pypi: HTSeq | Projects | Ecosyste.ms: Papers

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 7 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: over 8 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: almost 8 years ago

10.3389/fphys.2019.00278

Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome
Cited by: 14
Author(s): Jianbin Zhang, Qiangqiang Nie, Chaozeng Si, Wang Cheng, Yang Chen, Weiliang Sun, Pei Lin, Jing Guo, Jie Kong, Yiyao Cui, Feng Wang, Xueqiang Fan, Zhidong Ye, Jianyan Wen, Peng Liu
Software Mentions: 5
Published: over 5 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 3 years ago

10.3390/plants10071465

Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max
Cited by: 11
Author(s): Ramon de Koning, Raphaël Kiekens, Mary Esther Muyoka Toili, Geert Angenon
Software Mentions: 5
Published: over 3 years ago

10.3389/fnins.2019.00002

A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks
Cited by: 51
Author(s): Shradha Mukherjee, Christine Klaus, Mihaela Pricop-Jeckstadt, Jeremy A. Miller, Felix L Struebing
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: almost 5 years ago

10.3389/fcell.2021.669354

Transcriptomic Signature of Human Embryonic Thyroid Reveals Transition From Differentiation to Functional Maturation
Cited by: 7
Author(s): Geert Dom, Petr Dmitriev, Marie-Alexandra Lambot, Guy Van Vliet, Daniel Glinoer, Frédérick Libert, Anne Lefort, Jacques Emile Dumont, Carine Maenhaut
Software Mentions: 5
Published: over 3 years ago

10.3389/fneur.2020.00511

Drosophila Exhibit Divergent Sex-Based Responses in Transcription and Motor Function After Traumatic Brain Injury
Cited by: 14
Author(s): Ekta Shah, Katherine Gurdziel, Douglas M. Ruden
Software Mentions: 5
Published: over 4 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 8 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: almost 4 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: almost 11 years ago

10.3389/fgene.2021.625019

Novel Non-coding RNA Analysis in Multiple Myeloma Identified Through High-Throughput Sequencing
Cited by: 5
Author(s): Minqiu Lu, Yin Wu, Wen Gao, Ying Tian, Guorong Wang, Aijun Liu, Wen-Ming Chen
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.02075

Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis
Cited by: 14
Author(s): Gi Yoon Shin, Jeffrey K. Schachterle, Divine Yufetar Shyntum, Lucy N. Moleleki, Teresa A. Coutinho, George W. Sundin
Software Mentions: 5
Published: about 5 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: about 8 years ago

10.1371/journal.pbio.2003962

Design of synthetic bacterial communities for predictable plant phenotypes
Cited by: 157
Author(s): Sur Herrera Paredes, Tianxiang Gao, Theresa F. Law, Omri M. Finkel, Tatiana S. Mucyn, Paulo José Pereira Lima Teixeira, Isaí Salas González, Meghan E. Feltcher, Matthew J. Powers, Elizabeth A. Shank, Corbin D. Jones, Vladimir Jojic, Jeffery L. Dangl, Gabriel Castrillo
Software Mentions: 5
Published: almost 7 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 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 8 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: about 7 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: almost 6 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 3 years ago

10.1371/journal.pbio.1002585

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process
Cited by: 192
Author(s): Richard Angélique, Boullu Loïs, Ulysse Herbach, Bonnafoux Arnaud, Valérie Morin, Elodie Vallin, Anissa Guillemin, Nan Gao, Gunawan Rudiyanto, Jérémie Cosette, Ophélie Arnaud, Jean-Jacques Kupiec, Thibault Espinasse, Sandrine Gonin-Giraud, Olivier Gandrillon
Software Mentions: 5
Published: almost 8 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 3 years ago

10.3389/fmolb.2021.612881

Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach
Cited by: 7
Author(s): Jiali Yu, Dennis Bennett, Christopher Dardick, Tetyana Zhebentyayeva, Albert G. Abbott, Zongrang Liu, Margaret Staton
Software Mentions: 5
Published: over 3 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: almost 7 years ago

10.3389/fcell.2020.00639

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
Cited by: 14
Author(s): Anne M. Hahn, Daniel Pensold, Cathrin Bayer, Jessica Tittelmeier, Lourdes González-Bermúdez, Lisa Marx-Blümel, Jenice Linde, Jonas Groß, Gabriela Salinas-Riester, Thomas Lingner, Julia von Maltzahn, Marc Spehr, Tomas Pieler, Anja Urbach, Geraldine Zimmer-Bensch
Software Mentions: 5
Published: over 4 years ago

10.3389/fcell.2021.652408

Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver
Cited by: 21
Author(s): Xianliang Hou, Yane Yang, Ping Li, Zhipeng Zeng, Wenlong Hu, Ruilian Zhe, Xinqiong Liu, Donge Tang, Minglin Ou, Yong Dai
Software Mentions: 5
Published: over 3 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: about 5 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 8 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: over 9 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: almost 8 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: almost 9 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 7 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: over 5 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 7 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: 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: about 4 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 3 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 5 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 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: almost 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 7 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 6 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 11 years ago

10.1002/ece3.5924

Wild <i>Dictyostelium discoideum</i> 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: almost 5 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 9 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 8 years ago

10.7717/peerj.10818

Cytochrome P450 monooxygenase genes in the wild silkworm, <i>Bombyx mandarina</i>
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: almost 4 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 5 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 5 years ago

10.1098/rstb.2020.0107

Sex-biased gene expression and recent sex chromosome turnover
Cited by: 14
Author(s): Nicolás Lichilín, Athimed El Taher, Astrid Böhne
Software Mentions: 5
Published: over 3 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 4 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: about 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: about 4 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 7 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: over 4 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 9 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: about 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: over 7 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: about 4 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: almost 7 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 7 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 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: almost 4 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 4 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: about 6 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: almost 7 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: almost 11 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: almost 4 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 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: almost 4 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 5 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 3 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: about 3 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: almost 4 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 4 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: over 4 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: about 12 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 3 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: almost 4 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 5 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: almost 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: over 8 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: over 6 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: about 6 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 9 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 6 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: almost 4 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 3 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: about 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: over 7 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 6 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: over 4 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 6 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 3 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: over 4 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 4 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: about 7 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 4 years ago

Projects: pypi: HTSeq

Papers Mentioning HTSeq 3,071