pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.31557/APJCP.2020.21.9.2593

Transcriptome Related to Avoiding Immune Destruction in Nasopharyngeal Cancer in Indonesian Patients Using Next-Generation Sequencing
Cited by: 2
Author(s): Risky Hiskia Poluan, Digdo Sudigyo, Gisti Rahmawati, Dicka Wahyu Setiasari, Salsabila Luthfi Sesotyosari, Tirta Wardana, Indwiani Astuti, Didik Setyo Heriyanto, Sagung Rai Indrasari, Cita Herawati, FNU Afiahayati, Sofia Mubarika Haryana
Software Mentions: 4
Published: about 4 years ago

10.1186/s12967-021-02870-x

High copy number variations, particular transcription factors, and low immunity contribute to the stemness of prostate cancer cells
Cited by: 9
Author(s): Zao Dai, Ping Liu
Software Mentions: 4
Published: over 3 years ago

10.15252/embj.2018101430

Cyclin F‐dependent degradation of E2F7 is critical for <scp>DNA</scp> repair and G2‐phase progression
Cited by: 33
Author(s): Ruixue Yuan, Qingwu Liu, Hendrika A. Segeren, Laurensia Yuniati, Daniele Guardavaccaro, Robert Jan Lebbink, Bart Westendorp, Alain de Bruin
Software Mentions: 4
Published: about 5 years ago

10.1155/2020/5974157

Comparative Transcriptome Analysis Reveals the Protective Mechanism of Glycyrrhinic Acid for Deoxynivalenol-Induced Inflammation and Apoptosis in IPEC-J2 Cells
Cited by: 14
Author(s): Xiaoxiang Xu, Guorong Yan, Juan Chang, Ping Wang, Qingqiang Yin, Chaoqi Liu, Qun Zhu, Fushan Lu
Software Mentions: 4
Published: about 4 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

10.1128/JVI.00589-18

Transcriptional and Translational Landscape of Equine Torovirus
Cited by: 22
Author(s): Hazel Stewart, Katherine A. Brown, Adam M. Dinan, Nerea Irigoyen, Eric J. Snijder, Andrew E. Firth
Software Mentions: 4
Published: about 6 years ago

10.1523/ENEURO.0166-18.2018

Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress
Cited by: 45
Author(s): Mikaela Laine, Kalevi Trontti, Zuzanna Misiewicz, Ewa Sokołowska, Natalia Kulesskaya, Aino Heikkinen, Suvi Saarnio, Ingrid Balcells, Pierre Ameslon, Dario Greco, Pirkko Mattila, Pekka Ellonen, Lars Paulín, Petri Auvinen, Eija Jokitalo, Iiris Hovatta
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.23280

Validation of a hypoxia related gene signature in multiple soft tissue sarcoma cohorts
Cited by: 32
Author(s): Lingjian Yang, Laura Forker, Joely J. Irlam, Nischalan Pillay, Ananya Choudhury, Catharine M L West
Software Mentions: 4
Published: almost 7 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

10.18632/oncotarget.27632

Validated limited gene predictor for cervical cancer lymph node metastases
Cited by: 1
Author(s): Joshua Bloomstein, Rie von Eyben, Avis Chan, Erinn B. Rankin, Daniel R. Fregoso, Jing Wang-Chiang, Lisa Lee, Li Xie, Shannon MacLaughlan David, Henning Stehr, Mohammad Shahrokh Esfahani, Amato J. Giaccia, Elizabeth A. Kidd
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

10.7554/eLife.66014

Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses
Cited by: 18
Author(s): Stephan Wilmes, Polly-Anne Jeffrey, Jonathan Martínez-Fábregas, Maximillian Hafer, Paul K. Fyfe, Elizabeth Pöhler, Silvia Gaggero, Martín López‐García, Grant Lythe, Charles Taylor, Thomas Guerrier, David Launay, Suman Mitra, Jacob Piehler, Carmen Molina-Parı́s, Ignacio Moraga
Software Mentions: 4
Published: over 3 years ago

10.18632/oncotarget.20977

Selecting lncRNAs in gastric cancer cells for directed therapy with bioactive peptides and chemotherapy drugs
Cited by: 7
Author(s): Wenyan Han, Rui Xiao, Chuanling Zhang, Qimuge Suyila, Xian Li, Xiulan Su
Software Mentions: 4
Published: about 7 years ago

10.1242/dmm.042713

Leptin and fractalkine: Novel subcutaneous cytokines in burn injury
Cited by: 4
Author(s): Dominic Friston, Sini Junttila, Júlia Borges Paes Lemes, Helen Laycock, Jose Vicente Torres-Pérez, Elizabeth J. Want, Attila Gyenesei, I. Nagy
Software Mentions: 4
Published: almost 5 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

10.7554/eLife.46566

The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop
Cited by: 29
Author(s): Merve Deniz Abdusselamoglu, Elif Eroğlu, Thomas R Burkard, Juergen A. Knoblich
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

10.3389/fgene.2020.608325

Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation
Cited by: 1
Author(s): Xiaoli Ma, Mei Shang, Baofeng Su, Anne A. Wiley, Max R. Bangs, Veronica Alston, Rhoda Mae C. Simora, Mai Thi Thanh Nguyen, Nathan J. C. Backenstose, Anthony G. Moss, Dương Thúy Yên, Xiaozhu Wang, Rex A. Dunham
Software Mentions: 4
Published: almost 4 years ago

10.1155/2018/3028290

Stress-Adaptive Responses Associated with High-Level Carbapenem Resistance in KPC-ProducingKlebsiella pneumoniae
Cited by: 4
Author(s): Sheila Adams‐Sapper, Adam Gayoso, Lee W. Riley
Software Mentions: 4
Published: almost 7 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

10.7554/eLife.02734

Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer
Cited by: 102
Author(s): Sakari Vanharanta, Christina B. Marney, Weiqun Shu, Manuel Valiente, Yilong Zou, Aldo Mele, Robert B. Darnell, Joan Massagué
Software Mentions: 4
Published: over 10 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

10.1016/j.devcel.2020.09.025

Functional Diversification of SRSF Protein Kinase to Control Ubiquitin-Dependent Neurodevelopmental Signaling
Cited by: 27
Author(s): Francisco Bustos, Anna Segarra-Fas, Gino Nardocci, Andrew Cassidy, Odetta Antico, L. S. P. Davidson, Lennart Brandenburg, Thomas Macartney, Rachel Toth, Claire Hastie, Jennifer L. Moran, Robert Gourlay, Joby Varghese, Renata Soares, Martín Montecino, Greg M. Findlay
Software Mentions: 4
Published: almost 4 years ago

10.18632/aging.103442

TCF7L2 rs290487 C allele aberrantly enhances hepatic gluconeogenesis through allele-specific changes in transcription and chromatin binding
Cited by: 4
Author(s): Xueyou Zhang, Panpan Ye, Haitao Huang, Baohong Wang, Fengqin Dong, Qi Ling
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.02626

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways
Cited by: 80
Author(s): Benoît Ballester, Alejandra Medina-Rivera, Dominic Schmidt, Mar Gonzàlez-Porta, Matthew Carlucci, Marc E. Rothenberg, Kyle Chessman, Aline Faure, Alister P. W. Funnell, Ângela Gonçalves, Claudia Kutter, Margus Lukk, Suraj Menon, William McLaren, Klara Stefflova, Stephen Watt, Matthew T. Weirauch, Merlin Crossley, John C. Marioni, Duncan T. Odom, Paul Flicek, Michael D. Wilson
Software Mentions: 4
Published: about 10 years ago

10.7554/eLife.16220

Trisomy 21 consistently activates the interferon response
Cited by: 205
Author(s): Kelly D. Sullivan, Hannah C. Lewis, Amanda A. Hill, Ahwan Pandey, Leisa Jackson, Joseph M Cabral, Keith P Smith, L. Alexander Liggett, Eliana B. Gómez, Matthew D. Galbraith, James DeGregori, Joaquín M. Espinosa
Software Mentions: 4
Published: over 8 years ago

10.1186/s12870-018-1602-0

Dual RNA-seq analysis provides new insights into interactions between Norway spruce and necrotrophic pathogen Heterobasidion annosum s.l.
Cited by: 31
Author(s): Andriy Kovalchuk, Zhen Zeng, Rajendra P. Ghimire, Minna Kivimäenpää, Tommaso Raffaello, Mengxia Liu, Mukrimin Mukrimin, Risto Kasanen, Hui Sun, Riitta Julkunen‐Tiitto, Jarmo K. Holopainen, Fred O. Asiegbu
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.08851

Maternal LSD1/KDM1A is an essential regulator of chromatin and transcription landscapes during zygotic genome activation
Cited by: 99
Author(s): Katia Ancelin, Laurène Syx, Maud Borensztein, Noémie Ranisavljevic, Ivaylo Vassilev, Luis Briseño-Roa, Tao Liu, Eric Metzger, Nicolas Servant, Emmanuel Barillot, Chongjian Chen, Roland Schüle, Edith Heard
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.66522

Ketogenic diet restrains aging-induced exacerbation of coronavirus infection in mice
Cited by: 33
Author(s): Seungjin Ryu, Irina Shchukina, Yun‐Hee Youm, Hua Qing, Brandon Hilliard, Tamara Dlugos, Xinbo Zhang, Yuki Yasumoto, Carmen J. Booth, Carlos Fernández‐Hernando, Yajaira Suárez, Kamal M. Khanna, Tamás L. Horváth, Marcelo O Dietrich, Maxim N. Artyomov, Andrew Wang, Vishwa Deep Dixit
Software Mentions: 4
Published: over 3 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

10.1016/j.devcel.2021.07.018

Reprogrammed lipid metabolism protects inner nuclear membrane against unsaturated fat
Cited by: 28
Author(s): Anete Romanauska, Alwin Köhler
Software Mentions: 4
Published: about 3 years ago

10.7554/eLife.19406

Modeling susceptibility to drug-induced long QT with a panel of subject-specific induced pluripotent stem cells
Cited by: 79
Author(s): Francesca Stillitano, Jens Hansen, Chi-Wing Kong, Ioannis Karakikes, Christian Funck‐Brentano, Lin Geng, Stuart A. Scott, Stephan Reynier, Wu Ma, Yannick Valogne, Carole Desseaux, Joe‐Elie Salem, Dorota Jeziorowska, Noël Zahr, Ronald Li, Ravi Iyengar, Roger J. Hajjar, Jean‐Sébastien Hulot
Software Mentions: 4
Published: almost 8 years ago

10.1016/j.ydbio.2016.06.016

Developmentally regulated long non-coding RNAs in Xenopus tropicalis
Cited by: 17
Author(s): Elmira Forouzmand, Nick Owens, Ira L. Blitz, Kitt D. Paraiso, Mustafa K. Khokha, Michael J. Gilchrist, Xiaohui Xie, Ken W.Y. Cho
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1007905

Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment
Cited by: 21
Author(s): Alexandra Bezler, Fabian Braukmann, Sean M. West, Arthur Duplan, Raffaella Conconi, Frédéric Schütz, Pierre Gönczy, Fabio Piano, Kristin C. Gunsalus, Eric A. Miska, Laurent Keller
Software Mentions: 4
Published: almost 6 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

10.7554/eLife.39658

Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome
Cited by: 33
Author(s): Srivarsha Rajshekar, Jun Yao, Paige K. Arnold, Sara G. Payne, Yinwen Zhang, Teresa V. Bowman, Robert J. Schmitz, John Edwards, Mary Goll
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.60987

Adaptive evolution of an essential telomere protein restricts telomeric retrotransposons
Cited by: 9
Author(s): Bastien Saint-Leandre, Courtney J. Christopher, Mia T. Levine
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.66547

Dual expression of Atoh1 and Ikzf2 promotes transformation of adult cochlear supporting cells into outer hair cells
Cited by: 31
Author(s): Shuangwen Sun, Shuting Li, Zhengnan Luo, Minhui Ren, Shunji He, Guangqin Wang, Zhiyong Liu
Software Mentions: 4
Published: about 3 years ago

10.1186/s12859-019-2916-0

A multivariate Poisson-log normal mixture model for clustering transcriptome sequencing data
Cited by: 26
Author(s): Anjali Silva, Steven J. Rothstein, Paul D. McNicholas, Sanjeena Subedi
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

10.7554/eLife.63556

Deficient spermiogenesis in mice lacking Rlim
Cited by: 7
Author(s): Feng Wang, María Gracia Gervasi, Ana Bošković, Fengyun Sun, Vera D. Rinaldi, Jun Yu, Mary C. Wallingford, Darya A Tourzani, Jesse Mager, Lihua Julie Zhu, Oliver J. Rando, Pablo E. Visconti, Lara Strittmatter, Ingolf Bach
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.21697

Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ
Cited by: 43
Author(s): Lorenzo Rinaldi, Alexandra Avgustinova, Mercé Martı́n, Debayan Datta, Guiomar Solanas, Neus Prats, Salvador Aznar Benitah
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.67481

SORBS2 is a genetic factor contributing to cardiac malformation of 4q deletion syndrome patients
Cited by: 7
Author(s): Fei Liang, Bo Wang, Juan Geng, Guoling You, Jingjing Fa, Min Zhang, Hunying Sun, Huiwen Chen, Qin Fu, Xiaoqing Zhang, Zhen Zhang
Software Mentions: 4
Published: over 3 years ago

10.1038/s42003-021-02203-0

The chaperonin CCT8 controls proteostasis essential for T cell maturation, selection, and function
Cited by: 5
Author(s): Bergithe E. Oftedal, Stefano Maio, Adam E. Handel, White Mpj., Duncan Howie, Simon Davis, Nicolas Prevot, Ioanna A. Rota, Mary E. Deadman, Benedikt M. Kessler, Román Fischer, Nikolaus S. Trede, Erdinç Sezgin, Rick M. Maizels, G A Holländer
Software Mentions: 4
Published: over 3 years ago

10.1016/j.cub.2019.07.083

Genetically Defined Functional Modules for Spatial Orienting in the Mouse Superior Colliculus
Cited by: 60
Author(s): Laura Masullo, Letizia Mariotti, Nicolas Alexandre, Paula Freire-Pritchett, Jérôme Boulanger, Marco Tripodi
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.08411

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions
Cited by: 39
Author(s): Anne Plessis, Christoph Hafemeister, Olivia Wilkins, Zennia Jean Gonzaga, Rachel S. Meyer, Inês S. Pires, Christian Müller, Endang M. Septiningsih, Richard Bonneau, Michael D. Purugganan
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.08007

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome
Cited by: 129
Author(s): Yoong Wearn Lim, Lionel A. Sanz, Xiaoqin Xu, Stella R. Hartono, Frédéric Chédin
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.37892

DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis
Cited by: 57
Author(s): Amr Nassrallah, Martin Rougée, Clara Bourbousse, Stéphanie Drevensek, Sandra Fonseca, Elisa Iniesto, Ouardia Aït-Mohamed, Anne Flore Deton-Cabanillas, Gérald Zabulon, Ikhlak Ahmed, David Stroebel, Vanessa Masson, Bérangère Lombard, Dominique Eeckhout, Kris Gevaert, Damarys Loew, Auguste Genovesio, Cécile Breyton, Geert De Jaeger, Chris Bowler, Vicente Rubio, Frédy Barneche
Software Mentions: 4
Published: about 6 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

10.1007/s00239-020-09939-z

A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila
Cited by: 51
Author(s): Brennen Heames, Julia Schmitz, Erich Bornberg‐Bauer
Software Mentions: 4
Published: over 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

10.1186/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

10.7554/eLife.33084

Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs
Cited by: 23
Author(s): Michelle C. Ward, Siming Zhao, Kaixuan Luo, Bryan J. Pavlovic, Mehdi Karimi, Matthew Stephens, Yoav Gilad
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

10.7554/eLife.35551

Ssd1 and Gcn2 suppress global translation efficiency in replicatively aged yeast while their activation extends lifespan
Cited by: 54
Author(s): Zheng Hu, Bo Xia, Spike D. L. Postnikoff, Zih Jie Shen, Alin Tomoiaga, Troy A. A. Harkness, Ja Hwan Seol, Wei Li, Kaifu Chen, Jessica K. Tyler
Software Mentions: 4
Published: over 6 years ago

10.1016/j.ijpara.2018.01.004

Transcriptomic profiling of nematode parasites surviving vaccine exposure
Cited by: 19
Author(s): Guillaume Sallé, Roz Laing, James A. Cotton, Kirsty Maitland, Axel Martinelli, Nancy Holroyd, Alan S. Tracey, Matthew Berriman, William D. Smith, G. F. J. Newlands, Eve Hanks, Eileen Devaney, Collette Britton
Software Mentions: 4
Published: over 6 years ago

10.4049/jimmunol.1900940

Malat1 Suppresses Immunity to Infection through Promoting Expression of Maf and IL-10 in Th Cells
Cited by: 45
Author(s): James P. Hewitson, Katie A West, Kylie R. James, Gulab Fatima Rani, Nidhi Sharma Dey, Audrey Romano, Najmeeyah Brown, Sarah A. Teichmann, Paul M. Kaye, Dimitrios Lagos
Software Mentions: 4
Published: over 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/s40425-019-0609-x

Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma
Cited by: 22
Author(s): Sehhoon Park, Je‐Gun Joung, Min Ye, Jae‐Yong Nam, Daeun Ryu, Dongryul Oh, Woong-Yang Park, Sehoon Lee, Yoon La Choi, Jin Seok Ahn, Myung‐Ju Ahn, Keunchil Park, Jong‐Mu Sun
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

10.18632/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

10.1111/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

10.1084/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

10.1186/s12870-019-1708-z

The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development
Cited by: 30
Author(s): Ming Li, Songtao Yang, Wei Xü, Zhien Pu, Jiayi Feng, Zhangying Wang, Cong Zhang, Peng Ma, Chunguang Du, Feng Lin, Changhe Wei, Shuai Qiao, Hongda Zou, Lei Zhang, Yán Li, Huan Yang, Anzhong Liao, Wei Song, Zhongren Zhang, Ji Li, Kai Wang, Yizheng Zhang, Hao Lin, Jinbo Zhang, Wen-Fang Tan
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.02104

Mof-associated complexes have overlapping and unique roles in regulating pluripotency in embryonic stem cells and during differentiation
Cited by: 41
Author(s): Sarina Ravens, Marjorie Fournier, Tao Ye, Matthieu Stierlé, Doulaye Dembelé, Virginie Chavant, László Tora
Software Mentions: 4
Published: over 10 years ago

10.7554/eLife.68238

Neuronal calmodulin levels are controlled by CAMTA transcription factors
Cited by: 3
Author(s): Thanh Thi Kim Vuong-Brender, Sean M. Flynn, Yvonne Vallis, Mario de Bono
Software Mentions: 4
Published: about 3 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

10.1186/s40169-017-0150-9

Single‐cell RNA‐sequencing of the brain
Cited by: 46
Author(s): Raquel Durán, Haichao Wei, Jia Qian Wu
Software Mentions: 4
Published: over 7 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

10.1038/s42003-021-02059-4

Three-dimensional tissue-engineered human skeletal muscle model of Pompe disease
Cited by: 13
Author(s): Jason Wang, Chris J. Zhou, Alastair Khodabukus, Sabrina Tran, Sang-oh Han, Aaron L. Carlson, Lauran Madden, Priya S. Kishnani, Dwight D. Koeberl
Software Mentions: 4
Published: over 3 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.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

10.1128/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/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

10.1186/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

10.1038/s42003-019-0430-6

Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms
Cited by: 18
Author(s): Boxiang Liu, Melissa A. Calton, Nathan S. Abell, Gillie Benchorin, Michael J. Gloudemans, Ming Chen, Jane Hu, Xin Li, Brunilda Balliu, Dean Bok, Stephen B. Montgomery, Douglas Vollrath
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

10.1128/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

10.1186/s13046-018-0957-2

miR-296-5p suppresses EMT of hepatocellular carcinoma via attenuating NRG1/ERBB2/ERBB3 signaling
Cited by: 64
Author(s): Dongmin Shi, Lixin Li, Xinyu Bian, Xuejiang Shi, Lili Lü, Hongxin Zhou, Ting-Jia Pan, Jian Zhou, Jia Fan, Wei–Zhong Wu
Software Mentions: 4
Published: almost 6 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

10.1186/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

10.1128/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

10.3390/cells9122637

RNA-Seq Analysis of Cisplatin and the Monofunctional Platinum(II) Complex, Phenanthriplatin, in A549 Non-Small Cell Lung Cancer and IMR90 Lung Fibroblast Cell Lines
Cited by: 4
Author(s): Jerry D. Monroe, Satya A. Moolani, Elvin N. Irihamye, Joshua S. Speed, Yann Gibert, Michael E. Smith
Software Mentions: 4
Published: almost 4 years ago

10.1016/j.bbr.2017.04.007

Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis
Cited by: 6
Author(s): Hannah Scott, Mark F. Rogers, Helen L. Scott, Colin Campbell, E. Clea Warburton, James B. Uney
Software Mentions: 4
Published: over 7 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

10.1186/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

10.3390/cells9081793

Molecular Changes in the Non-Inflamed Terminal Ileum of Patients with Ulcerative Colitis
Cited by: 3
Author(s): Ho‐Su Lee, Maaike Vancamelbeke, Sare Verstockt, Tom Wilms, Bram Verstockt, João Sabino, Marc Ferrante, Séverine Vermeire, Isabelle Cleynen
Software Mentions: 4
Published: over 4 years ago

10.3390/cells9122593

Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors
Cited by: 3
Author(s): Silvin Lito, Adama Sidibé, Sten Ilmjärv, Patricie Burda, Matthias R. Baumgartner, Bernhard Wehrle-Haller, Karl‐Heinz Krause, Antoine Marteyn
Software Mentions: 4
Published: almost 4 years ago

10.1093/bioinformatics/btx143

The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data
Cited by: 26
Author(s): Robert Petryszak, Nuno A. Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y. Amy Tang, Alvis Brāzma
Software Mentions: 4
Published: over 7 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

10.1186/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

10.1016/j.dib.2016.05.007

Whole transcriptome data analysis of zebrafish mutants affecting muscle development
Cited by: 7
Author(s): Olivier Armant, Victor Gourain, Christelle Etard, Uwe Strähle
Software Mentions: 4
Published: about 8 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

Projects: pypi: HTSeq

Papers Mentioning HTSeq 3,071