dorsal Horn
Cited by: 43
Author(s): Alexander Chamessian, Michael Young, Yawar J. Qadri, Temugin Berta, Ru-Rong Ji, Thomas Van de Ven
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-16603-y

RNA-seq of serial kidney biopsies obtained during progression of chronic kidney disease from dogs with X-linked hereditary nephropathy
Cited by: 11
Author(s): Candice P. Chu, Jessica A. Hokamp, Rachel E. Cianciolo, Alan R. Dabney, Candice Brinkmeyer-Langford, George E. Lees, Mary B. Nabity
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-017-17337-7

Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes
Cited by: 2
Author(s): Enrico Capobianco, Camilo Valdes, Samanta Sarti, Zhijie Jiang, Laura Poliseno, Nicolas F. Tsinoremas
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0212755

Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing
Cited by: 9
Author(s): Fátima Gomes, Luciana Watanabe, João L.S.G. Vianez, Márcio Roberto Teixeira Nunes, Jedson Ferreira Cardoso, Clayton Pereira Silva de Lima, Horácio Schneider, Iracilda Sampaio
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0216679

Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel
Cited by: 8
Author(s): Fatma Zohra Djazouli Alim, Elena V. Romanova, Yea Ling Tay, Ahmad Yamin bin Abdul Rahman, Kok‐Gan Chan, Kar‐Wai Hong, Mark F. Rogers, Bruce R. Southey, Michael Greenwood, André Souza Mecawi, Mohammad Rais Mustafa, Nicole Mahy, Colin Campbell, José Antunes‐Rodrigues, Jonathan V. Sweedler, David Murphy, Charles C.T. Hindmarch
Software Mentions: 4
Published: over 5 years ago

10.1111/acer.14259

Chronic Voluntary Ethanol Drinking in Cynomolgus Macaques Elicits Gene Expression Changes in Prefrontal Cortical Area 46
Cited by: 4
Author(s): Nicole A.R. Walter, Christina Zheng, Robert P. Searles, Shannon K. McWeeney, Kathleen A. Grant, Robert Hitzemann
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-017-18480-x

RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients
Cited by: 51
Author(s): Jungmok You, Susan M. Corley, Li Wen, Chris Hodge, Roland Hӧllhumer, Michele C. Madigan, Marc R. Wilkins, Gerard Sutton
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-018-25302-1

Egr2-independent, Klf1-mediated induction of PD-L1 in CD4+ T cells
Cited by: 8
Author(s): Shuzo Teruya, Tomohisa Okamura, Takashi Komai, Mariko Inoue, Yukiko Iwasaki, Shuji Sumitomo, Hirofumi Shoda, Kazuhiko Yamamoto, Keishi Fujio
Software Mentions: 4
Published: over 6 years ago

10.1186/1755-8794-7-57

Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model
Cited by: 79
Author(s): Lisette J. A. Kogelman, Susanna Cirera, Daria V. Zhernakova, Merete Fredholm, Lude Franke, Haja N. Kadarmideen
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.ppat.1008633

Dynamic chromatin accessibility profiling reveals changes in host genome organization in response to baculovirus infection
Cited by: 9
Author(s): Xiaodong Kong, Guisheng Wei, Nan Chen, Shudi Zhao, Yongrong Shen, Jianjia Zhang, Li Yang, Xiaoqun Zeng, Xiaoxia Wu
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-019-2676-x

SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package
Cited by: 5
Author(s): Taewoon Joo, Ji-Hye Choi, Jihye Lee, So Eun Park, Youngsic Jeon, Sae Hoon Jung, Hyun Goo Woo
Software Mentions: 4
Published: almost 6 years ago

10.1186/1755-8794-7-32

Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers
Cited by: 45
Author(s): Zhifu Sun, Liang Wang, Bruce W. Eckloff, Bo Deng, Yi Wang, Jason A. Wampfler, Jiseon Jang, Eric D. Wieben, Jin Jen, Ming You, Ping Yang
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.ppat.1008066

Linking the effects of helminth infection, diet and the gut microbiota with human whole-blood signatures
Cited by: 25
Author(s): Soo Ching Lee, Mei Tang, Alice V. Easton, Joseph C. Devlin, Ling Ling Chua, Ilseung Cho, Foong Ming Moy, Tsung Fei Khang, Yvonne Ai Lian Lim, P’ng Loke
Software Mentions: 4
Published: almost 5 years ago

10.18632/aging.102034

A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass
Cited by: 5
Author(s): Xuehui Li, Lei Wei, Qiongye Dong, Liyang Liu, Michael Q. Zhang, Zhen Xie, Xiaowo Wang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1006391

Microbiota-induced peritrophic matrix regulates midgut homeostasis and prevents systemic infection of malaria vector mosquitoes
Cited by: 114
Author(s): Faye H. Rodgers, Mathilde Gendrin, Claudia A. S. Wyer, George K. Christophides
Software Mentions: 4
Published: over 7 years ago

10.1002/cne.24994

Identification of regenerative processes in neonatal spinal cord injury in the opossum ( <scp> Monodelphis domestica </scp> ): A transcriptomic study
Cited by: 6
Author(s): Benjamin Wheaton, Johnny A. Sena, Anitha Sundararajan, Pooja Umale, Faye Schilkey, Robert D. Miller
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0199902

Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome
Cited by: 8
Author(s): Tina Ilc, Gautier Arista, Raquel Tavares, Nicolas Navrot, Éric Duchêne, Amandine Velt, Frédéric Choulet, Etienne Paux, Marc Fischer, David R. Nelson, Philippe Hugueney, Danièle Werck‐Reichhart, Camille Rustenholz
Software Mentions: 4
Published: over 6 years ago

10.3390/jcm8081158

Role of MYC-miR-29-B7-H3 in Medulloblastoma Growth and Angiogenesis
Cited by: 29
Author(s): Ian J. Purvis, Avilala Janardhan, Maheedhara R. Guda, Sujatha Venkataraman, Rajeev Vibhakar, Andrew J. Tsung, Kiran Kumar Velpula, Swapna Asuthkar
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0226057

Estrogen receptor β exerts tumor suppressive effects in prostate cancer through repression of androgen receptor activity
Cited by: 16
Author(s): Surendra Chaurasiya, Scott Widmann, Cindy Botero, Chin-Yo Lin, Jan‐Åke Gustafsson, Anders Ström
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-019-6018-1

Transcriptome profile of Corynebacterium pseudotuberculosis in response to iron limitation
Cited by: 19
Author(s): Izabela Coimbra Ibraim, Mariana Teixeira Dornelles Parise, Doglas Parise, Michelle Zibetti Tadra Sfeir, Thiago Luiz de Paula Castro, Alice R. Wattam, Preetam Ghosh, Debmalya Barh, Emannuel Maltempi Souza, Aristóteles Goés-Neto, Anne Cybelle Pinto Gomide, Vasco Azevedo
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-018-4632-y

Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils
Cited by: 18
Author(s): Marcella Sabino, Victor Adriano Okstoft Carmelo, Gianluca Mazzoni, Katia Cappelli, Stefano Capomaccio, Paolo Ajmone‐Marsan, Andrea Verini-Supplizi, Massimo Trabalza‐Marinucci, Haja N. Kadarmideen
Software Mentions: 4
Published: over 6 years ago

10.1172/jci.insight.142980

Treating ICB-resistant glioma with anti-CD40 and mitotic spindle checkpoint controller BAL101553 (lisavanbulin)
Cited by: 5
Author(s): Vassilis Genoud, Felipe I Espinoza, Eliana Marinari, Viviane Rochemont, Pierre‐Yves Dietrich, Paul M.J. McSheehy, Felix Bachmann, Heidi A. Lane, Paul R Walker
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-017-07757-w

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Cited by: 63
Author(s): Ann H. Ryu, Walter L. Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
Software Mentions: 4
Published: over 7 years ago

10.1038/s41438-020-00432-8

Transcriptional regulation of bark freezing tolerance in apple (Malus domestica Borkh.)
Cited by: 9
Author(s): Yin Liang, Shanshan Wang, Chang Zhao, Xinwei Ma, Yiyong Zhao, Jing Shao, Yuebo Li, Honglian Li, Song Hong‐wei, Hong Mā, Hao Li, Bingbing Zhang, Liangsheng Zhang
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2164-15-221

From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism
Cited by: 119
Author(s): Inès Zouari, Alessandra Salvioli, Matteo Chialva, Mara Novero, Laura Miozzi, Gian Carlo Tenore, Paolo Bagnaresi, Paola Bonfante
Software Mentions: 4
Published: over 10 years ago

10.1016/j.ajhg.2016.05.030

BCL11A Haploinsufficiency Causes an Intellectual Disability Syndrome and Dysregulates Transcription
Cited by: 116
Author(s): Cristina Dias, Sara Busquets Estruch, Sarah A. Graham, Jeremy F. McRae, Stephen J. Sawiak, Jane A. Hurst, Shelagh Joss, Susan Holder, Jenny Morton, Claire Turner, Julien Thévenon, Kelly Mellul, Gabriela Sánchez-Andrade, Ximena Ibarra-Soria, Pelagia Derizioti, Rui F. Santos, Song-Choon Lee, Laurence Faivre, Tjitske Kleefstra, Pentao Liu, Mathew E. Hurles, Simon E. Fisher, Darren W. Logan
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-018-24227-z

A new way of producing pediocin in Pediococcus acidilactici through intracellular stimulation by internalized inulin nanoparticles
Cited by: 19
Author(s): Whee-Soo Kim, Jun-Yeong Lee, Bijay Singh, Sushila Maharjan, Liang Hong, Sang-Mok Lee, Lianhua Cui, Ki-June Lee, Girak Kim, Cheol‐Heui Yun, Seoung-Hun Kang, Yun‐Jaie Choi, Chong‐Su Cho
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-016-2618-1

Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage
Cited by: 107
Author(s): Irene da Cruz, Rosana Rodríguez-Casuriaga, Federico F. Santiñaque, Joaquina Farías, Gianni Curti, Carlos A. Capoano, Gustavo A. Folle, Ricardo Benavente, José Sotelo‐Silveira, Adriana Geisinger
Software Mentions: 4
Published: over 8 years ago

10.1038/s41438-020-00416-8

Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles
Cited by: 66
Author(s): Muhammad Umer, Luqman Bin Safdar, Haileslassie Gebremeskel, Shengjie Zhao, Pingli Yuan, Huiling Zhu, Mohamed Omar Kaseb, Muhammad Anees, Xingrong Lu, Nan He, Chengsheng Gong, Wenge Liu
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0210672

Identification of new regulators through transcriptome analysis that regulate anthocyanin biosynthesis in apple leaves at low temperatures
Cited by: 28
Author(s): Tingting Song, Keting Li, Ting Wu, Yi Wang, Xinzhong Zhang, Xuefeng Xu, Yuncong Yao, Zhenhai Han
Software Mentions: 4
Published: almost 6 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-017-3967-0

Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq
Cited by: 15
Author(s): Miriam Payá‐Milans, Gerardo H. Nunez, James W. Olmstead, Timothy A. Rinehart, Margaret Staton
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-020-07141-5

Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii
Cited by: 9
Author(s): Peter M. Henry, Sukhwinder Kaur, Quyen Anh Tran Pham, Radwan Barakat, Samuel Brinker, Hannah Haensel, Oleg Daugovish, Lynn Epstein
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0141225

A catalogue of novel bovine long noncoding RNA across 18 tissues
Cited by: 76
Author(s): Lambros T. Koufariotis, Yi‐Ping Phoebe Chen, Amanda J. Chamberlain, Christy Vander Jagt, Ben J. Hayes
Software Mentions: 4
Published: about 9 years ago

10.1038/s41438-018-0073-7

Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV
Cited by: 39
Author(s): Tian Wang, Zhiqi Deng, Xi Zhang, Hongzheng Wang, Yu Wang, Xiuying Liu, Songyu Liu, Feng Xu, Tao Li, Daqi Fu, Beiwei Zhu, Yunbo Luo, Hongliang Zhu
Software Mentions: 4
Published: about 6 years ago

10.1172/jci.insight.138443

Epigenetic regulation of the PGE2 pathway modulates macrophage phenotype in normal and pathologic wound repair
Cited by: 31
Author(s): Frank M. Davis, Lam C. Tsoi, Rachael Wasikowski, Aaron D. denDekker, Amrita Joshi, Carol A. Wilke, Hongping Deng, Sonya Wolf, Andrea Obi, Steven K. Huang, Allison C. Billi, Scott T. Robinson, Jay H Lipinski, William J. Melvin, Christopher O. Audu, Stephan Weidinger, Steven L. Kunkel, Andrew M. Smith, Jóhann E. Guðjónsson, Bethany B. Moore, Katherine A. Gallagher
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-017-4411-1

A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees
Cited by: 22
Author(s): Ogonna Obudulu, Niklas Mähler, Tomas Skotare, Joakim Bygdell, Ilka Nacif Abreu, Maria Ahnlund, Madhavi Latha Gandla, Anna Petterle, Thomas Moritz, Torgeir R. Hvidsten, Leif J. Jönsson, Gunnar Wingsle, Johan Trygg, Hannele Tuominen
Software Mentions: 4
Published: almost 7 years ago

Projects: pypi: HTSeq

Papers Mentioning HTSeq 3,071