pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0255066

First transcriptome profiling of D. melanogaster after development in a deep underground low radiation background laboratory
Cited by: 8
Author(s): Mikhail Zarubin, A. M. Gangapshev, Yuri Gavriljuk, V. V. Kazalov, Е. В. Кравченко
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1006704

Meioc maintains an extended meiotic prophase I in mice
Cited by: 85
Author(s): Y. Q. Shirleen Soh, Maria M. Mikedis, Mina Kojima, Alexander K. Godfrey, Dirk G. de Rooij, David C. Page
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0128041

Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions
Cited by: 85
Author(s): Lei Gong, Hongxia Zhang, Xiaoyan Gan, Li Zhang, Yuchao Chen, Fengjie Nie, Lei Shi, Miao Li, Zhiqian Guo, Guohui Zhang, Song Yao
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.56890

Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung at single cell resolution
Cited by: 27
Author(s): Racquel Domingo-Gonzalez, Fabio Zanini, Xibing Che, Min Liu, Robert C. Jones, Michael Swift, Stephen R. Quake, David N. Cornfield, Cristina M. Alvira
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2017.01695

AR-13, a Celecoxib Derivative, Directly Kills Francisella In Vitro and Aids Clearance and Mouse Survival In Vivo
Cited by: 4
Author(s): Ky V. Hoang, Haley E. Adcox, James Fitch, David Gordon, Heather M. Curry, Larry S. Schlesinger, Peter White, John S. Gunn
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.48767

Induction of Sertoli-like cells from human fibroblasts by NR5A1 and GATA4
Cited by: 35
Author(s): Jianlin Liang, Nan Wang, Jing He, Jian Du, Yin Guo, Lin Li, Wenbo Wu, Chencheng Yao, Zheng Li, Kehkooi Kee
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0188285

DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions
Cited by: 7
Author(s): Yoshimasa Aoto, Tsuyoshi Hachiya, Kazuhiro Okumura, Sumitaka Hase, Kengo Sato, Yuichi Wakabayashi, Yasubumi Sakakibara
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2017.02683

Desert Dust as a Source of Iron to the Globally Important Diazotroph Trichodesmium
Cited by: 19
Author(s): Despo Polyviou, Alison J. Baylay, Andrew Hitchcock, Julie Robidart, C. Mark Moore, Thomas S. Bibby
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0219272

Global gene expression analysis in etiolated and de-etiolated seedlings in conifers
Cited by: 9
Author(s): Sonali Sachin Ranade, Nicolas Delhomme, María Rosario García‐Gil
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.135576

Lack of miR-378 attenuates muscular dystrophy in mdx mice
Cited by: 18
Author(s): Paulina Podkalicka, Olga Mucha, Iwona Bronisz-Budzyńska, Magdalena Kozakowska, Katarzyna Pietraszek-Gremplewicz, Anna Cetnarowska, Urszula Głowniak-Kwitek, Karolina Bukowska-Straková, Maciej Cieśla, Maria Kulecka, Jerzy Ostrowski, Michał Mikula, Anna Potulska‐Chromik, Anna Kostera‐Pruszczyk, Alicja Józkowicz, Agnieszka Łoboda, Józef Dulak
Software Mentions: 3
Published: over 4 years ago

10.1172/jci.insight.97219

Unique features and clinical importance of acute alloreactive immune responses
Cited by: 8
Author(s): Charlotte Inman, Suzy Eldershaw, Joanne E. Croudace, Nathaniel J. Davies, Archana Sharma-Oates, Tanuja Rai, Hayden Pearce, Mirjana Sirovica, Y. L. Tracey Chan, Kriti Verma, Jianmin Zuo, Sandeep Nagra, Francesca Kinsella, Jane Nunnick, Rasoul Amel-Kashipaz, Charles Craddock, Ram Malladi, Paul Moss
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2016.00636

Transcriptomic Analysis Reveals Adaptive Responses of an Enterobacteriaceae Strain LSJC7 to Arsenic Exposure
Cited by: 17
Author(s): Yingjiao Zhang, Songcan Chen, Xiuli Hao, Jian‐Qiang Su, Xudong Xue, Yu Yan, Yan Zhu, Jun Ye
Software Mentions: 3
Published: almost 9 years ago

10.3389/fmicb.2017.00716

Effects of Inhibitors on the Transcriptional Profiling of Gluconobater oxydans NL71 Genes after Biooxidation of Xylose into Xylonate
Cited by: 16
Author(s): Yuanyuan Miao, Yi Shen, Yong Xu
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0192945

Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death
Cited by: 16
Author(s): Salim Hossain Reza, Nicolas Delhomme, Nathaniel R. Street, Prashanth Ramachandran, Kerstin Dalman, Ove Nilsson, Elena A. Minina, Peter V. Bozhkov
Software Mentions: 3
Published: almost 7 years ago

10.1172/jci.insight.125679

Angiocrine signals regulate quiescence and therapy resistance in bone metastasis
Cited by: 51
Author(s): Amit Singh, Vimal Veeriah, Pengjun Xi, Rossella Labella, Junyu Chen, Sara Romeo, Saravana K. Ramasamy, Anjali P. Kusumbe
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2019.02064

Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome
Cited by: 16
Author(s): Martin Fischer, Andrea Ulbricht, Sven C. Neulinger, Sarah Refai, Kati Waßmann, Sven Künzel, Ruth A. Schmitz
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.48718

Receptor-specific interactome as a hub for rapid cue-induced selective translation in axons
Cited by: 40
Author(s): Max Koppers, Roberta Cagnetta, Toshiaki Shigeoka, Lucia Cs Wunderlich, Pedro P. Vallejo Ramirez, Julie Qiaojin Lin, Sixian Zhao, Maximilian Ah Jakobs, Asha Dwivedy, Michael S. Minett, Anaïs Bellon, Clemens F. Kaminski, William A. Harris, John G. Flanagan, Christine E. Holt
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.125377

Keratinocyte growth factor impairs human thymic recovery from lymphopenia
Cited by: 14
Author(s): Alasdair Coles, Laura Azzopardi, Onajite Kousin-Ezewu, Harpreet Kaur Mullay, Sara Thompson, Lorna B. Jarvis, John Q. Davies, Sarah Howlett, Daniel B. Rainbow, Judith Babar, Timothy J Sadler, J William L Brown, Edward Needham, Karen May, Zoya Georgieva, A E Handel, Stefano Maio, Mary E. Deadman, Ioanna A. Rota, G A Holländer, Sarah Dawson, David Jayne, Ruth Seggewiß-Bernhardt, Daniel C. Douek, John D. Isaacs, Joanne L. Jones
Software Mentions: 3
Published: over 5 years ago

10.1038/s41389-018-0108-9

Atypical GATA transcription factor TRPS1 represses gene expression by recruiting CHD4/NuRD(MTA2) and suppresses cell migration and invasion by repressing TP63 expression
Cited by: 24
Author(s): Yuzhi Wang, Xue Lü, Xue Gong, Lixian Wu, Jun Zhang, Weiguang Li, Jian Li, Liming Chen
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2017.01830

A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro
Cited by: 18
Author(s): J. Wallis Marsh, Michael S. Humphrys, Garry Myers
Software Mentions: 3
Published: over 7 years ago

10.1016/j.jacep.2020.09.012

Evidence of Superior and Inferior Sinoatrial Nodes in the Mammalian Heart
Cited by: 42
Author(s): Jaclyn A. Brennan, Qing Chen, BS Anna Gams, Jhansi Dyavanapalli, David Mendelowitz, Weiqun Peng, Igor R. Efimov
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.29736

CDK9-dependent RNA polymerase II pausing controls transcription initiation
Cited by: 157
Author(s): Saskia Gressel, Björn Schwalb, Tim-Michael Decker, Weihua Qin, Heinrich Leonhardt, Dirk Eick, Patrick Cramer
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.63731

CEP78 functions downstream of CEP350 to control biogenesis of primary cilia by negatively regulating CP110 levels
Cited by: 24
Author(s): André Gonçalves, Sarah Kirstine Hasselbalch, Beinta Biskopstø Joensen, Sebastian Patzke, Pernille Martens, Signe Krogh Ohlsen, Mathieu Quinodoz, Konstantinos Nikopoulos, Reem Suleiman, Magnus Per Damsø Jeppesen, Catja Weiss, Søren Tvorup Christensen, Carlo Rivolta, Jens S. Andersen, Pietro Farinelli, Lotte B. Pedersen
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.64061

Basis of specificity for a conserved and promiscuous chromatin remodeling protein
Cited by: 10
Author(s): Drake A Donovan, Johnathan G. Crandall, Vi N. Truong, Abigail L Vaaler, Thomas B Bailey, Devin Dinwiddie, Orion Gb Banks, Laura E. McKnight, Jeffrey N. McKnight
Software Mentions: 3
Published: about 4 years ago

10.3390/insects12090809

Solitary Living Brings a Decreased Weight and an Increased Agility to the Domestic Silkworm, Bombyx mori
Cited by: 2
Author(s): Zhenglin Zhu, Yuting Tan, Siyu Xiao, Zhufen Guan, Wen Zhao, Zhijun Dai, Gexin Liu, Ze Zhang
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2015.00569

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates
Cited by: 27
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, Anup Mahurkar, Owen White, James B. Kaper, David A. Rasko
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2018.01261

Transcriptional Regulation of Cysteine and Methionine Metabolism in Lactobacillus paracasei FAM18149
Cited by: 17
Author(s): Daniel Wüthrich, Claudia Wenzel, Tharmatha Bavan, Rémy Bruggmann, Hélène Berthoud, Stefan Irmler
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2015.01199

A detailed view of the intracellular transcriptome of Listeria monocytogenes in murine macrophages using RNA-seq
Cited by: 23
Author(s): Tilman Schultze, Rolf Hilker, Gopala Krishna Mannala, Katrin Gentil, Markus Weigel, Neda Farmani, Anita Windhorst, Alexander Goesmann, Trinad Chakraborty, Torsten Hain
Software Mentions: 3
Published: over 9 years ago

10.1093/insilicoplants/diaa005

Within- and cross-species predictions of plant specialized metabolism genes using transfer learning
Cited by: 7
Author(s): Bethany M. Moore, Peipei Wang, Pengxiang Fan, Aaron Lee, Bryan J. Leong, Yann‐Ru Lou, Craig A. Schenck, Koh‐ichi Sugimoto, Melissa D. Lehti-Shiu, Cornelius S. Barry, Shin-Han Shiu
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.66288

Repressing Ago2 mRNA translation by Trim71 maintains pluripotency through inhibiting let-7 microRNAs
Cited by: 17
Author(s): Qiuying Liu, Xiaoli Chen, Mariah K Novak, Shaojie Zhang, Wenqian Hu
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-021-96374-9

Integrative genetic, genomic and transcriptomic analysis of heat shock protein and nuclear hormone receptor gene associations with spontaneous preterm birth
Cited by: 10
Author(s): Johanna M. Huusko, Heli Tiensuu, Antti M. Haapalainen, Anu Pasanen, Pinja Tissarinen, Minna K. Karjalainen, Ge Zhang, Kaare Christensen, Kelli K. Ryckman, Bo Jacobsson, Jeffrey C. Murray, Stephen F. Kingsmore, Mikko Hallman, Louis J. Muglia, Mika Rämet
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2020.01978

Sound Vibration-Triggered Epigenetic Modulation Induces Plant Root Immunity Against Ralstonia solanacearum
Cited by: 7
Author(s): Jihye Jung, Seon‐Kyu Kim, Sung‐Hee Jung, Mi‐Jeong Jeong, Choong-Min Ryu
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0178281

Gene and metabolite time-course response to cigarette smoking in mouse lung and plasma
Cited by: 18
Author(s): Mikaela Miller, Thomas Danhorn, Charmion Cruickshank‐Quinn, Sonia M. Leach, Sean Jacobson, Matthew Strand, Nichole Reisdorph, Russell P. Bowler, Irina Petrache, Katerina Kechris
Software Mentions: 3
Published: over 7 years ago

10.1016/j.heliyon.2017.e00381

Metabolic and transcriptomic analysis of Huntington’s disease model reveal changes in intracellular glucose levels and related genes
Cited by: 11
Author(s): Gepoliano Chaves, Rıfat Emrah Özel, Namrata V. Rao, Hana Hadiprodjo, Yvonne Da Costa, Zachary Tokuno, Nader Pourmand
Software Mentions: 3
Published: over 7 years ago

10.3389/fnmol.2017.00090

RNA-Seq Analysis of Microglia Reveals Time-Dependent Activation of Specific Genetic Programs following Spinal Cord Injury
Cited by: 52
Author(s): Harun N. Noristani, Yannick Nicolas Gerber, Jean-Charles Sabourin, Marine Le Corre, Nicolas Lonjon, Nadine Mestre‐Francés, Hélène Hirbec, Florence E. Perrin
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pgen.1005495

Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript
Cited by: 22
Author(s): Marta Puig, David Castellano, Lorena Pantano, Carla Giner-Delgado, David Izquierdo, Magdalena Gayà-Vidal, José Ignacio Lucas-Lledó, Tõnu Esko, Chikashi Terao, Fumihiko Matsuda, Mario Cáceres
Software Mentions: 3
Published: over 9 years ago

10.3389/fnmol.2017.00275

Divergence in Morris Water Maze-Based Cognitive Performance under Chronic Stress Is Associated with the Hippocampal Whole Transcriptomic Modification in Mice
Cited by: 19
Author(s): Soo Yeon Jung, Milene Brownlow, Matteo Pellegrini, Ryan Jankord
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-021-97013-z

Electronic cigarette smoke reduces ribosomal protein gene expression to impair protein synthesis in primary human airway epithelial cells
Cited by: 5
Author(s): Hae-Ryung Park, Jose Vallarino, Michael J. O’Sullivan, Charlotte Wirth, Ronald Allan M Panganiban, Gabrielle Webb, Maya Shumyatcher, Blanca E. Himes, Jin‐Ah Park, David C. Christiani, Joseph G. Allen, Quan Lu
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.65797

Stress resets ancestral heritable small RNA responses
Cited by: 56
Author(s): Leah Houri-Zeevi, Guy Teichman, Hila Gingold, Oded Rechavi
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.32697

A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila
Cited by: 13
Author(s): Joana Torres, Remo Monti, Ariane L. Moore, Makiko Seimiya, Yanrui Jiang, Niko Beerenwinkel, Christian Beisel, Jorge V. Beira, Renato Paro
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41438-021-00612-0

A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis
Cited by: 37
Author(s): Jianye Chen, Fangfang Xie, Yanze Cui, Canbin Chen, Wang-jin Lu, Xiaodi Hu, Qian Hua, Jing Zhao, Zhengkai Wu, Gao Da, Zhi-ke Zhang, Wenkai Jiang, Sun Qi-zhong, Guibing Hu, Yonghua Qin
Software Mentions: 3
Published: over 3 years ago

10.3389/fneur.2015.00045

Long Non-Coding RNA Expression during Aging in the Human Subependymal Zone
Cited by: 37
Author(s): Guy Barry, Boris Guennewig, Samantha J. Fung, Dominik C. Kaczorowski, Cynthia Shannon Weickert
Software Mentions: 3
Published: almost 10 years ago

10.3389/fneur.2020.00091

A Moderate Blast Exposure Results in Dysregulated Gene Network Activity Related to Cell Death, Survival, Structure, and Metabolism
Cited by: 6
Author(s): Katie A. Edwards, Vida Motamedi, Nicole Danielle Osier, Hyung-Suk Kim, Sijung Yun, Young-Eun Cho, Chen Lai, Kristine C. Dell, Walter Carr, Peter B. Walker, Stephen T. Ahlers, Matthew L. LoPresti, Angela M Yarnell, Anna Tschiffley, Jessica Gill
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41438-021-00543-w

Integration of early disease-resistance phenotyping, histological characterization, and transcriptome sequencing reveals insights into downy mildew resistance in impatiens
Cited by: 2
Author(s): Ze Peng, Yan‐Hong He, Saroj Parajuli, Qi You, Weining Wang, Krishna Bhattarai, Aaron J. Palmateer, Zhanao Deng
Software Mentions: 3
Published: almost 4 years ago

10.3389/fnins.2020.580524

miRNA Alterations Elicit Pathways Involved in Memory Decline and Synaptic Function in the Hippocampus of Aged Tg4-42 Mice
Cited by: 5
Author(s): Yvonne Bouter, Tim Kacprowski, Fanny L M Rößler, Lars Riff Jensen, Andreas W. Kuß, Thomas A. Bayer
Software Mentions: 3
Published: over 4 years ago

10.1038/s41388-018-0661-x

Lineage-specific control of TFIIH by MITF determines transcriptional homeostasis and DNA repair
Cited by: 17
Author(s): Marcos Seoane, Sophia Buhs, Pablo A. Iglesias, Julia Strauß, Ann-Christin Puller, Jürgen Müller, Helwe Gerull, Susanne Feldhaus, Malik Alawi, Johanna M. Brandner, Dennis Eggert, Jinyan Du, Jürgen Thomale, Peter J. Wild, Martin Zimmermann, Thomas Sternsdorf, Udo Schumacher, Peter Nollau, David E. Fisher, Martin Horstmann
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0148039

Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks
Cited by: 27
Author(s): Rebecca A. Nebel, Dejian Zhao, Erika Pedrosa, Jill Kirschen, Herbert M. Lachman, Deyou Zheng, Brett S. Abrahams
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0138782

Transcriptome Profiling of Pediatric Core Binding Factor AML
Cited by: 13
Author(s): Chih Hao Hsu, Cu Nguyen, Chunhua Yan, Rhonda E. Ries, Qing Rong Chen, Ying Hu, Fabiana Ostronoff, Derek L. Stirewalt, George A. Komatsoulis, Shawn Levy, Daoud Meerzaman, Soheil Meshinchi
Software Mentions: 3
Published: over 9 years ago

10.1038/s41438-021-00597-w

Transcriptional profiling reveals multiple defense responses in downy mildew-resistant transgenic grapevine expressing a TIR-NBS-LRR gene located at the MrRUN1/MrRPV1 locus
Cited by: 3
Author(s): Junjie Qu, Ian B. Dry, Lulu Liu, Zhanbao Guo, Ling Yin
Software Mentions: 3
Published: over 3 years ago

10.3389/fnins.2019.01324

A Targeted Gene Panel That Covers Coding, Non-coding and Short Tandem Repeat Regions Improves the Diagnosis of Patients With Neurodegenerative Diseases
Cited by: 4
Author(s): Allen Chi Shing Yu, Aldrin Kay-Yuen Yim, Anna Chan, Liz Y P Yuen, Wing Chi Au, Timothy Cheng, Xiao Lin, Jing‐Woei Li, Larry Wl Chan, Vincent Chung Tong Mok, Ting-Fung Chan, Ho Yin Chan
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1009003

Serotonergic modulation of visual neurons in Drosophila melanogaster
Cited by: 11
Author(s): Maureen M. Sampson, Katherine M. Myers Gschweng, Ben J. Hardcastle, Shivan L. Bonanno, Tyler R. Sizemore, Rebecca C. Arnold, Fuying Gao, Andrew M. Dacks, Mark A. Frye, David E. Krantz
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.08298

Starvation promotes concerted modulation of appetitive olfactory behavior via parallel neuromodulatory circuits
Cited by: 142
Author(s): Kang I. Ko, Cory M. Root, Scott A. Lindsay, Orel A. Zaninovich, Andrew K. Shepherd, Steven A. Wasserman, Susy M. Kim, Jing W. Wang
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0221634

Comparative multi-omics systems analysis reveal the glycolysis / gluconeogenesis signal pathway play an important role in virulence attenuation in fish-derived GBS YM001
Cited by: 2
Author(s): Yu Liu, Liping Li, Ting Huang, Rui Wang, Weizheng Liang, Qiong Yang, Aiying Lei, Ming Chen
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.00215

A Novel Long Non-coding RNA, MSTRG.51053.2 Regulates Cisplatin Resistance by Sponging the miR-432-5p in Non-small Cell Lung Cancer Cells
Cited by: 24
Author(s): Jie Zhang, Chuanqin Xu, Y Gao, Yi Wang, Zongli Ding, Yueming Zhang, Wenyi Shen, Yulong Zheng, Yufeng Wan
Software Mentions: 3
Published: almost 5 years ago

10.3389/fonc.2021.712041

RhoC Modulates Cell Junctions and Type I Interferon Response in Aggressive Breast Cancers
Cited by: 3
Author(s): Hannah Abraham, Peter Ulintz, Laura Goo, Joel A. Yates, Andrew C. Little, Liwei Bao, Zhifen Wu, Sofía D. Merajver
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2020.586567

Multi-Lineage BCR-ABL Expression in Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia Is Associated With Improved Prognosis but No Specific Molecular Features
Cited by: 5
Author(s): Satoshi Nishiwaki, Jeong Hui Kim, Masafumi Ito, Matsuyoshi Maeda, Yusuke Okuno, Daisuke Koyama, Yukiyasu Ozawa, Masaharu Gunji, Masahide Osaki, Kazuo Kïtamura, Yoko Ushijima, Yuichi Ishikawa, Koichi Miyamura, Isamu Sugiura, Hitoshi Kiyoi
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.54919

Transposase-assisted tagmentation of RNA/DNA hybrid duplexes
Cited by: 34
Author(s): Bo Lu, Liting Dong, Danyang Yi, Meiling Zhang, Chenxu Zhu, Xiaoyu Li, Chengqi Yi
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.ppat.1006026

Transcriptomic Analysis Implicates the p53 Signaling Pathway in the Establishment of HIV-1 Latency in Central Memory CD4 T Cells in an In Vitro Model
Cited by: 25
Author(s): Cory H. White, Bastiaan Moesker, Nadejda Beliakova-Bethell, Laura J. Martins, Celsa A. Spina, David M. Margolis, Douglas D. Richman, Vicente Planelles, Alberto Bosque, Christopher H. Woelk
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-021-86795-x

Distinct transcriptomic response to Newcastle disease virus infection during heat stress in chicken tracheal epithelial tissue
Cited by: 2
Author(s): Perot Saelao, Ying Wang, Ganrea Chanthavixay, Vivian M. Yu, Rodrigo A. Gallardo, Jack C. M. Dekkers, Susan J. Lamont, T. Ross Kelly, Huaijun Zhou
Software Mentions: 3
Published: almost 4 years ago

10.3390/cells9010090

PP2A Deficiency Enhances Carcinogenesis of Lgr5+ Intestinal Stem Cells Both in Organoids and In Vivo
Cited by: 3
Author(s): Yu–Ting Yen, May B. Chien, Yung-Chih Lai, Dao-Peng Chen, Cheng‐Ming Chuong, Mien‐Chie Hung, Shih‐Chieh Hung
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0079874

Phenotypic and Transcriptional Fidelity of Patient-Derived Colon Cancer Xenografts in Immune-Deficient Mice
Cited by: 31
Author(s): Jeffrey Chou, Matthew Fitzgibbon, Christie-Lynn Mortales, Andrea M. H. Towlerton, Melissa P. Upton, Raymond S. Yeung, Martin W. McIntosh, Edus H. Warren
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.ppat.1007397

The RNA helicase DDX3X is an essential mediator of innate antimicrobial immunity
Cited by: 59
Author(s): Daniel Szappanos, Roland Tschismarov, Thomas Perlot, Sandra Westermayer, Katrin Fischer, Ekaterini Platanitis, Fabian Kallinger, Maria Novatchkova, Caroline Lassnig, Mathias Müller, Veronika Sexl, Keiryn L. Bennett, Michelle Foong-Sobis, Josef Penninger, Thomas Decker
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-021-84138-4

Transcriptome analysis of ciliary-dependent MCH signaling in differentiating 3T3-L1 pre-adipocytes
Cited by: 4
Author(s): Lloyd Allen Cook, Henry D. Ophardt, Rongkun Shen, Bryan H. Pratt, Lucas A. Galbier
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41438-020-0238-z

MdMYB8 is associated with flavonol biosynthesis via the activation of the MdFLS promoter in the fruits of Malus crabapple
Cited by: 32
Author(s): Hua Li, Li Yu, Jiaxuan Yu, Ting Wu, Jie Zhang, Ji Tian
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.ppat.1008035

Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize
Cited by: 35
Author(s): Pascal Pecher, Gabriele Moro, Maria Cristina Canale, Sylvain Capdevielle, Archana Archana, Allyson M. MacLean, Akiko Sugio, Chih-Horng Kuo, João Roberto Spotti Lopes, Saskia A. Hogenhout
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.ppat.1008079

P200 family protein IFI204 negatively regulates type I interferon responses by targeting IRF7 in nucleus
Cited by: 22
Author(s): Liu Cao, Yanxi Ji, Lanyi Zeng, Qianyun Liu, Zhen Zhang, Shuting Guo, Xiaolong Guo, Yunguang Tong, Xiaolu Zhao, Chunmei Li, Yu Chen, Deyin Guo
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.38621

CD95/Fas ligand mRNA is toxic to cells
Cited by: 32
Author(s): William Putzbach, Ashley Haluck-Kangas, Quan Gao, Aishe A. Sarshad, Elizabeth T. Bartom, Austin Stults, Abdul Qadir, Markus Hafner, Marcus E. Peter
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1008397

Distinct epigenomic and transcriptomic modifications associated with Wolbachia-mediated asexuality
Cited by: 15
Author(s): Xin Wu, Amelia R.I. Lindsey, Paramita Chatterjee, John H. Werren, Richard Stouthamer, Soojin V. Yi
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0240253

Systems genetics analysis of the LXS recombinant inbred mouse strains:Genetic and molecular insights into acute ethanol tolerance
Cited by: 0
Author(s): Richard A. Radcliffe, Robin D. Dowell, Aaron Odell, Phillip A. Richmond, Beth Bennett, Colin Larson, Katerina Kechris, Laura Saba, Pratyaydipta Rudra, Wenmei Shi
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-87278-9

Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
Cited by: 8
Author(s): Lingshu Han, Yuena Sun, Yue Cao, Peng Gao, Zijiao Quan, Yaqing Chang, Jun Ding
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.ppat.1008781

Gene expression network analyses during infection with virulent and avirulent Trypanosoma cruzi strains unveil a role for fibroblasts in neutrophil recruitment and activation
Cited by: 8
Author(s): Antônio Edson Rocha Oliveira, Milton Pereira, Ashton T. Belew, Ludmila Rodrigues Pinto Ferreira, Larissa M. N. Pereira, Eula G. A. Neves, Maria do Carmo Pereira Nunes, Barbara A. Burleigh, Walderez Ornelas Dutra, Najib M. El-Sayed, Ricardo T. Gazzinelli, Santuza Maria Ribeiro Teixeira
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.ppat.1008660

Identification of oncolytic vaccinia restriction factors in canine high-grade mammary tumor cells using single-cell transcriptomics
Cited by: 3
Author(s): Béatrice Cambien, Kévin Lebrigand, Alberto Baeri, Nicolas Nottet, Catherine Compin, Audrey Lamit, Olivier Ferraris, Christophe N. Peyrefitte, Virginie Magnone, Jérôme Henriques, Laure‐Emmanuelle Zaragosi, Sophie Giorgetti‐Peraldi, Fréd́eric Bost, Marine Gautier-Isola, Roger Rezzonico, Pascal Barbry, Robert Barthel, Bernard Mari, Georges Vassaux
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.10518

Temporal transcriptomics suggest that twin-peaking genes reset the clock
Cited by: 58
Author(s): William G Pembroke, Arran Babbs, Kay E. Davies, Chris P. Ponting, Peter L. Oliver
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-019-50618-x

Comparisons of lung and gluteus transcriptome profiles between yaks at different ages
Cited by: 1
Author(s): Jinwei Xin, Zhixin Chai, Chengfu Zhang, Qiang Zhang, Yong Zhu, Hanwen Cao, Qiumei Ji, Jincheng Zhong
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.39234

Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources
Cited by: 38
Author(s): Bram Cerulus, Abbas Jariani, Gemma Perez-Samper, Lieselotte Vermeersch, Julian Pietsch, Matthew M. Crane, Aaron M. New, Brigida Gallone, Miguel Roncoroni, Maria C. Dzialo, Sander K. Govers, Jhana O. Hendrickx, Eva Galle, Maarten Coomans, Pieter Berden, Sara Verbandt, Peter S. Swain, Kevin J. Verstrepen
Software Mentions: 3
Published: over 6 years ago

10.3390/cells10040906

Induced Torpor as a Countermeasure for Low Dose Radiation Exposure in a Zebrafish Model
Cited by: 7
Author(s): Thomas J. Cahill, Willian A. da Silveira, Ludivine Renaud, Tucker Williamson, Hao Wang, Dongjun Chung, Ian M. Overton, Sherine S.L. Chan, Gary Hardiman
Software Mentions: 3
Published: almost 4 years ago

10.3390/cells10030635

Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana
Cited by: 12
Author(s): Ruchika, Chisato Okudaira, Matomo Sakari, Toshifumi Tsukahara
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-019-51535-9

Transcriptomic analysis reveals potential genes involved in tanshinone biosynthesis in Salvia miltiorrhiza
Cited by: 29
Author(s): Yuan‐Jen Chang, Meizhen Wang, Jiang Li, Shanfa Lu
Software Mentions: 3
Published: over 5 years ago

10.3390/cells10020452

Upregulation of COX4-2 via HIF-1α in Mitochondrial COX4-1 Deficiency
Cited by: 7
Author(s): Liza Douiev, Chaya Miller, Shmuel Ruppo, Hadar Benyamini, Bassam Abu‐Libdeh, Ann Saada
Software Mentions: 3
Published: almost 4 years ago

10.3389/fphar.2021.750352

Quinacrine Has Preferential Anticancer Effects on Mesothelioma Cells With Inactivating NF2 Mutations
Cited by: 3
Author(s): Derek B. Oien, Sayantani Sarkar Bhattacharya, Jeremy Chien, Julian R. Molina, Viji Shridhar
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1004922

Genome-wide Association Study Identifies Shared Risk Loci Common to Two Malignancies in Golden Retrievers
Cited by: 60
Author(s): Noriko Tonomura, Ingegerd Elvers, Rachael Thomas, Kate Megquier, Jason Turner-Maier, Cédric Howald, Aaron L. Sarver, Ross Swofford, Aric M. Frantz, Daisuke Ito, Evan Mauceli, Maja L. Arendt, Hyun Ji Noh, Michele Koltookian, Tara Biagi, Sarah Fryc, Christina L. Williams, Anne C. Avery, Jong Hyuk Kim, Lisa G. Barber, Kristine Burgess, Eric S. Lander, Elinor K. Karlsson, Chieko Azuma, Jaime F. Modiano, Matthew Breen, Kerstin Lindblad‐Toh
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-021-83541-1

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
Cited by: 23
Author(s): Ammar Zaghlool, Adnan Niazi, Åsa K. Björklund, Jakub Orzechowski Westholm, Adam Ameur, Lars Feuk
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.ppat.1004365

Comparative Phenotypic Analysis of the Major Fungal Pathogens Candida parapsilosis and Candida albicans
Cited by: 100
Author(s): Linda Holland, Markus Schröder, Siobhán A. Turner, Heather T. Taff, David R. Andes, Zsuzsanna Grózer, Attila Gácser, Lauren Ames, Ken Haynes, Desmond G. Higgins, Geraldine Butler
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0246679

Effects of glyphosate residues and different concentrate feed proportions in dairy cow rations on hepatic gene expression, liver histology and biochemical blood parameters
Cited by: 11
Author(s): Ann-Katrin Heymann, Karina Schnabel, Fabian Billenkamp, Susanne Bühler, Jana Frahm, Susanne Kersten, Liane Hüther, Ulrich Meyer, Dirk von Soosten, Nares Trakooljul, Jens Peter Teifke, Sven Dänicke
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1006336

Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes
Cited by: 76
Author(s): Yuheng Huang, Aneil F. Agrawal
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-021-82905-x

Transcriptional response to the host cell environment of a multidrug-resistant Mycobacterium tuberculosis clonal outbreak Beijing strain reveals its pathogenic features
Cited by: 9
Author(s): Pakorn Aiewsakun, Pinidphon Prombutara, Tegar Adriansyah Putra Siregar, Thanida Laopanupong, Phongthon Kanjanasirirat, Tanawadee Khumpanied, Suparerk Borwornpinyo, Pirut Tong-ngam, Alisa Tubsuwan, Prapaporn Srilohasin, Angkana Chaiprasert, Wuthiwat Ruangchai, Prasit Palittapongarnpim, Therdsak Prammananan, Brian C. VanderVen, Marisa Ponpuak
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.24523

Synergistic interactions with PI3K inhibition that induce apoptosis
Cited by: 23
Author(s): Yaara Zwang, Oliver Jonas, Casandra Chen, Mikael L. Rinne, John G. Doench, Federica Piccioni, Tan Li, Hai‐Tsang Huang, Jinhua Wang, Young Jin Ham, Joyce T. O’Connell, Patrick Bhola, Mihir B. Doshi, Matthew A. Whitman, Michael J. Cima, Anthony Letaï, David E. Root, Robert Langer, Nathanael S. Gray, William C. Hahn
Software Mentions: 3
Published: over 7 years ago

10.1186/s13148-017-0381-z

Transcriptomics and methylomics in chronic periodontitis with tobacco use: a pilot study
Cited by: 21
Author(s): Young‐Dan Cho, Pil-Jong Kim, Hong-Gee Kim, Yang‐Jo Seol, Yong-Moo Lee, In‐Chul Rhyu, Hyun‐Mo Ryoo
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1008562

Mutations on ent-kaurene oxidase 1 encoding gene attenuate its enzyme activity of catalyzing the reaction from ent-kaurene to ent-kaurenoic acid and lead to delayed germination in rice
Cited by: 20
Author(s): Hui Zhang, Ming Li, Dongli He, Kun Wang, Pingfang Yang
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-81611-y

Absence of S100A4 in the mouse lens induces an aberrant retina-specific differentiation program and cataract
Cited by: 3
Author(s): Rupalatha Maddala, Junyuan Gao, Richard T. Mathias, Tylor R. Lewis, Vadim Y. Arshavsky, Adriana Levine, Jonathan M. Backer, Anne R. Bresnick, Ponugoti Vasantha Rao
Software Mentions: 3
Published: about 4 years ago

10.1002/cti2.1144

Transcriptional profiling and immunophenotyping show sustained activation of blood monocytes in subpatent <i>Plasmodium falciparum</i> infection
Cited by: 9
Author(s): Jessica R. Loughland, Tonia Woodberry, Matthew A. Field, Dean Andrew, Arya SheelaNair, Nicholas Dooley, Kim A. Piera, Fiona H. Amante, Enny Kenangalem, Ric N. Price, Christian Engwerda, Nicholas M. Anstey, James S. McCarthy, Michelle J. Boyle, Gabriela Minigo
Software Mentions: 3
Published: about 5 years ago

10.1093/jxb/erx219

Transcriptomic and metabolomics responses to elevated cell wall invertase activity during tomato fruit set
Cited by: 36
Author(s): Lei Ru, Sonia Osorio, Lu Wang, Alisdair R. Fernie, John W. Patrick, Yong‐Ling Ruan
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-020-80168-6

Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish
Cited by: 14
Author(s): Wei Gan, Yu Wen Chung-Davidson, Zelin Chen, Shiying Song, Weicheng Cui, Wei He, Qinghua Zhang, Weiming Li, Mingyou Li, Jianfeng Ren
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-60656-5

Genomic alterations and abnormal expression of APE2 in multiple cancers
Cited by: 20
Author(s): Katherine A. Jensen, Xinghua Shi, Yan Shen Shan
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-61305-7

Root transcriptome reveals efficient cell signaling and energy conservation key to aluminum toxicity tolerance in acidic soil adapted rice genotype
Cited by: 12
Author(s): Wricha Tyagi, Julia S. Yumnam, Debashish Sen, Mayank Rai
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-62150-4

Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions
Cited by: 15
Author(s): Abbot O. Oghenekaro, Andriy Kovalchuk, Tommaso Raffaello, Susana Camarero, Markus Gressler, Bernard Henrissat, Juna Lee, Mengxia Liu, Ángel T. Martı́nez, Otto Miettinen, Sirma Mihaltcheva, Jasmyn Pangilinan, Fei Ren, Robert Riley, Francisco J. Ruiz‐Dueñas, Ana Serrano, Michael R. Thon, Zilan Wen, Zhen Zeng, Kerrie Barry, I. V. Grigoriev, Francis Martin, Fred O. Asiegbu
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1007025

Widespread epistasis regulates glucose homeostasis and gene expression
Cited by: 14
Author(s): Anlu Chen, Yang Liu, Scott M. Williams, Nathan Morris, David A. Buchner
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-020-65593-x

Detrimental effects of flame retardant, PBB153, exposure on sperm and future generations
Cited by: 29
Author(s): Katherine W. Greeson, Kristen L. Fowler, Paige M. Estave, S. Kate Thompson, Chelsea Wagner, R. Clayton Edenfield, Krista Maye Symosko, Alyse N. Steves, M. Elizabeth Marder, Metrecia L. Terrell, Hillary Barton, Michael Koval, Michele Marcus, Charles A. Easley
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-79082-8

Human extrahepatic and intrahepatic cholangiocyte organoids show region-specific differentiation potential and model cystic fibrosis-related bile duct disease
Cited by: 37
Author(s): Monique M A Verstegen, Floris J.M. Roos, Ksenia Burka, Helmuth Gehart, Myrthe Jager, Maaike de Wolf, Marcel J. C. Bijvelds, Hugo R. de Jonge, Arif Ibrahim Ardisasmita, Nick A. van Huizen, Henk P. Roest, Jeroen de Jonge, Michael Koch, Francesco Pampaloni, Sabine A. Fuchs, Imre F. Schene, Theo M. Luider, Hubert P.J. van der Doef, Frank Bodewes, Ruben H J de Kleine, Bart Spee, Gert‐Jan Kremers, Hans Clevers, Jan N. M. IJzermans, Edwin Cuppen, Luc J. W. van der Laan
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-66988-6

A Transcriptome Analysis Reveals that Hepatic Glycolysis and Lipid Synthesis Are Negatively Associated with Feed Efficiency in DLY Pigs
Cited by: 8
Author(s): Cineng Xu, Xingwang Wang, Zhanwei Zhuang, Jie Wu, Shenping Zhou, Jianping Quan, Rongrong Ding, Yong Ye, Longlong Peng, Zhenfang Wu, Enqin Zheng, Jie Yang
Software Mentions: 3
Published: over 4 years ago

Projects: pypi: HTSeq

Papers Mentioning HTSeq 3,071