pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1186/s12864-015-2174-0

Extensive variation between tissues in allele specific expression in an outbred mammal
Cited by: 67
Author(s): Amanda J. Chamberlain, Christy J. Vander Jagt, Ben J. Hayes, Majid Khansefid, L. C. Marett, Catriona A. Millen, Thuy Thi Thu Nguyen, Michael E. Goddard
Software Mentions: 5
Published: almost 11 years ago

10.7717/peerj.10818

Cytochrome P450 monooxygenase genes in the wild silkworm, Bombyx mandarina
Cited by: 5
Author(s): Linrong Wan, Zhou Anlian, Wen‐Fu Xiao, Bangxing Zou, Yaming Jiang, Jing Xiao, Cao Deng, Youhong Zhang, Mengjia Liu
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.6499

Transcriptional profiling in the livers of rats after hypobaric hypoxia exposure
Cited by: 5
Author(s): Zhenguo Xu, Zhilong Jia, Jianxin Shi, Zeyu Zhang, Xiaojian Gao, Qi Jia, Bohan Liu, Jixuan Liu, Chunlei Liu, Xiaojing Zhao, Kunlun He
Software Mentions: 5
Published: over 7 years ago

10.1093/gigascience/giz145

Benchmark of long non-coding RNA quantification for RNA sequencing of cancer samples
Cited by: 31
Author(s): Hong Zheng, Kevin Brennan, Mikel Hernáez, Olivier Gevaert
Software Mentions: 5
Published: almost 7 years ago

10.1007/s11357-021-00329-x

Are the 50’s, the transition decade, in choroid plexus aging?
Cited by: 5
Author(s): Ana Carolina Tahira, Fernanda Marques, Bianca Cristina Garcia Lisbôa, Arthur Sant’Anna Feltrin, André Rocha Barbosa, Kátia C. Oliveira, Carlos Alberto de Bragança Pereira, Renata Leite, Lea T. Grinberg, Cláudia Kimie Suemoto, Renata Eloah de Lucena Ferretti‐Rebustini, Carlos Augusto Pasqualucci, Wilson Jacob‐Filho, Helena Brentani, Joana Almeida Palha
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-021-07924-4

Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella)
Cited by: 10
Author(s): Yan He, Hongyan Yu, Hongling Zhao, Hua Zhu, Qingjing Zhang, Anqi Wang, Yubang Shen, Xiaoyan Xu, Jiale Li
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.48216

Cis-regulatory basis of sister cell type divergence in the vertebrate retina
Cited by: 28
Author(s): Daniel P. Murphy, Andrew Hughes, Karen A. Lawrence, Connie A. Myers, Joseph C. Corbo
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.11418

An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells
Cited by: 212
Author(s): Marius Walter, Aurélie Teissandier, Raquel Pérez-Palacios, Déborah Bourc’his
Software Mentions: 5
Published: over 10 years ago

10.1186/s13072-017-0137-1

Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid
Cited by: 32
Author(s): Gautier Richard, Fabrice Legeai, Nathalie Prunier-Leterme, Anthony Bretaudeau, Denis Tagu, Julie Jaquiéry, Gaël Le Trionnaire
Software Mentions: 5
Published: over 9 years ago

10.1002/ece3.6899

Insights into the genetic basis of predator‐induced response inDaphnia galeata
Cited by: 9
Author(s): Verena Tams, Jana Nickel, Anne Ehring, Mathilde Cordellier
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13072-020-00359-3

UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells
Cited by: 5
Author(s): Beisi Xu, Brett B. Mulvey, Muneeb Salie, Xiaoyang Yang, Yurika Matsui, Anjana Nityanandam, Yiping Fan, Jamy C. Peng
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.13926

Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci
Cited by: 122
Author(s): Claude Philippe, Dulce B Vargas-Landin, Aurélien J. Doucet, Dominic van Essen, Jorge Vera-Otárola, Monika Kuciak, Antoine Corbin, Pilvi Nigumann, Gaël Cristofari
Software Mentions: 5
Published: over 10 years ago

10.7554/eLife.21049

Proliferation-independent regulation of organ size by Fgf/Notch signaling
Cited by: 36
Author(s): Agnė Kozlovskaja-Gumbrienė, Yi Ren, Alexander Richard, Andy Aman, Ryan Jiskra, Danielle Nagelberg, Holger Knaut, Melainia McClain, Tatjana Piotrowski
Software Mentions: 5
Published: over 9 years ago

10.7717/peerj.6660

Music-performance regulates microRNAs in professional musicians
Cited by: 7
Author(s): Preethy Sasidharan Nair, Tuire Kuusi, Minna Ahvenainen, Anju K. Philips, Irma Järvelä
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.3091

Effect of method of deduplication on estimation of differential gene expression using RNA-seq
Cited by: 20
Author(s): Anna V. Klepikova, Artem S. Kasianov, Mikhail S. Chesnokov, Н. Л. Лазаревич, Aleksey A. Penin, Maria D. Logacheva
Software Mentions: 5
Published: over 9 years ago

10.1155/2021/5320445

Predicting Target Genes of San-Huang-Chai-Zhu Formula in Treating ANIT-Induced Acute Intrahepatic Cholestasis Rat Model via Bioinformatics Analysis Combined with Experimental Validation
Cited by: 6
Author(s): Jiaming Yao, Junbin Yan, Jinting Wu, Jianshun Yu, Beihui He, Xi Chen
Software Mentions: 5
Published: about 5 years ago

10.12688/wellcomeopenres.14735.2

Mapping targets for small nucleolar RNAs in yeast
Cited by: 16
Author(s): Tatiana Dudnakova, Hywel Dunn-Davies, Rosie Peters, David Tollervey
Software Mentions: 5
Published: almost 8 years ago

10.7554/eLife.23645

Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation
Cited by: 27
Author(s): Sarah Elizabeth Albritton, Anna Lena Kranz, Lara Winterkorn, Lena Annika Street, Sevinç Ercan
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-017-4364-4

Pronounced strain-specific chemosensory receptor gene expression in the mouse vomeronasal organ
Cited by: 16
Author(s): Kyle Duyck, Vasha DuTell, Limei Ma, Ariel Paulson, Chong Yu
Software Mentions: 5
Published: almost 9 years ago

10.7554/eLife.42499

A combination of transcription factors mediates inducible interchromosomal contacts
Cited by: 15
Author(s): Seungsoo Kim, Maitreya J. Dunham, Jay Shendure
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.21476

Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated
Cited by: 67
Author(s): Ximena Ibarra-Soria, Thiago S. Nakahara, Jingtao Lilue, Yue Jiang, Casey Trimmer, Mateus A.A. Souza, Paulo H.M. Netto, Kentaro Ikegami, Nicolle R. Murphy, Mairi Kusma, Andrea Kirton, Luís R. Saraiva, Thomas Keane, Hiroaki Matsunami, Joel D. Mainland, Fábio Papes, Darren W. Logan
Software Mentions: 5
Published: over 9 years ago

10.15252/emmm.202013328

Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients
Cited by: 11
Author(s): Mirko Signorelli, Mitra Ebrahimpoor, Olga Veth, Kristina Hettne, Nisha Verwey, R. García-Rodríguez, Christa L Tanganyika-deWinter, Luz Berenice López-Hernández, Rosa Escobar Cedillo, Benjamín Gómez-D́iaz, Ólafur Þ. Magnússon, Hailiang Mei, Roula Tsonaka, Annemieke Aartsma‐Rus, Pietro Spitali
Software Mentions: 5
Published: over 5 years ago

10.3390/brainsci10050275

Transcriptome Analysis of Alcohol Drinking in Non-Dependent and Dependent Mice Following Repeated Cycles of Forced Swim Stress Exposure
Cited by: 10
Author(s): Sean P. Farris, Gayatri R. Tiwari, Olga N. Ponomareva, Marcelo F. López, R. Dayne Mayfield, Howard C. Becker
Software Mentions: 5
Published: over 6 years ago

10.15252/embj.2020105479

Repression of Irs2 by let‐7 mi <scp>RNA</scp> s is essential for homeostasis of the telencephalic neuroepithelium
Cited by: 9
Author(s): Virgínia Fernández, Maria Ángeles Martínez-Martinez, Anna Prieto-Colomina, Adrián Cárdenas, Rafael Soler, Martina Dori, Ugo Tomasello, Yuki Nomura, José P. López‐Atalaya, Federico Calegari, Vı́ctor Borrell
Software Mentions: 5
Published: almost 6 years ago

10.1186/1471-2164-15-917

Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut
Cited by: 37
Author(s): Matan Shelomi, W. Cameron Jasper, Joel Atallah, Lynn S. Kimsey, Brian R. Johnson
Software Mentions: 5
Published: over 12 years ago

10.1002/ece3.5924

Wild Dictyostelium discoideum social amoebae show plastic responses to the presence of nonrelatives during multicellular development
Cited by: 10
Author(s): Suegene Noh, Lauren Christopher, Joan E. Strassmann, David C. Queller
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.14997

Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons
Cited by: 326
Author(s): Mark S. Cembrowski, Lihua Wang, Ken Sugino, Brenda C. Shields, Nelson Spruston
Software Mentions: 5
Published: over 10 years ago

10.7554/eLife.38619

Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain
Cited by: 52
Author(s): Ken Sugino, Erin Clark, Anton Schulmann, Yasuyuki Shima, Lihua Wang, David Hunt, Bryan M. Hooks, Dimitri Tränkner, Jayaram Chandrashekar, Serge Picard, Andrew Lemire, Nelson Spruston, Adam W. Hantman, Sacha B. Nelson
Software Mentions: 5
Published: over 7 years ago

10.1111/1751-7915.13313

Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis
Cited by: 16
Author(s): Martin Fischer, Simon Güllert, Sarah Refai, Sven Künzel, Uwe Deppenmeier, Wolfgang R. Streit, Ruth A. Schmitz
Software Mentions: 5
Published: almost 8 years ago

10.1186/s12864-019-5504-9

Streamlined computational pipeline for genetic background characterization of genetically engineered mice based on next generation sequencing data
Cited by: 5
Author(s): Carlos Farkas, Francisco Fuentes-Villalobos, Boris Rebolledo‐Jaramillo, Fernando Benavides, Ariel F. Castro, Roxana Pincheira
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.47214

In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation
Cited by: 15
Author(s): Daniel Andergassen, Zachary D. Smith, Jordan P. Lewandowski, Chiara Gerhardinger, Alexander Meissner, John L. Rinn
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12864-019-5496-5

OMICfpp: a fuzzy approach for paired RNA-Seq counts
Cited by: 1
Author(s): Alberto Berral-González, Ángela L. Riffo‐Campos, Guillermo Ayala
Software Mentions: 5
Published: over 7 years ago

10.1016/j.devcel.2021.07.019

Genetically variant human pluripotent stem cells selectively eliminate wild-type counterparts through YAP-mediated cell competition
Cited by: 25
Author(s): Christopher J. Price, Dylan Stavish, Paul J. Gokhale, Ben A. Stevenson, Samantha Sargeant, Joanne Lacey, Tristan A. Rodríguez, Ivana Barbaric
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.47980

Controlling gene activation by enhancers through a drug-inducible topological insulator
Cited by: 5
Author(s): Taro Tsujimura, Osamu Takase, Masahide Yoshikawa, Etsuko Sano, Matsuhiko Hayashi, Kazuto Hoshi, Tsuyoshi Takato, Atsushi Toyoda, Hideyuki Okano, Keiichi Hishikawa
Software Mentions: 5
Published: over 6 years ago

10.15252/msb.20167058

Mechanism for microbial population collapse in a fluctuating resource environment
Cited by: 21
Author(s): Serdar Turkarslan, Arjun V. Raman, Anne Thompson, Christina E. Arens, Mark A. Gillespie, Frederick von Netzer, Kristina L. Hillesland, Sergey Stolyar, Adrián López García de Lomana, David J Reiss, Drew Gorman‐Lewis, Grant M. Zane, Jeffrey A. Ranish, Judy D. Wall, David A. Stahl, Nitin S. Baliga
Software Mentions: 5
Published: over 9 years ago

10.7554/eLife.43627

Flura-seq identifies organ-specific metabolic adaptations during early metastatic colonization
Cited by: 42
Author(s): Harihar Basnet, Lin Tian, Karuna Ganesh, Yun-Han Huang, Danilo G. Macalinao, Edi Brogi, Lydia W.S. Finley, Joan Massagué
Software Mentions: 5
Published: over 7 years ago

10.15252/msb.20145776

A high‐throughput <scp>C</scp> h <scp>IP</scp> ‐ <scp>S</scp> eq for large‐scale chromatin studies
Cited by: 28
Author(s): Christophe D. Chabbert, Sophie H. Adjalley, Bernd Klaus, E. Fritsch, Ishaan Gupta, Vicent Pelechano, Lars M. Steinmetz
Software Mentions: 5
Published: over 11 years ago

10.15252/msb.20209888

Gene expression profiling reveals insights into infant immunological and febrile responses to group B meningococcal vaccine
Cited by: 6
Author(s): Daniel O’Connor, Marta Pinto, Dylan Sheerin, Adriana Tomić, Ruth Drury, Samuel Channon‐Wells, Ushma Galal, Christina Dold, Hannah Robinson, Simon Kerridge, Emma Plested, Henry J. Hughes, Lisa Stockdale, Manish Sadarangani, Matthew D. Snape, Christine S. Rollier, Michael Levin, Andrew J. Pollard
Software Mentions: 5
Published: almost 6 years ago

10.1093/jmcb/mjaa061

RNF219 interacts with CCR4–NOT in regulating stem cell differentiation
Cited by: 6
Author(s): Hao Du, Chen Chen, Yan Wang, Yang Yang, Zhuanzhuan Che, Xiaoxu Liu, Siyan Meng, Chenghao Guo, Manman Xu, Haitong Fang, Fengchao Wang, Chengqi Lin, Zhuojuan Luo
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-020-06795-5

Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality
Cited by: 27
Author(s): Alessandra Zombardo, Cristina Crosatti, Paolo Bagnaresi, Laura Bassolino, Noam Reshef, Sergio Puccioni, Primetta Faccioli, Alessio Tafuri, Massimo Delledonne, Aaron Fait, Paolo Storchi, Luigi Cattivelli, Erica Mica
Software Mentions: 5
Published: about 6 years ago

10.1186/1471-213X-12-33

Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst
Cited by: 82
Author(s): Manabu Ozawa, Miki Sakatani, Jiqiang Yao, Savita Shanker, Fahong Yu, Rui Yamashita, Shokichi Wakabayashi, Kenta Nakai, Kyle B. Dobbs, Mateus José Sudano, William G. Farmerie, Peter J. Hansen
Software Mentions: 5
Published: almost 14 years ago

10.1038/onc.2016.382

Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer
Cited by: 125
Author(s): Alison Harrod, Janet S. Fulton, Van Nguyen, Manikandan Periyasamy, L Ramos-Garcia, C-F Lai, Gergana Metodieva, Alex de Giorgio, Richard Williams, Delfran Batista dos Santos, Pablo Gómez, M-L Lin, Metodi V. Metodiev, Justin Stebbing, Leandro Castellano, Luca Magnani, R. Charles Coombes, Laki Buluwela, Simak Ali
Software Mentions: 5
Published: almost 10 years ago

10.1093/hmg/ddab031

Sexual dimorphism in cancer: insights from transcriptional signatures in kidney tissue and renal cell carcinoma
Cited by: 10
Author(s): Ruhina Shirin Laskar, Peng Li, Szilvia Ecsedi, Behnoush Abedi‐Ardekani, G. Durand, Nivonirina Robinot, Jean-Noël Hubert, Vladimír Janout, Давид Заридзе, Anush Mukeria, Dana Mateș, Ivana Holcátová, Lenka Foretová, Beata Świątkowska, Zoran Džamić, Saša Milosavljević, Robert Olaso, Anne Boland, Jean‐François Deleuze, David C. Muller, James McKay, Paul Brennan, Florence Le Calvez-Kelm, Ghislaine Scélo, Estelle Chanudet
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-020-01181-z

Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt
Cited by: 27
Author(s): Amber N. Habowski, Jessica L. Flesher, Jennifer Bates, Chia‐Feng Tsai, Kendall J. Martin, Rui Zhao, Anand K. Ganesan, Robert A. Edwards, Tujin Shi, H. Steven Wiley, Yongsheng Shi, Klemens J. Hertel, Marian L. Waterman
Software Mentions: 5
Published: about 6 years ago

10.1038/s42003-021-02167-1

JAK inhibitors dampen activation of interferon-stimulated transcription of ACE2 isoforms in human airway epithelial cells
Cited by: 15
Author(s): Hye Kyung Lee, Olive Jung, Lothar Hennighausen
Software Mentions: 5
Published: over 5 years ago

10.1038/s41396-020-00794-w

Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity
Cited by: 17
Author(s): Sean Meaden, Loris Capria, Ellinor O. Alseth, Sylvain Gandon, Ambarish Biswas, Luca Lenzi, Stineke van Houte, Edze R. Westra
Software Mentions: 5
Published: almost 6 years ago

10.1002/1878-0261.12655

Transcriptome profiling of Ewing sarcomas – treatment resistance pathways and IGF‐dependency
Cited by: 6
Author(s): Yi Chen, Asle Charles Hesla, Yingbo Lin, Mehran Ghaderi, Mingzhi Liu, Yang Chen, Yifan Zhang, Panagiotis Tsagozis, Olle Larsson, Felix Haglund
Software Mentions: 5
Published: over 6 years ago

10.1038/s42003-018-0037-3

The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization
Cited by: 18
Author(s): Lisa Lindström, Tongbin Li, Darina Malycheva, Arun Kancharla, Helén Nilsson, Neelanjan Vishnu, Hindrik Mulder, Martin Johansson, Catalina Ana Rosselló, María Alvarado-Kristensson
Software Mentions: 5
Published: over 8 years ago

10.1084/jem.20171738

A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets
Cited by: 75
Author(s): Ángel F. Álvarez-Prado, Pablo Pérez-Durán, Arantxa Pérez-García, Alberto Benguría, Carlos Torroja, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 5
Published: over 8 years ago

10.1186/s12864-015-2246-1

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants
Cited by: 12
Author(s): Anna Aulicino, Adam M. Dinan, Aleksandra A. Miranda-CasoLuengo, John A. Browne, Kévin Rue-Albrecht, David E. MacHugh, Brendan J. Loftus
Software Mentions: 5
Published: almost 11 years ago

10.1242/dev.146811

Epigenetic resetting of human pluripotency
Cited by: 210
Author(s): Ge Guo, Ferdinand von Meyenn, Maria Rostovskaya, James Clarke, Sabine Dietmann, Duncan Baker, Anna Sahakyan, Samuel A. Myers, Paul Bertone, Wolf Reik, Kathrin Plath, Austin Smith
Software Mentions: 5
Published: about 9 years ago

10.1038/s42003-020-01398-y

Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation
Cited by: 2
Author(s): Michal Schwartz, Avital Sarusi Portugez, Bracha Zukerman Attia, Miriam Tannenbaum, Leslie E. Cohen, Olga Loza, Emily Chase, Yousef Turman, Tommy Kaplan, Zaidoun Salah, Ofir Hakim
Software Mentions: 5
Published: almost 6 years ago

10.3390/cells8080919

The Combination of IFN β and TNF Induces an Antiviral and Immunoregulatory Program via Non-Canonical Pathways Involving STAT2 and IRF9
Cited by: 11
Author(s): Mélissa K. Mariani, Pouria Dasmeh, Audray Fortin, Élise Caron, Mario Kalamujic, Alexander N. Harrison, Diana Ioana Hotea, Dacquin M. Kasumba, Sandra Cervantes-Ortiz, Espérance Mukawera, Adrian W.R. Serohijos, Nathalie Grandvaux
Software Mentions: 5
Published: about 7 years ago

10.1186/s13148-020-00879-5

G9a regulates tumorigenicity and stemness through genome-wide DNA methylation reprogramming in non-small cell lung cancer
Cited by: 25
Author(s): Rajendra P. Pangeni, Lu Yang, Keqiang Zhang, Jinhui Wang, Wendong Li, Chao Guo, Xinwei Yun, Ting Sun, Jami Wang, Dan J. Raz
Software Mentions: 5
Published: over 6 years ago

10.1186/s13024-018-0261-9

Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model
Cited by: 37
Author(s): Lodewijk J.A. Toonen, Maurice Overzier, Melvin M. Evers, Leticia G. León, Sander A.J. van der Zeeuw, Hailiang Mei, Szymon M. Kiełbasa, Jelle J. Goeman, Kristina Hettne, Ólafur Þ. Magnússon, Marion Poirel, Alexandre Seyer, Peter A.C. ’t Hoen, Willeke M. C. van Roon‐Mom
Software Mentions: 5
Published: about 8 years ago

10.1186/s40478-019-0805-4

Profiling the unique protective properties of intracranial arterial endothelial cells
Cited by: 7
Author(s): Dorien Hermkens, Olga C.G. Stam, Nienke M. de Wit, Ruud D. Fontijn, Aldo Jongejan, Perry D. Moerland, Claire Mackaaij, Ingeborg S. E. Waas, M. J. A. P. Daemen, Helga E. de Vries
Software Mentions: 5
Published: almost 7 years ago

10.3390/cells10081971

PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen
Cited by: 8
Author(s): Carolin Seyfferth, Bernard A. Wessels, Jorma Vahala, Jaakko Kangasjärvi, Nicolas Delhomme, Torgeir R. Hvidsten, Hannele Tuominen, Judith Lundberg‐Felten
Software Mentions: 5
Published: about 5 years ago

10.1038/s42003-021-01892-x

Transcriptomic analyses of the termite, Cryptotermes secundus, reveal a gene network underlying a long lifespan and high fecundity
Cited by: 15
Author(s): Silu Lin, Jana Werle, Judith Korb
Software Mentions: 5
Published: over 5 years ago

10.7150/thno.60031

Astrocytic YAP protects the optic nerve and retina in an experimental autoimmune encephalomyelitis model through TGF-β signaling
Cited by: 27
Author(s): Wei Qian, Xuemeng Miao, Jingjing Zhang, Ludan Xiang, Xiuchun Li, Xiaomei Bao, Siyu Du, Mianxian Wang, Shuangda Miao, Yiren Fan, Wei Wang, Xingxing Xu, Xiya Shen, Dongren Yang, Xiwu Wang, Yuanyuan Fang, Li‐Xin Hu, Xuyi Pan, Haoru Dong, Hui Wang, Ying Wang, Jia Li, Zhihui Huang
Software Mentions: 5
Published: over 5 years ago

10.1016/j.cels.2018.06.011

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data
Cited by: 63
Author(s): Nils Eling, Alison F. Richard, Sylvia Richardson, John C. Marioni, Catalina A. Vallejos
Software Mentions: 5
Published: about 8 years ago

10.3390/ani11092606

Jejunal Transcriptomic Profiling for Differences in Feed Conversion Ratio in Slow-Growing Chickens
Cited by: 2
Author(s): Panpradub Sinpru, Cindy Riou, Shin Kubota, Chotima Poompramun, Wittawat Molee, Amonrat Molee
Software Mentions: 5
Published: about 5 years ago

10.3390/v13081540

Multi-Tissue Transcriptomic-Informed In Silico Investigation of Drugs for the Treatment of Dengue Fever Disease
Cited by: 1
Author(s): Beatríz Sierra, Ana C. Magalhães, Daniel Lemos Soares, Bruno Cavadas, Ana B. Pérez, Mayling Álvarez, Eglys Aguirre, Claudia Bracho, Luı́sa Pereira, María G. Guzmán
Software Mentions: 5
Published: about 5 years ago

10.1007/s00122-020-03759-x

Multi-omics-based prediction of hybrid performance in canola
Cited by: 19
Author(s): Dominic Knoch, Christian R. Werner, Rhonda C. Meyer, David Riewe, Amine Abbadi, Sophie Lücke, Rod J. Snowdon, Thomas Altmann
Software Mentions: 5
Published: over 5 years ago

10.1101/2021.01.15.426908

Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules
Cited by: 2
Author(s): Jakub Jankowski, Hye Kyung Lee, Julia Wilflingseder, Lothar Hennighausen
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-33718-y

A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat
Cited by: 40
Author(s): Yongpeng Li, Xing Fu, Meicheng Zhao, Wei Zhang, Bo Li, Diaoguo An, Junming Li, Aimin Zhang, Renyi Liu, Xigang Liu
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13041-020-00603-7

Ocular hypertension suppresses homeostatic gene expression in optic nerve head microglia of DBA/2 J mice
Cited by: 28
Author(s): James R. Tribble, Jeffrey M. Harder, Pete A. Williams, Simon W. M. John
Software Mentions: 5
Published: over 6 years ago

10.1186/s12943-017-0653-4

Human germ/stem cell-specific gene TEX19 influences cancer cell proliferation and cancer prognosis
Cited by: 18
Author(s): Vicente Planells-Palop, Ali Hazazi, Julia Feichtinger, Jana Jezkova, Gerhard G. Thallinger, Naif Alsiwiehri, Mikhlid H. Almutairi, Lee Parry, Jane A. Wakeman, Ramsay J. McFarlane
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-018-29993-4

Analysis of diet-induced differential methylation, expression, and interactions of lncRNA and protein-coding genes in mouse liver
Cited by: 10
Author(s): José P. Silva, Derek Van Booven
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-018-38209-8

Differentially expressed gene networks, biomarkers, long noncoding RNAs, and shared responses with cocaine identified in the midbrains of human opioid abusers
Cited by: 30
Author(s): Manal H. Saad, Matthew Rumschlag, Michael H. Guerra, Candace Savonen, Alaina M Jaster, Philip D. Olson, Adnan Alazizi, Francesca Luca, Roger Piqué-Regi, Carl J. Schmidt, Michael J. Bannon
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0182270

Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegans
Cited by: 4
Author(s): Kapil Dev Singh, Xue Zheng, Stuart Milstein, Martin Keller, Bernd Roschitzki, Jonas Grossmann, Michael O. Hengartner
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0204234

Large scale changes in the transcriptome of Eisenia fetida during regeneration
Cited by: 28
Author(s): Aksheev Bhambri, Neeraj Dhaunta, Surendra Singh Patel, Mitali Hardikar, Abhishek Bhatt, Nagesh Srikakulam, Shruti Shridhar, Shamsudheen Karuthedath Vellarikkal, Rajesh Pandey, Rijith Jayarajan, Ankit Verma, Vikram Kumar, Pradeep Gautam, Yukti Khanna, Jameel Ahmed Khan, Bastian Fromm, Kevin J. Peterson, Vinod Scaria, Sridhar Sivasubbu, Beena Pillai
Software Mentions: 5
Published: almost 8 years ago

10.18632/aging.202582

Pan-cancer investigation reveals mechanistic insights of planar cell polarity gene Fuz in carcinogenesis
Cited by: 5
Author(s): Zhefan Stephen Chen, Xiao Lin, Ting-Fung Chan, Ho Yin Chan
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-27078-w

Global miRNA expression profile reveals novel molecular players in aneurysmal subarachnoid haemorrhage
Cited by: 19
Author(s): Kátia de Paiva Lopes, Tatiana Vinasco-Sandoval, Ricardo Assunção Vialle, Fernando Mendes Paschoal, Vanessa Albuquerque Paschoal Aviz Bastos, Edson Bor‐Seng‐Shu, Manoel Jacobsen Teixeira, Elizabeth Sumi Yamada, Pablo Diego do Carmo Pinto, Amanda Ferreira Vidal, André M. Ribeiro-dos-Santos, Fabiano Cordeiro Moreira, Sidney Emanuel Batista dos Santos, Eric Homero Albuquerque Paschoal, Ândrea Ribeiro‐dos‐Santos
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-019-40375-2

Transcriptome analysis of rumen epithelium and meta-transcriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis
Cited by: 21
Author(s): Wenli Li, S.L. Gelsinger, Andrea Edwards, Christina Riehle, Daniel C. Koch
Software Mentions: 5
Published: over 7 years ago

10.1128/mBio.00575-18

Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis
Cited by: 76
Author(s): Emily M. Nowicki, Raghav Shroff, Jacqueline A. Singleton, Diane E. Renaud, Debra L. Wallace, Julie Drury, Jolene Zirnheld, Brock Colleti, Andrew D. Ellington, Richard J. Lamont, David A. Scott, Marvin Whiteley
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.ppat.1009349

PD-1 is imprinted on cytomegalovirus-specific CD4+ T cells and attenuates Th1 cytokine production whilst maintaining cytotoxicity
Cited by: 15
Author(s): Helen Parry, Alexander C. Dowell, Jianmin Zuo, Kriti Verma, Francesca Kinsella, Jusnara Begum, Wayne Croft, Archana Sharma-Oates, Guy Pratt, Paul Moss
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-020-06911-5

Wild mice with different social network sizes vary in brain gene expression
Cited by: 2
Author(s): Patrícia C. Lopes, Barbara König
Software Mentions: 5
Published: about 6 years ago

10.1080/22221751.2020.1738277

Competing endogenous RNA network profiling reveals novel host dependency factors required for MERS-CoV propagation
Cited by: 50
Author(s): Xi Zhang, Hin Chu, Lei Wen, Huiping Shuai, Dong Yang, Yixin Wang, Yuxin Hou, Zheng Zhu, Shuofeng Yuan, Feifei Yin, Jasper Fuk‐Woo Chan, Kwok‐Yung Yuen
Software Mentions: 5
Published: over 6 years ago

10.1210/endocr/bqz044

Dysregulation of Hypothalamic Gene Expression and the Oxytocinergic System by Soybean Oil Diets in Male Mice
Cited by: 8
Author(s): Poonamjot Deol, Elena Kozlova, Matthew C. Valdez, Catherine Ho, Ei-Wen Yang, H.J. Richardson, Gwendolyn Michelle Gonzalez, Edward Truong, Jack Reid, Joseph M. Valdez, Jonathan Deans, Jose Martinez-Lomeli, Jane R. Evans, Tao Jiang, Frances M. Sladek, Margarita Curras‐Collazo
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0252685

Expanded transcriptomic view of strawberry fruit ripening through meta-analysis
Cited by: 0
Author(s): Gibum Yi, Hosub Shin, Kyeonglim Min, Eun Jin Lee
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-017-08094-8

CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo
Cited by: 14
Author(s): D. Craig Ayre, Ian C. Chute, Andrew P. Joy, David A. Barnett, Andrew M. Hogan, Marc P. Grüll, Lourdes Peña‐Castillo, Andrew S. Lang, Stephen M. Lewis, Sherri L. Christian
Software Mentions: 5
Published: about 9 years ago

10.1186/s12915-021-01084-3

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis
Cited by: 31
Author(s): Andrey N. Shkoporov, Е. В. Хохлова, Niamh Stephens, Cara M. Hueston, Samuel Seymour, Andrew J. Hryckowian, Dimitri Scholz, R. Paul Ross, Colin Hill
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-019-5974-9

Comparison of gene expression profile of the spinal cord of sprouting-capable neonatal and sprouting-incapable adult mice
Cited by: 9
Author(s): Hiroshi Tsujioka, Toshio Yamashita
Software Mentions: 5
Published: about 7 years ago

10.1186/s12915-018-0558-8

Clonal raider ant brain transcriptomics identifies candidate molecular mechanisms for reproductive division of labor
Cited by: 27
Author(s): Romain Libbrecht, Peter R. Oxley, Daniel J. C. Kronauer
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.ppat.1008444

Surfing motility is a complex adaptation dependent on the stringent stress response in Pseudomonas aeruginosa LESB58
Cited by: 16
Author(s): Daniel Pletzer, Evelyn Sun, Caleb Ritchie, Lauren Wilkinson, Leo T. Liu, Michael J. Trimble, Heidi Wolfmeier, Travis M. Blimkie, Robert E. W. Hancock
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-017-09335-6

Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis
Cited by: 85
Author(s): Julia Steinberg, Graham R. S. Ritchie, Theodoros I. Roumeliotis, Raveen L Jayasuriya, Matthew Clark, Roger A. Brooks, Abbie L. A. Binch, Karan M. Shah, Rachael Coyle, Mercedes Pardo, Christine Le Maitre, Yolande F M Ramos, Rob G H H Nelissen, Ingrid Meulenbelt, Andrew W. McCaskie, Jyoti S. Choudhary, J. Mark Wilkinson, Eleftheria Zeggini
Software Mentions: 5
Published: about 9 years ago

10.1186/s40168-021-01037-6

When your host shuts down: larval diapause impacts host-microbiome interactions in Nasonia vitripennis
Cited by: 15
Author(s): Jessica Dittmer, Robert M. Brucker
Software Mentions: 5
Published: over 5 years ago

10.1093/jxb/eraa124

Transcriptomics in Erigeron canadensis reveals rapid photosynthetic and hormonal responses to auxin herbicide application
Cited by: 19
Author(s): Cara L. McCauley, Scott A. M. McAdam, Ketaki P. Bhide, Jyothi Thimmapuram, Jo Ann Banks, Bryan G. Young
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1006699

The yeast form of the fungus Candida albicans promotes persistence in the gut of gnotobiotic mice
Cited by: 70
Author(s): Lena Böhm, Sanda Torsin, Su Hlaing Tint, Marie Therese Eckstein, Tobias Ludwig, J. Christian Pérez
Software Mentions: 5
Published: almost 9 years ago

10.1242/dev.131664

Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β‑catenin recruitment
Cited by: 99
Author(s): Yukio Nakamura, Eduardo Rodrigues Alves, Gert Jan C. Veenstra, Stefan Hoppler
Software Mentions: 5
Published: over 10 years ago

10.1186/s12864-018-4746-2

SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma
Cited by: 19
Author(s): Antonio Jordán-Pla, Simei Yu, Johan Waldholm, Thomas Källman, Ann‐Kristin Östlund Farrants, Neus Visa
Software Mentions: 5
Published: over 8 years ago

10.3390/biom11020291

Determination of Genotoxicity Attributed to Diesel Exhaust Particles in Normal Human Embryonic Lung Cell (WI-38) Line
Cited by: 4
Author(s): Joong Won Lee, Hee Jae Lee, Young Joo Lee, Yong Beom Lim, Woo Jong Sim, Ji Hye Jang, Hye Ryeon Heo, Hyunwoo Lim, Ji Won Jung, Jin Sik Kim
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms9020347

Global Transcriptional Response of Methylorubrum extorquens to Formaldehyde Stress Expands the Role of EfgA and Is Distinct from Antibiotic Translational Inhibition
Cited by: 3
Author(s): Jannell V. Bazurto, Siavash Riazi, Simon D’Alton, Daniel E. Deatherage, Eric L. Bruger, Jeffrey E. Barrick, Christopher J. Marx
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.27159

Development of Bag-1L as a therapeutic target in androgen receptor-dependent prostate cancer
Cited by: 29
Author(s): Laura Cato, Antje Neeb, Adam Sharp, Víctor Buzón, Scott B. Ficarro, Linxiao Yang, Claudia Muhle‐Goll, Nane C. Kuznik, Ruth Riisnaes, Daniel Nava Rodrigues, Olivier Armant, Victor Gourain, Guillaume Adelmant, Emmanuel Amankwah Ntim, Thomas Westerling, David Dolling, Pasquale Rescigno, Ines Figueiredo, Friedrich Fauser, Jiansheng Wu, Jaice T. Rottenberg, L. Shatkina, Claudia Ester, Burkhard Luy, Holger Puchta, Jakob Troppmair, Nicole Jung, Stefan Bräse, Uwe Strähle, Jarrod A. Marto, G. Ulrich Nienhaus, Bissan Al‐Lazikani, Xavier Salvatella, Johann S. de Bono, Andrew C. B. Cato, Myles Brown
Software Mentions: 5
Published: about 9 years ago

10.1186/s13073-020-00760-3

ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer
Cited by: 32
Author(s): Aileen P. Szczepanski, Zibo Zhao, Victoria Sosnowski, Young Ah Goo, Elizabeth T. Bartom, Lu Wang
Software Mentions: 5
Published: about 6 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 8 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 6 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 6 years ago

10.1016/j.heliyon.2020.e03493

Efficient differentiation and purification of human induced pluripotent stem cell-derived endothelial progenitor cells and expansion with the use of inhibitors of ROCK, TGF-β, and GSK3β
Cited by: 9
Author(s): Hiromasa Aoki, Misaki Yamashita, Tadahiro Hashita, Koichi Ogami, Shin‐ichi Hoshino, Takahiro Iwao, Tamihide Matsunaga
Software Mentions: 4
Published: over 6 years ago

10.3390/md17030181

Comparative Transcriptome Analyses Provide Potential Insights into the Molecular Mechanisms of Astaxanthin in the Protection against Alcoholic Liver Disease in Mice
Cited by: 12
Author(s): Huilin Liu, Huimin Liu, Liang Zhu, Ziqi Zhang, Xin Zheng, Jingsheng Liu, Xueqi Fu
Software Mentions: 4
Published: over 7 years ago

Projects: pypi: HTSeq

Science Score: 65/100

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Papers Mentioning HTSeq 3,071