pypi: HTSeq | Projects | Ecosyste.ms: Papers

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

10.1186/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

10.1084/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

10.1007/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

10.1186/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

10.1186/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

10.1186/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: about 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

10.1080/22221751.2020.1738277

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

10.1002/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

10.1155/2018/2439527

RNA-seq Reveals the Overexpression of IGSF9 in Endometrial Cancer
Cited by: 11
Author(s): Zonggao Shi, Chunyan Li, Laura Tarwater, Jun Li, Yang Li, William Kaliney, Darshan S. Chandrashekar, M. Sharon Stack
Software Mentions: 5
Published: over 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

10.1210/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

10.1186/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

10.1186/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

10.1186/1471-2164-15-76

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.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/s41419-021-03644-5

Eradication of specific donor-dependent variations of mesenchymal stem cells in immunomodulation to enhance therapeutic values
Cited by: 19
Author(s): Chunxue Zhang, Liqiang Zhou, Zhen Wang, Wenxia Gao, Wei Chen, Huina Zhang, Bo Jing, Zhu Xu, Lei Chen, Changhong Zheng, Kaiyan Shi, Wu Li, Liming Cheng, Kunshan Zhang, Yi Sun
Software Mentions: 5
Published: over 5 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

10.15252/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

10.1002/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

10.15252/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/s41420-019-0184-4

A six-inhibitor culture medium for improving naïve-type pluripotency of porcine pluripotent stem cells
Cited by: 15
Author(s): Ye Yuan, Jin‐Kyu Park, Yuchen Tian, Jungmin Choi, Rolando Pasquariello, Andrei P. Alexenko, Aihua Dai, Susanta K. Behura, R. Michael Roberts, Toshihiko Ezashi
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

10.1016/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

10.15252/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

10.18632/oncotarget.16493

ERK signalling modulates epigenome to drive epithelial to mesenchymal transition
Cited by: 20
Author(s): Mohit Navandar, Angela Garding, Sanjeeb Kumar Sahu, Abhijeet Pataskar, Sandra Schick, Vijay Tiwari
Software Mentions: 5
Published: over 9 years ago

10.18632/oncotarget.13062

Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Cited by: 29
Author(s): Lei Wei, Sreenivasulu Chintala, Eric Ciamporcero, Swathi Ramakrishnan, May Elbanna, Jianmin Wang, Qiang Hu, Sean T. Glenn, Mitsuko Murakami, Lu Liu, Eduardo Cortes Gomez, Yuchen Sun, Jacob Conroy, Kiersten Marie Miles, Malathi Kullappan, Sudha Ramaiah, Anand Anbarasu, Anna Woloszynska‐Read, Candace S. Johnson, Jeffrey M. Conroy, Song Liu, Carl Morrison, Роберто Пили
Software Mentions: 5
Published: almost 10 years ago

10.18632/oncotarget.21031

Genome-wide analysis and functional prediction of long non-coding RNAs in mouse uterus during the implantation window
Cited by: 22
Author(s): Qi Wang, Nan Wang, Rui Cai, Fan Zhao, Yi Xiong, Xiao Li, Aihua Wang, Peng Lin, Yaping Jin
Software Mentions: 5
Published: almost 9 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

10.1186/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

10.18632/oncotarget.8192

Integrated analysis of long non-coding RNAs in human colorectal cancer
Cited by: 32
Author(s): Xiaohua Chen, Binjian Liu, Rui Yang, Yong Guo, Feng Li, Lin Wang, Hanyang Hu
Software Mentions: 5
Published: over 10 years ago

10.1186/s12864-017-4380-4

Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome
Cited by: 36
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, David Bunn, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 5
Published: almost 9 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/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

10.3390/ijms22052353

ATF3-Induced Mammary Tumors Exhibit Molecular Features of Human Basal-Like Breast Cancer
Cited by: 3
Author(s): Leqin Yan, Sally Gaddis, Luis Della Coletta, John Repass, Katherine Powell, Melissa S. Simper, Yueping Chen, Michelle Byrom, Yi Zhong, Kevin Lin, Bin Liu, Yao Lu, Jianjun Shen, Michael C. MacLeod
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms20133315

Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts
Cited by: 10
Author(s): Simona Cantarella, Davide Carnevali, Marco Morselli, Anastasia Conti, Matteo Pellegrini, Barbara Montanini, Giorgio Dieci
Software Mentions: 5
Published: about 7 years ago

10.3390/ijms22052738

Identification of Overexpressed Genes in Malignant Pleural Mesothelioma
Cited by: 11
Author(s): Federica Morani, Luisa Bisceglia, Giulia Rosini, Luciano Mutti, Ombretta Melaiu, Stefano Landi, Federica Gemignani
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

10.1093/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

10.3390/ijms22115858

Calreticulin Deficiency Disturbs Ribosome Biogenesis and Results in Retardation in Embryonic Kidney Development
Cited by: 4
Author(s): Nazli Serin, Gry H. Dihazi, Asima Tayyeb, Christof Lenz, Gerhard A. Müller, Michael Zeisberg, Hassan Dihazi
Software Mentions: 5
Published: over 5 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

10.1186/1471-2164-14-230

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

10.1186/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

10.7150/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/s41598-021-97258-8

Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
Cited by: 3
Author(s): Cristina Cheroni, Lara Manganaro, Lorena Donnici, Valeria Bevilacqua, Raoul J. P. Bonnal, Riccardo Rossi, Raffaele De Francesco
Software Mentions: 5
Published: almost 5 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

10.1038/s41598-021-84270-1

Serial transplantation unmasks galectin-9 contribution to tumor immune escape in the MB49 murine model
Cited by: 4
Author(s): Valentin Baloche, Julie Rivière, Thi Bao Tram Tran, Aurore Gelin, Olivia Bawa, Nicolas Signolle, Mouhamadou Diop, Philippe Dessen, Stéphanie Beq, Muriel D. David, P. Busson
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

10.1038/s41598-021-81472-5

Drosophila Hox genes induce melanized pseudo-tumors when misexpressed in hemocytes
Cited by: 6
Author(s): Titus Ponrathnam, Ravina Saini, Sofia Banu, Rakesh Mishra
Software Mentions: 5
Published: over 5 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

10.1038/s41598-020-70131-w

Transcriptomic profile of adverse neurodevelopmental outcomes after neonatal encephalopathy
Cited by: 6
Author(s): Paolo Montaldo, Aubrey J. Cunnington, Vânia Oliveira, Ravi Swamy, Prathik Bandya, Stuti Pant, Peter J Lally, Phoebe Ivain, Josephine Mendoza, Gaurav Atreja, Padmesh Vadakepat, Mythili Baburaj, Monica Sebastian, Indiramma Yasashwi, Chinnathambi Kamalarathnam, Rema Chandramohan, Mangalabharathi Sundaram, Kumutha Kumaraswami, Shobha Kumar, Naveen Benakappa, Swati Manerkar, Jayashree Mondhkar, Vinayagam Prakash, Mohammed Sajjid, Arasar Seeralar, Ismat Jahan, Sadeka Choudhury Moni, Mohammod Shahidullah, Radhika Sujatha, M Chandrasekaran, Siddarth Ramji, Seetha Shankaran, Myrsini Kaforou, Jethro Herberg, Sudhin Thayyil
Software Mentions: 5
Published: about 6 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

10.1101/2021.01.15.426908

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

10.1111/1751-7915.13313

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

10.1371/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

10.1186/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

10.1038/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

10.1371/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/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

10.1186/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

10.1038/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

10.1128/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/s12864-019-5496-5

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.pone.0153932

Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis
Cited by: 24
Author(s): Randy J. Hempel, John P. Bannantine, Judith R. Stabel
Software Mentions: 5
Published: over 10 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

10.1186/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

10.1371/journal.pone.0235218

Transcriptome profiling of longissimus lumborum in Holstein bulls and steers with different beef qualities
Cited by: 17
Author(s): Yan Li, Meimei Wang, Qiufeng Li, Yanxia Gao, Qian Li, Jianguo Li, Yong Cao
Software Mentions: 5
Published: about 6 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

10.1186/1471-213X-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

10.1371/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

10.1098/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

10.1126/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

10.1093/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

10.1038/s41437-020-00398-2

Sex-specific responses to cold in a very cold-tolerant, northern Drosophila species
Cited by: 12
Author(s): Darren J. Parker, Tapio Envall, Michael G. Ritchie, Maaria Kankare
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0101374

Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads
Cited by: 21
Author(s): Shanrong Zhao
Software Mentions: 5
Published: about 12 years ago

10.1371/journal.pgen.1006498

Genetic Variation in the Social Environment Contributes to Health and Disease
Cited by: 73
Author(s): Amelie Baud, Megan K. Mulligan, Francesco Paolo Casale, Jesse Ingels, Casey Bohl, Jacques Crinon, Jean Marie Launay, Jon P. Krohn, Andrés Legarra, Robert W. Williams, Oliver Stegle
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0088515

Extensive Expression Differences along Porcine Small Intestine Evidenced by Transcriptome Sequencing
Cited by: 29
Author(s): Núria Mach, Mustapha Berri, Diane Esquerré, Claire Chevaleyre, Gaëtan Lemonnier, Yvon Billon, Patricia Lepage, Isabelle P. Oswald, Joël Doré, Claire Rogel–Gaillard, Jordi Estellé
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pone.0139868

NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data
Cited by: 31
Author(s): Mohan A. V. S. K. Katta, Aamir W. Khan, Dadakhalandar Doddamani, Mahendar Thudi, Rajeev K. Varshney
Software Mentions: 5
Published: almost 11 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

10.1172/jci.insight.143469

Activation of skeletal muscle–resident glial cells upon nerve injury
Cited by: 17
Author(s): Daisy Proietti, Lorenzo Giordani, Marco De Bardi, Chiara D’Ercole, Biliana Lozanoska-Ochser, Susanna Amadio, Cinzia Volonté, Sara Marinelli, Antoine Muchir, Marina Bouchè, Giovanna Borsellino, Alessandra Sacco, Pier Lorenzo Puri, Luca Madaro
Software Mentions: 5
Published: over 5 years ago

10.1093/gigascience/giy132

Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species
Cited by: 21
Author(s): Miriam Payá‐Milans, James W. Olmstead, Gerardo H. Nunez, Timothy A. Rinehart, Margaret Staton
Software Mentions: 5
Published: almost 8 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

10.3390/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

10.1371/journal.pone.0182507

A comprehensive simulation study on classification of RNA-Seq data
Cited by: 26
Author(s): Gökmen Zararsız, Dinçer Göksülük, Selçuk Korkmaz, Vahap Eldem, Gözde Ertürk Zararsız, İzzet Paruğ Duru, Ahmet Öztürk
Software Mentions: 5
Published: about 9 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

10.1007/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

10.3390/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

10.1093/gigascience/giaa112

A molecular map of lung neuroendocrine neoplasms
Cited by: 15
Author(s): Aurélie Gabriel, Emilie Mathian, Lise Mangiante, Catherine Voegele, Vincent Cahais, Akram Ghantous, James McKay, Nicolas Alcala, Lynnette Fernández-Cuesta, Matthieu Foll
Software Mentions: 5
Published: almost 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

10.1038/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

Projects: pypi: HTSeq

Science Score: 65/100

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Papers Mentioning HTSeq 3,071