pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1186/s12859-019-2728-2

UTAP: User-friendly Transcriptome Analysis Pipeline
Cited by: 88
Author(s): Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran, Dena Leshkowitz
Software Mentions: 5
Published: over 7 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

10.3390/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

10.7554/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

10.7554/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

10.1186/s12864-016-2745-8

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq
Cited by: 17
Author(s): Yongxian Yuan, Huaiqian Xu, Rufina Leung
Software Mentions: 5
Published: over 10 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

10.1186/s12864-017-3810-7

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species
Cited by: 27
Author(s): Ezra Lencer, Wesley C. Warren, Richard G. Harrison, Amy R. McCune
Software Mentions: 5
Published: over 9 years ago

10.1186/s12859-016-1154-y

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016
Cited by: 0
Author(s): Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park, Xueyuan Cao, Stanley Pounds, Susana C. Raimondi, James R. Downing, Raul C. Ribeiro, Jeffery Rubnitz, Jatinder K. Lamba, Bernie J. Daigle, Deborah C. Hay Burgess, Stephanie Gehrlich, John C. Carmen, Nicholas Johnson, Chandrakanth Emani, Kalpani De Silva, Michael P. Heaton, Theodore S. Kalbfleisch, Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun T. Ajayi, Fatih Şen, Eunice Y. Huang, Mohammad Mohebbi, Luaire Florian, Douglas Jackson, John Naber, Akm Sabbir, Sally R. Ellingson, Yuping Lu, Charles Phillips, Michael A. Langston, Rahul Kumar Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui, Mohammed Sayed, Jing Wang, Qi Liu, Yu Shyr, Xiaofei Zhang, Naresh Prodduturi, Gavin R. Oliver, Diane E. Grill, Jie Na, Jeanette E. Eckel‐Passow, Eric W. Klee, Michael M. Goodin, Mark L. Farman, Harrison A Inocencio, Chanyong Jang, Jerzy W. Jaromczyk, Neil Moore, Kelly L Sovacool, Leon Dent, Mike Izban, Sammed N. Mandape, Shruti S. Sakhare, Siddharth Pratap, Dana Marshall, M Scotty DePriest, James N. MacLeod, H. Marblestone Adam, Ethan Blandford, Joel Campbell, Joshua Castlen, Brittany Dixon, Ginger Gilbert, Aaron Smalter Hall, Philip Kreisle, Jessica Lasher, B.K. Oakes, Allison Speer, Maximilian Valentine, Naga Satya V Rao Nagisetty, Rony Jose, Robert J. Rooney, David S. Hains
Software Mentions: 5
Published: about 10 years ago

10.1186/s40478-017-0414-z

Serum microRNA miR-501-3p as a potential biomarker related to the progression of Alzheimer’s disease
Cited by: 118
Author(s): Norikazu Hara, Masataka Kikuchi, Akinori Miyashita, Hiroyuki Hatsuta, Yuko Saito, Kensaku Kasuga, Shigeo Murayama, Takeshi Ikeuchi, Ryozo Kuwano
Software Mentions: 5
Published: over 9 years ago

10.3389/fgene.2018.00441

Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle
Cited by: 30
Author(s): Tassia M. Goncalves, Luciana Correia de Almeida Regitano, James E. Koltes, Aline Silva Mello Cesar, Sónia Cristina da Silva Andrade, Gérson Barreto Mourão, G. Gasparin, Gabriel Costa Monteiro Moreira, Eric R. Fritz-Waters, James M. Reecy
Software Mentions: 5
Published: almost 8 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

10.1038/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

10.1038/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

10.1007/s10456-021-09788-4

The endosomal RIN2/Rab5C machinery prevents VEGFR2 degradation to control gene expression and tip cell identity during angiogenesis
Cited by: 20
Author(s): Lanette Kempers, Yuki Wakayama, Ivo van der Bijl, Charita Furumaya, Iris M. De Cuyper, Aldo Jongejan, Marije Kat, Anne-Marieke D. van Stalborch, Antonius L. van Boxtel, Marvin Hubert, Dirk Geerts, Jaap D. van Buul, Dirk de Korte, Wiebke Herzog, Coert Margadant
Software Mentions: 5
Published: over 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

10.7554/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

10.1038/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

10.7554/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/s12864-020-6495-2

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features
Cited by: 8
Author(s): Yang Li, Menggen Dalai, Rongguo Su, Weili Lin, Myagmarsuren Erdenedalai, Batkhuu Luvsantseren, Chimedragchaa Chimedtseren, Zhen Wang, Surong Hasi
Software Mentions: 5
Published: over 6 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

10.7554/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

10.3390/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

10.3390/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

10.7554/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

10.1186/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: about 6 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/s12864-020-07313-3

The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation
Cited by: 7
Author(s): Longsheng Xing, Yu X, Xi Qiao, Cong Huang, Qiang Wu, Yang Ni, Jiao Guo, Wan‐Xue Liu, Wei Fan, Fang‐Hao Wan, Wanqiang Qian
Software Mentions: 5
Published: over 5 years ago

10.1016/j.stem.2015.04.004

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations
Cited by: 369
Author(s): Nicola K. Wilson, David G. Kent, Florian Buettner, Mona Shehata, Iain C. Macaulay, Fernando J. Calero-Nieto, Manuel Sánchez Castillo, Caroline A. Oedekoven, Evangelia Diamanti, Reiner Schulte, Chris P. Ponting, Thierry Voet, Carlos Caldas, John Stingl, Anthony Green, Fabian J. Theis, Berthold Göttgens
Software Mentions: 5
Published: over 11 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

10.1186/1471-2164-15-76

Combinatorial epigenetic patterns as quantitative predictors of chromatin biology
Cited by: 16
Author(s): Marcin Cieślik, Stefan Bekiranov
Software Mentions: 5
Published: over 12 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

10.1038/s41422-020-0385-7

Stabilization of heterochromatin by CLOCK promotes stem cell rejuvenation and cartilage regeneration
Cited by: 51
Author(s): Chuqian Liang, Zunpeng Liu, Moshi Song, Wei Li, Zeming Wu, Zehua Wang, Qiaoran Wang, Si Wang, Yan Ke, Liang Sun, Tomoaki Hishida, Yanning Cai, Juan Carlos Izpisúa Belmonte, Pedro Guillén, Piu Chan, Qi Zhou, Weiqi Zhang, Jing Qu, Guanghui Liu
Software Mentions: 5
Published: about 6 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

10.1093/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/s12864-016-3283-0

Tsetse fly tolerance to T. brucei infection: transcriptome analysis of trypanosome-associated changes in the tsetse fly salivary gland
Cited by: 25
Author(s): Irina Matetovici, Guy Caljon, Jan Van Den Abbeele
Software Mentions: 5
Published: almost 10 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

10.1016/j.celrep.2018.04.004

mRNA Cap Methyltransferase, RNMT-RAM, Promotes RNA Pol II-Dependent Transcription
Cited by: 32
Author(s): Dhaval Varshney, Olivia Lombardi, Gabriele Schweikert, Sianadh Dunn, Olga Suska, Victoria H. Cowling
Software Mentions: 5
Published: over 8 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

10.15252/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

10.1038/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

10.7554/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

10.7150/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

10.1007/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

10.1038/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

10.1038/s41419-021-03739-z

WNT/β-catenin-suppressed FTO expression increases m6A of c-Myc mRNA to promote tumor cell glycolysis and tumorigenesis
Cited by: 61
Author(s): Xueying Yang, Fei Shao, Dong Guo, Wei Wang, Juhong Wang, Rongxuan Zhu, Yibo Gao, Jie He, Zhimin Lu
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-015-0670-5

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments
Cited by: 211
Author(s): Stephen W. Hartley, James C. Mullikin
Software Mentions: 5
Published: about 11 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

10.1186/s12864-017-3589-6

Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activity
Cited by: 14
Author(s): Michael Chambers, Wiam Turki-Judeh, Min Woo Kim, Kenny Chen, Sean D. Gallaher, Albert J. Courey
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-019-5960-2

Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT
Cited by: 19
Author(s): Matteo Schiavinato, Richard Strasser, Lukas Mach, Juliane C. Dohm, Heinz Himmelbauer
Software Mentions: 5
Published: about 7 years ago

10.1038/s41421-017-0003-0

ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
Cited by: 46
Author(s): Si Wang, Boqiang Hu, Zicheng Ding, Yujiao Dang, Jun Wu, Di Li, Xiaoling Liu, Bailong Xiao, Weiqi Zhang, Rui Ren, Jinghui Lei, Huifang Hu, Chang Chen, Piu Chan, Dong Liu, Jing Qu, Fuchou Tang, Guang Hui Liu
Software Mentions: 5
Published: over 8 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/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/s41598-018-33718-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

10.1101/2021.01.15.426908

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/s41598-017-09335-6

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

10.1038/s41598-017-03489-z

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli
Cited by: 38
Author(s): Tracy H. Hazen, Jane Michalski, Qingwei Luo, Amol C. Shetty, Sean C. Daugherty, James M. Fleckenstein, David A. Rasko
Software Mentions: 5
Published: about 9 years ago

10.1038/srep33813

Contrasting diets reveal metabolic plasticity in the tree-killing beetle, Anoplophora glabripennis (Cerambycidae: Lamiinae)
Cited by: 20
Author(s): Charles J. Mason, Erin D. Scully, Scott M. Geib, Kelli Hoover
Software Mentions: 5
Published: almost 10 years ago

10.1038/sdata.2016.51

Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome
Cited by: 40
Author(s): Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser‐Klopp, J. J. Arranz
Software Mentions: 5
Published: about 10 years ago

10.1038/srep25948

Integrated metabolomic and transcriptome analyses reveal finishing forage affects metabolic pathways related to beef quality and animal welfare
Cited by: 58
Author(s): José A. Carrillo, Yanghua He, Yaokun Li, Jianan Liu, R.A. Erdman, Tad S. Sonstegard, Jiuzhou Song
Software Mentions: 5
Published: over 10 years ago

10.1038/srep46156

Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chickens
Cited by: 18
Author(s): Xi Lan, Yan Wang, Kai Tian, Fei Ye, Huadong Yin, Xiaoling Zhao, Hengyong Xu, Yong Huang, Haibo Li, John Hsieh, Susan J. Lamont, Qing Zhu
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-2164-14-230

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro
Cited by: 39
Author(s): Nicolas C. Nalpas, Stephen D. E. Park, David A. Magee, Maria Taraktsoglou, John A. Browne, Kevin M. Conlon, Kévin Rue-Albrecht, Kate E. Killick, Karsten Hokamp, Amanda J. Lohan, Brendan J. Loftus, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 5
Published: over 13 years ago

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

10.1371/journal.pone.0160925

The 4p16.3 Parkinson Disease Risk Locus Is Associated with GAK Expression and Genes Involved with the Synaptic Vesicle Membrane
Cited by: 16
Author(s): Michael W. Nagle, Jeanne C. Latourelle, Adam Labadorf, Alexandra Dumitriu, Tiffany C. Hadzi, Thomas G. Beach, Richard H. Myers
Software Mentions: 5
Published: about 10 years ago

10.1016/j.cmet.2020.03.003

Microbiota-Derived Metabolites Suppress Arthritis by Amplifying Aryl-Hydrocarbon Receptor Activation in Regulatory B Cells
Cited by: 247
Author(s): Elizabeth C. Rosser, Christopher Piper, Diana E. Matei, Paul A. Blair, André F. Rendeiro, Michael Orford, Dagmar Alber, Thomas Krausgruber, Diego Catalán, Nigel Klein, Jessica Manson, Ignat Drozdov, Christoph Bock, Lucy R. Wedderburn, Simon Eaton, Claudia Mauri
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

10.1126/sciadv.abd7819

High-resolution 3D imaging uncovers organ-specific vascular control of tissue aging
Cited by: 54
Author(s): Junyu Chen, Unnikrishnan Sivan, Sin Lih Tan, Luciana Lippo, Jessica De Angelis, Rossella Labella, Amit Singh, Alexandros Chatzis, Stanley Cheuk, Mino Medhghalchi, Jesús Gil, Georg A. Holländer, Brian D. Marsden, R. J. P. Williams, Saravana K. Ramasamy, Anjali P. Kusumbe
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

10.1128/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

10.1186/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

10.1098/rsos.200792

Tissue-specific developmental regulation and isoform usage underlie the role ofdoublesexin sex differentiation and mimicry inPapilioswallowtails
Cited by: 13
Author(s): Riddhi Deshmukh, Dhanashree Lakhe, Krushnamegh Kunte
Software Mentions: 5
Published: about 6 years ago

10.21203/rs.3.rs-119695/v1

Activation of Interferon-Stimulated Transcriptomes and ACE2 Isoforms in Human Airway Epithelium Is Curbed by Janus Kinase Inhibitors
Cited by: 5
Author(s): Hye Kyung Lee, Olive Jung, Lothar Hennighausen
Software Mentions: 5
Published: over 5 years ago

10.1016/j.gpb.2020.08.001

G9a/GLP-sensitivity of H3K9me2 Demarcates Two Types of Genomic Compartments
Cited by: 3
Author(s): Zixiang Yan, Luzhang Ji, Xiangru Huo, Qianfeng Wang, Yuwen Zhang, Bo Wen
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0197162

A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells
Cited by: 15
Author(s): Alexander Wolff, Michaela Bayerlová, Jochen Gaedcke, Dieter Kube, Tim Beißbarth
Software Mentions: 5
Published: over 8 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

10.1186/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

10.1186/s13073-016-0348-2

Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring
Cited by: 9
Author(s): José P. Silva, Guerline Lambert, Derek Van Booven, Claes Wahlestedt
Software Mentions: 5
Published: about 10 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/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

10.1186/s13073-021-00938-3

The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability
Cited by: 9
Author(s): Jennifer Derrien, Catherine Guérin‐Charbonnel, Victor Gaborit, Loı̈c Campion, Martine Devic, Elise Douillard, Nathalie Roi, Hervé Avet‐Loiseau, Olivier Decaux, Thierry Facon, Jan‐Philipp Mallm, Roland Eils, Nikhil C. Munshi, Philippe Moreau, Carl Herrmann, Florence Magrangeas, Stέphane Minvielle
Software Mentions: 5
Published: about 5 years ago

10.1111/1751-7915.13441

Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. <scp>BAL</scp>341
Cited by: 12
Author(s): Christofer M. G. Karlsson, Elena Cerro‐Gálvez, Daniel Lundin, Camilla Karlsson, Maria Vila‐Costa, Jarone Pinhassi
Software Mentions: 5
Published: about 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

10.1016/j.cmet.2018.07.005

A Role for p53 in the Adaptation to Glutamine Starvation through the Expression of SLC1A3
Cited by: 144
Author(s): Mylène Tajan, A. Höck, Julianna Blagih, Neil Robertson, Christiaan F. Labuschagne, Flore Kruiswijk, Timothy J. Humpton, Peter D. Adams, Karen H. Vousden
Software Mentions: 5
Published: almost 8 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

10.1371/journal.pone.0232963

Identifying the key regulators that promote cell-cycle activity in the hearts of early neonatal pigs after myocardial injury
Cited by: 11
Author(s): Eric Zhang, Thanh Nguyen, Meng Zhao, Son Do Hai Dang, Jake Y. Chen, Weihua Bian, Gregory P. Walcott
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-020-02175-0

Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity
Cited by: 32
Author(s): Won‐Chul Lee, Alexandre Reuben, Xin Hu, Nicholas McGranahan, Runzhe Chen, Ali Jalali, Marcelo V. Negrão, Shawna M. Hubert, Chad Tang, Chia-Chin Wu, Anthony San Lucas, Whijae Roh, Kenichi Suda, Jihye Kim, Aik-Choon Tan, David H. Peng, Wei Lü, Ximing Tang, Chi-Wan Chow, Junya Fujimoto, Carmen Behrens, Neda Kalhor, Kazutaka Fukumura, Marcus Coyle, Rebecca Thornton, Curtis Gumbs, Jun Li, Chang-Jiun Wu, Latasha Little, Emily Roarty, Xingzhi Song, J. Jack Lee, Erik P. Sulman, Ganesh Rao, Stephen G. Swisher, Lixia Diao, Jing Wang, John V. Heymach, Jason T. Huse, Paul Scheet, Ignacio I. Wistuba, Don L. Gibbons, P. Andrew Futreal, Jianhua Zhang, Daniel R. Gomez, Jianjun Zhang
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13059-021-02397-w

A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion
Cited by: 4
Author(s): Franziska Witte, Jorge Ruiz-Orera, Camilla Ciolli Mattioli, Susanne Blachut, Eleonora Adami, Jana Felicitas Schulz, Valentin Schneider-Lunitz, Oliver Hummel, Giannino Patone, Michael Mücke, Jan Šilhavý, Matthias Heinig, Leonardo Bottolo, Daniel Sanchı́s, Martin Vingron, Marina Chekulaeva, Michal Pravenec, Norbert Hübner, Sebastiaan van Heesch
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pntd.0009587

Transcriptomic analysis and molecular docking reveal genes involved in the response of Aedes aegypti larvae to an essential oil extracted from Eucalyptus
Cited by: 9
Author(s): Ivana Sierra, José Manuel Latorre-Estivalis, Lucila Traverso, Paula Valeria Gonzalez, Ariel A Aptekmann, Alejandro D. Nadra, Héctor Mario Masuh, Sheila Ons
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1008611

A non-canonical RNAi pathway controls virulence and genome stability in Mucorales
Cited by: 17
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Eusebio Navarro, Victoriano Garre
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pntd.0004992

Meta-transcriptome Profiling of the Human-Leishmania braziliensis Cutaneous Lesion
Cited by: 54
Author(s): Stephen M Christensen, Laura A. L. Dillon, Lucas P. Carvalho, Sara Passos, Fernanda O. Novais, V. K. Hughitt, Daniel P. Beiting, Edgar M. Carvalho, Phillip Scott, Najib M. El-Sayed, David M. Mosser
Software Mentions: 5
Published: almost 10 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

10.1186/1471-2164-15-917

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

10.1371/journal.pntd.0002905

Dual RNA-seq of Parasite and Host Reveals Gene Expression Dynamics during Filarial Worm–Mosquito Interactions
Cited by: 59
Author(s): Young Jun Choi, Matthew T. Aliota, George F. Mayhew, Sara M. Erickson, Bruce M. Christensen
Software Mentions: 5
Published: over 12 years ago

10.1186/s13059-021-02464-2

Systematic functional interrogation of human pseudogenes using CRISPRi
Cited by: 11
Author(s): Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Xu Han, Yiwen Chen
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-017-1285-0

Chromosome contacts in activated T cells identify autoimmune disease candidate genes
Cited by: 66
Author(s): Oliver S. Burren, Arcadio Rubio Garćıa, Biola M. Javierre, Daniel B. Rainbow, Jonathan Cairns, Nicholas Cooper, John Lambourne, Ellen Schofield, Xaquín Castro Dopico, Ricardo C. Ferreira, Richard M. R. Coulson, Frances Burden, Sophia Rowlston, Kate Downes, Steven W. Wingett, Mattia Frontini, Willem H. Ouwehand, Peter Fraser, Mikhail Spivakov, John A. Todd, Linda S. Wicker, Antony J. Cutler, Chris Wallace
Software Mentions: 5
Published: about 9 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.ccell.2019.02.009

Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets
Cited by: 533
Author(s): Luca Cassetta, Stamatina Fragkogianni, Andrew H. Sims, Agnieszka Swierczak, Lesley M. Forrester, Hui Zhang, Daniel Soong, Tiziana Cotechini, Pavana Anur, Elaine Y. Lin, A Fidanza, Martha Lopez‐Yrigoyen, Michael Millar, Alexandra Urman, Zhichao Ai, Paul T. Spellman, E. Shelley Hwang, JM Dixon, Lisa Wiechmann, Lisa M. Coussens, Harriet O. Smith, Jeffrey W. Pollard
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pgen.1006222

KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans
Cited by: 68
Author(s): Agnieszka Gacek‐Matthews, Harald Berger, Takahiko Sasaki, Kathrin Wittstein, Clemens Gruber, Zachary A. Lewis, Joseph Strauss
Software Mentions: 5
Published: about 10 years ago

10.1186/s13059-015-0734-x

Errors in RNA-Seq quantification affect genes of relevance to human disease
Cited by: 128
Author(s): Christelle Robert, Michael Watson
Software Mentions: 5
Published: about 11 years ago

Projects: pypi: HTSeq

Science Score: 65/100

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Papers Mentioning HTSeq 3,071