Ecosyste.ms: Papers

10.3389/fncel.2020.00144

MicroRNA-124 Overexpression in Schwann Cells Promotes Schwann Cell-Astrocyte Integration and Inhibits Glial Scar Formation Ability
Cited by: 4
Author(s): Zhijun Li, Yifei Yu, Juanjuan Kang, Yangyang Zheng, Jinying Xu, Kan Xu, Kun Hou, Yi Hou, Guangfan Chi
Software Mentions: 3
Published: over 4 years ago

10.3389/fendo.2019.00676

Sleep Deprivation Alters the Pituitary Stress Transcriptome in Male and Female Mice
Cited by: 6
Author(s): Mario G. Oyola, Elizabeth A. Shupe, Anthony R. Soltis, Gauthaman Sukumar, Marcelo Páez-Pereda, Darwin O. Larco, Matthew D. Wilkerson, Stephen W. Rothwell, Clifton L. Dalgard, T. John Wu
Software Mentions: 3
Published: about 5 years ago

10.3389/fimmu.2020.00708

Transcriptome Profiling of Lung Innate Immune Responses Potentially Associated With the Pathogenesis of Acinetobacter baumannii Acute Lethal Pneumonia
Cited by: 10
Author(s): Xi Zeng, Hao Gu, Peng Li, Yang Yao, Ning Wang, Yun Shi, Quanming Zou
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2017.01634

Dynamic Changes in Host Gene Expression following In Vitro Viral Mimic Stimulation in Crocodile Cells
Cited by: 1
Author(s): Subir Sarker, Yinan Wang, Brenden Warren-Smith, Karla J. Helbig
Software Mentions: 3
Published: almost 7 years ago

10.3389/fimmu.2020.01219

Hemophilia A Inhibitor Subjects Show Unique PBMC Gene Expression Profiles That Include Up-Regulated Innate Immune Modulators
Cited by: 6
Author(s): Ahmad Faisal Karim, Anthony R. Soltis, Gauthaman Sukumar, Christoph Königs, Nadia P. Ewing, Clifton L. Dalgard, Matthew D. Wilkerson, Kathleen P. Pratt
Software Mentions: 3
Published: over 4 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: over 7 years ago

10.3389/fnmol.2019.00005

Global Gene Knockout of Kcnip3 Enhances Pain Sensitivity and Exacerbates Negative Emotions in Rats
Cited by: 12
Author(s): Yupeng Guo, Yu-Ru Zhi, Tingting Liu, Yun Wang, Ying Zhang
Software Mentions: 3
Published: almost 6 years ago

10.3389/fnins.2018.00243

Adar3 Is Involved in Learning and Memory in Mice
Cited by: 48
Author(s): Dessislava Mladenova, Guy Barry, Lyndsey M. Konen, Sandy S. Pineda, Boris Guennewig, Lotta Avesson, Raphael Zinn, Nicole Schönrock, Mainá Bitar, Nicky Jonkhout, Lauren Crumlish, Dominik C. Kaczorowski, Andrew Gong, Mark Pinese, Glória Regina Franco, Carl R. Walkley, Bryce Vissel, John S. Mattick
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2016.01692

A Developmental and Molecular View of Formation of Auxin-Induced Nodule-Like Structures in Land Plants
Cited by: 19
Author(s): Ryan Hiltenbrand, Jacklyn Thomas, Hannah McCarthy, Karl Dykema, Ashley Spurr, Hamilton Newhart, Mary E. Winn, Arijit Mukherjee
Software Mentions: 3
Published: about 8 years ago

10.1093/g3journal/jkab030

Transcriptomic analysis of gonadal development in parasitic and non-parasitic lampreys (Ichthyomyzon spp.), with a comparison of genomic resources in these non-model species
Cited by: 1
Author(s): Nisha Ajmani, Tahirah Yasmin, Margaret F. Docker, Sara V. Good
Software Mentions: 3
Published: almost 4 years ago

10.3390/genes10120948

Source of Dietary Fat in Pig Diet Affects Adipose Expression of Genes Related to Cancer, Cardiovascular, and Neurodegenerative Diseases
Cited by: 6
Author(s): Maria Oczkowicz, Tomasz Szmatoła, Małgorzata Świątkiewicz
Software Mentions: 3
Published: about 5 years ago

10.3390/genes11091087

3′quant mRNA-Seq of Porcine Liver Reveals Alterations in UPR, Acute Phase Response, and Cholesterol and Bile Acid Metabolism in Response to Different Dietary Fats
Cited by: 3
Author(s): Maria Oczkowicz, Tomasz Szmatoła, Małgorzata Świątkiewicz, Anna Koseniuk, Grzegorz Smołucha, Wojciech Witarski, Alicja Wierzbicka
Software Mentions: 3
Published: about 4 years ago

10.3390/genes12060939

Two RECK Splice Variants (Long and Short) Are Differentially Expressed in Patients with Stable and Unstable Coronary Artery Disease: A Pilot Study
Cited by: 3
Author(s): Chiara Vancheri, Elena Morini, Francesca Romana Prandi, Elie Alkhoury, Roberto Celotto, Francesco Romeo, Giuseppe Novelli, Francesca Amati
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-015-0208-5

Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance
Cited by: 74
Author(s): William R. Swindell, Henriette A. Remmer, Mrinal K. Sarkar, Xianying Xing, Drew H. Barnes, Liza Wolterink, John J. Voorhees, Rajan P. Nair, Andrew Johnston, James T. Elder, Jóhann E. Guðjónsson
Software Mentions: 3
Published: over 9 years ago

10.1186/s13073-017-0415-3

Imiquimod has strain-dependent effects in mice and does not uniquely model human psoriasis
Cited by: 103
Author(s): William R. Swindell, Kellie A. Michaels, Andrew J. Sutter, Doina Diaconu, Yi Fritz, Xianying Xing, Mrinal K. Sarkar, Yun Liang, Lam C. Tsoi, Jóhann E. Guðjónsson, Nicole L. Ward
Software Mentions: 3
Published: over 7 years ago

10.1074/jbc.M116.751644

Bromodomain and extraterminal inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps
Cited by: 25
Author(s): Kristin M. Keck, S. Moquin, Amanda He, Samantha G. Fernandez, Jessica J. Somberg, Stephanie M. Liu, Delsy M. Martinez, JJ L. Miranda
Software Mentions: 3
Published: over 7 years ago

10.1074/jbc.RA120.014960

mTOR kinase inhibition disrupts neuregulin 1-ERBB3 autocrine signaling and sensitizes NF2-deficient meningioma cellular models to IGF1R inhibition
Cited by: 7
Author(s): Roberta L. Beauchamp, Serkan Erdin, Luke Witt, Justin T. Jordan, Scott R. Plotkin, James F. Gusella, Vijaya Ramesh
Software Mentions: 3
Published: almost 4 years ago

10.5334/jcr.213

Genes Relevant to Tissue Response to Cancer Therapy Display Diurnal Variation in mRNA Expression in Human Oral Mucosa
Cited by: 3
Author(s): Fangyi Gu, Eduardo Cortes Gomez, Jianhong Chen, Matthew F. Buas, Nicolas F. Schlecht, Karen Hulme, Shweta Vishwas Kulkarni, Prashant Singh, Richard J. O’Connor, Christine B. Ambrosone, Anurag Singh, Jianmin Wang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1009215

Injection site vaccinology of a recombinant vaccinia-based vector reveals diverse innate immune signatures
Cited by: 11
Author(s): Jessamine E. Hazlewood, Troy Dumenil, Thuy T. Le, Andrii Slonchak, Stephen H. Kazakoff, Ann‐Marie Patch, Lesley-Ann Gray, Paul M. Howley, Liang Liu, John D. Hayball, Kexin Yan, Daniel J. Rawle, Natalie A. Prow, Andreas Suhrbier
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-06281-1

Transcriptome Analysis of Canine Cutaneous Melanoma and Melanocytoma Reveals a Modulation of Genes Regulating Extracellular Matrix Metabolism and Cell Cycle
Cited by: 25
Author(s): Chiara Brachelente, Katia Cappelli, Stefano Capomaccio, Ilaria Porcellato, Serenella Silvestri, Laura Bongiovanni, Raffaella De Maria, Andrea Verini Supplizi, Luca Mechelli, Monica Sforna
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-07746-z

Whole transcriptome profiling of taste bud cells
Cited by: 67
Author(s): Sunil K. Sukumaran, Brian C. Lewandowski, Yumei Qin, Ramana Kotha, Alexander A. Bachmanov, Robert F. Margolskee
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-39591-7

Altered splicing and cytoplasmic levels of tRNA synthetases in SF3B1-mutant myelodysplastic syndromes as a therapeutic vulnerability
Cited by: 13
Author(s): Fabio G. Liberante, Katrina M. Lappin, Eliana M. Barros, Jekaterina Vohhodina, Florian Grebien, Kienan I. Savage, Ken I. Mills
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-45821-9

Skeletal muscle in MuRF1 null mice is not spared in low-gravity conditions, indicating atrophy proceeds by unique mechanisms in space
Cited by: 39
Author(s): Samuel M. Cadena, Yunyu Zhang, Jian Fang, Sophie Brachat, Pia Kuss, E. Giorgetti, Louis S. Stodieck, Michaela Kneissel, David J. Glass
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-76705-y

Human transcription factors responsive to initial reprogramming predominantly undergo legitimate reprogramming during fibroblast conversion to iPSCs
Cited by: 8
Author(s): Ricardo R. Cevallos, Yvonne J. K. Edwards, John M. Parant, Bradley K. Yoder, Kejin Hu
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-78416-w

A biomimetic engineered bone platform for advanced testing of prosthetic implants
Cited by: 3
Author(s): Martina Sladkova‐Faure, Michael Pujari-Palmer, Caroline Öhman‐Mägi, Alejandro López, Hanbin Wang, Håkan Engqvist, Giuseppe Maria de Peppo
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-020-79624-0

Ascending dorsal column sensory neurons respond to spinal cord injury and downregulate genes related to lipid metabolism
Cited by: 12
Author(s): Eric E. Ewan, Oshri Avraham, Dan Carlin, Tassia M. Goncalves, Guoyan Zhao, Valeria Cavalli
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-83459-8

Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
Cited by: 5
Author(s): M. Joseph Tomlinson, Shawn W. Polson, Jing Qiu, Juniper A. Lake, William Lee, Behnam Abasht
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-94341-y

Genome-wide chromatin accessibility analyses provide a map for enhancing optic nerve regeneration
Cited by: 10
Author(s): Wolfgang Pita-Thomas, Tassia M. Goncalves, Abdhesh Kumar, Guoyan Zhao, Valeria Cavalli
Software Mentions: 3
Published: over 3 years ago

10.1038/s41398-018-0355-8

Cell type-specific gene expression patterns associated with posttraumatic stress disorder in World Trade Center responders
Cited by: 79
Author(s): Pei‐Fen Kuan, Xiaohua Yang, Sean Clouston, Ruwei Xu, Roman Kotov, Monika A. Waszczuk, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 3
Published: almost 6 years ago

10.1128/mBio.00024-18

<i>In Vitro</i> Culture of the Insect Endosymbiont <i>Spiroplasma poulsonii</i> Highlights Bacterial Genes Involved in Host-Symbiont Interaction
Cited by: 49
Author(s): Florent Masson, Sandra Calderon Copete, Fanny Schüpfer, Mario Gonzalo Garcia-Arraez, Bruno Lemaître
Software Mentions: 3
Published: over 6 years ago

10.1128/mBio.01628-20

Pathogenesis of Human Papillomaviruses Requires the ATR/p62 Autophagy-Related Pathway
Cited by: 11
Author(s): Siqi Hong, Yan Li, Paul J. Kaminski, Jorge Andrade, Laimonis A. Laimins
Software Mentions: 3
Published: about 4 years ago

10.1002/ijc.31053

Neuroblastoma cells undergo transcriptomic alterations upon dissemination into the bone marrow and subsequent tumor progression
Cited by: 25
Author(s): Fikret Rifatbegovic, Christian Frech, Mojtaba Abbasi, Sabine Taschner‐Mandl, Tamara Weiss, Wolfgang M. Schmidt, Iris Schmidt, Ruth Ladenstein, Inge M. Ambros, Peter F. Ambros
Software Mentions: 3
Published: about 7 years ago

10.3390/jof7030198

Innate Resistance and Phosphite Treatment Affect Both the Pathogen’s and Host’s Transcriptomes in the Tanoak-Phytophthora ramorum Pathosystem
Cited by: 9
Author(s): Takao Kasuga, Katherine J. Hayden, Catherine A. Eyre, Peter J.P. Croucher, Shannon Schechter, Jessica W. Wright, Matteo Garbelotto
Software Mentions: 3
Published: over 3 years ago

10.1016/j.jhepr.2021.100237

Aramchol downregulates stearoyl CoA-desaturase 1 in hepatic stellate cells to attenuate cellular fibrogenesis
Cited by: 26
Author(s): Dipankar Bhattacharya, Brittany Basta, José M. Mato, Amanda Craig, David Fernández–Ramos, Fernando Lopitz‐Otsoa, Darya Tsvirkun, Liat Hayardeny, Vasuretha Chandar, Robert E. Schwartz, Augusto Villanueva, Scott L. Friedman
Software Mentions: 3
Published: over 3 years ago

10.1038/s41388-020-01614-3

Comprehensive characterisation of intronic mis-splicing mutations in human cancers
Cited by: 20
Author(s): Hyunchul Jung, Kang Seon Lee, Jung Kyoon Choi
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41389-021-00339-6

Disruptor of telomeric silencing 1-like promotes ovarian cancer tumor growth by stimulating pro-tumorigenic metabolic pathways and blocking apoptosis
Cited by: 9
Author(s): Suresh Chava, Suresh Bugide, Yvonne J. K. Edwards, Romi Gupta
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.58515

Functional specification of CCK+ interneurons by alternative isoforms of Kv4.3 auxiliary subunits
Cited by: 9
Author(s): Viktor János Oláh, David Lukacsovich, Jochen Winterer, Antónia Arszovszki, Andrea Lőrincz, Zoltán Nusser, Csaba Földy, János Szabadics
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.43821

HDAC3 restrains CD8-lineage genes to maintain a bi-potential state in CD4+CD8+ thymocytes for CD4-lineage commitment
Cited by: 23
Author(s): Rachael Laura Philips, Jeong Heon Lee, Krutika S. Gaonkar, Pritha Chanana, Ji Young Chung, Sinibaldo Romero Arocha, Aaron Schwab, Tamás Ördög, Virginia Smith Shapiro
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.63266

Dissecting the DNA binding landscape and gene regulatory network of p63 and p53
Cited by: 23
Author(s): Konstantin Riege, Helene Kretzmer, Arne Sahm, Simon S. McDade, Steve Hoffmann, Martin Fischer
Software Mentions: 3
Published: almost 4 years ago

10.3390/ijms18081709

Systematic Selection of Reference Genes for the Normalization of Circulating RNA Transcripts in Pregnant Women Based on RNA-Seq Data
Cited by: 20
Author(s): Stephen S.C. Chim, Kwan-Yiu Wong, C.Y. Chung, Stephanie Lam, Jamie Sui-Lam Kwok, Chit-Ying Lai, Yvonne Kwun Yue Cheng, Shuk Yi Annie Hui, Meng Meng, Oi-Ka Chan, Stephen Kwok‐Wing Tsui, Keun-Young Lee, Ting-Fung Chan, Tse Ngong Leung
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms19082300

Transcriptomic Analyses of Root Restriction Effects on Phytohormone Content and Signal Transduction during Grape Berry Development and Ripening
Cited by: 12
Author(s): Lu Feng, Ji Cao, Shiping Wang, Ling Jiang, Xian Li, Chongde Sun
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms21155191

A Genome-Wide View of Transcriptional Responses during Aphis glycines Infestation in Soybean
Cited by: 5
Author(s): Luming Yao, Biyun Yang, Xiao‐Pan Ma, Shuangshuang Wang, Zhe Guan, Biao Wang, Yan‐Yi Jiang
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms21197086

Transcriptome-Wide Analysis of Interplay between mRNA Stability, Translation and Small RNAs in Response to Neuronal Membrane Depolarization
Cited by: 3
Author(s): Dylan Kiltschewskij, Murray J. Cairns
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms21239145

Distinctive Features of Orbital Adipose Tissue (OAT) in Graves’ Orbitopathy
Cited by: 7
Author(s): Lei Zhang, Anna Evans, Christopher Von Ruhland, Mohd Shazli Draman, Sarah Edkins, Amy E. Vincent, Rolando Berlinguer‐Palmini, Aled Rees, Anjana Haridas, Diane H. Morris, Andrew R. Tee, Marian Ludgate, D.M. Turnbull, Fredrik Karpe, Colin Dayan
Software Mentions: 3
Published: almost 4 years ago

10.3390/ijms22136963

Aberrant Alternative Splicing in U2af1/Tet2 Double Mutant Mice Contributes to Major Hematological Phenotypes
Cited by: 4
Author(s): Cristina Martínez-Valiente, Cristian García-Ruiz, Beatriz Rosón, Alessandro Liquori, Elisa González-Romero, Raúl Fernández‐González, Isabel Gómez-Redondo, José Cervera, Alfonso Gutiérrez‐Adán, Alejandra Sanjuán-Pla
Software Mentions: 3
Published: over 3 years ago

10.1016/j.isci.2021.102741

Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra syndrome
Cited by: 3
Author(s): Ayumi Yamada, Takae Hirasawa, Kayako Nishimura, Chikako Shimura, Naomi Kogo, Kei Fukuda, Madoka Kato, Masaki Yokomori, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Yoichiro Iwakura, Itoshi Nikaido, Shigeyoshi Itohara, Yoichi Shinkai
Software Mentions: 3
Published: over 3 years ago

10.18632/oncotarget.7097

Bevacizumab specifically decreases elevated levels of circulating KIT+CD11b+ cells and IL-10 in metastatic breast cancer patients
Cited by: 13
Author(s): Sarah Cattin, Benoı̂t Fellay, Sylvain Pradervand, Andreas Trojan, Thomas Ruhstaller, Curzio Rüegg, G. Fürstenberger
Software Mentions: 3
Published: almost 9 years ago

10.18632/oncotarget.14050

Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer
Cited by: 12
Author(s): Yanxiao Zhang, Jie Yu, Vladimir Grachtchouk, Tingting Qin, Carey N. Lumeng, Maureen A. Sartor, Ronald J. Koenig
Software Mentions: 3
Published: almost 8 years ago

10.18632/oncotarget.26988

Investigating the role of LSD2 as an epigenetic regulator in Ewing sarcoma
Cited by: 3
Author(s): Priyal Patel, Kathleen I. Pishas, Cenny Taslim, Julia Selich‐Anderson, Emily R. Theisen, Stephen L. Lessnick
Software Mentions: 3
Published: over 5 years ago

10.1186/s12967-020-02247-6

CLEAR: coverage-based limiting-cell experiment analysis for RNA-seq
Cited by: 12
Author(s): Logan A. Walker, Michael G. Sovic, Chi‐Ling Chiang, Eileen Hu, Jiyeon K. Denninger, Xi Chen, Elizabeth D. Kirby, John C. Byrd, Natarajan Muthusamy, Ralf Bundschuh, Pearlly S. Yan
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pntd.0004334

Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq
Cited by: 73
Author(s): Letícia Anderson, Murilo Sena Amaral, Felipe Beckedorff, Lucas F. Silva, Bianca Dazzani, Kátia C. Oliveira, Giulliana T. Almeida, Maria de Lourdes Contente Gomes, David S. Pires, João Carlos Setúbal, Ricardo DeMarco, Sérgio Verjovski-Almeida
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.37202

tp53 deficiency causes a wide tumor spectrum and increases embryonal rhabdomyosarcoma metastasis in zebrafish
Cited by: 47
Author(s): Myron S. Ignatius, Madeline Hayes, Finola Moore, Qin Tang, Sara P. Garcia, Patrick R. Blackburn, Kunal Baxi, Long Wang, Alexander Jin, Ashwin Ramakrishnan, Sophia Reeder, Yidong Chen, G. Petur Nielsen, Eleanor Chen, Robert P. Hasserjian, Franck Tirode, Stephen C. Ekker, David M. Langenau
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0125718

Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study
Cited by: 51
Author(s): Christine Poitou, Claire Perret, François Mathieu, Vinh Truong, Yuna Blum, H Durand, Rohia Alili, Nadjim Chelghoum, Véronique Pelloux, Judith Aron‐Wisnewsky, Adriana Torcivia, Jean‐Luc Bouillot, Brian W. Parks, Ewa Ninio, Karine Clément, Laurence Tiret
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0059582

Transcriptome Sequencing of Gene Expression in the Brain of the HIV-1 Transgenic Rat
Cited by: 38
Author(s): Ming D. Li, Jun Cao, Shaolin Wang, Wang Ju, Saeed Sarkar, Michael Vigorito, Z. Jennie, Sulie L. Chang
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-15-842

New gene models and alternative splicing in the maize pathogen Colletotrichum graminicola revealed by RNA-Seq analysis
Cited by: 29
Author(s): Ivo Schliebner, Rayko Becher, Marcus Hempel, H. B. Deising, Ralf Horbach
Software Mentions: 2
Published: about 10 years ago

10.3390/jcm10010126

Fenofibrate Reduces the Severity of Neuroretinopathy in a Type 2 Model of Diabetes without Inducing Peroxisome Proliferator-Activated Receptor Alpha-Dependent Retinal Gene Expression
Cited by: 11
Author(s): Jennifer M. Enright, Sheng Zhang, Christina Thebeau, Emily Siebert, Alexander Jin, Veda Gadiraju, Xiaodong Zhang, Shiming Chen, Clay F. Semenkovich, Rithwick Rajagopal
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.ppat.1005747

Post-Transcriptional Regulation of KLF4 by High-Risk Human Papillomaviruses Is Necessary for the Differentiation-Dependent Viral Life Cycle
Cited by: 29
Author(s): Vignesh Gunasekharan, Yan Li, Jorge Andrade, Laimonis A. Laimins
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.54659

Osterix-Cre marks distinct subsets of CD45- and CD45+ stromal populations in extra-skeletal tumors with pro-tumorigenic characteristics
Cited by: 9
Author(s): Biancamaria Ricci, Eric Tycksen, Hamza Celik, Jad I. Belle, Francesca Fontana, Roberto Civitelli, Roberta Faccio
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0201822

RNA variant identification discrepancy among splice-aware alignment algorithms
Cited by: 7
Author(s): Ji Hyung Hong, Yoon Ho Ko, Keunsoo Kang
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms21134662

Putative Roles for Peptidylarginine Deiminases in COVID-19
Cited by: 24
Author(s): Elif Damla Arısan, Pinar Uysal-Onganer, Sigrun Lange
Software Mentions: 2
Published: over 4 years ago

10.1186/s13058-019-1177-1

Neoadjuvant neratinib promotes ferroptosis and inhibits brain metastasis in a novel syngeneic model of spontaneous HER2+ve breast cancer metastasis
Cited by: 79
Author(s): Aadya Nagpal, Richard P. Redvers, Xiawei Ling, Scott Ayton, Miriam Fuentes, Elnaz Tavancheh, Irmina Diala, Alshad S. Lalani, Sherene Loi, Steven David, Robin L. Anderson, Yvonne E. Smith, Delphine Mérino, Delphine Denoyer, Normand Pouliot
Software Mentions: 2
Published: over 5 years ago

10.1186/s13075-021-02477-z

Periostin loss-of-function protects mice from post-traumatic and age-related osteoarthritis
Cited by: 18
Author(s): Mukundan Attur, Xin Duan, Lei Cai, Tianzhen Han, Weili Zhang, Eric Tycksen, Jonathan Samuels, Robert H. Brophy, Steven B. Abramson, Muhammad Farooq
Software Mentions: 2
Published: over 3 years ago

10.18632/oncotarget.20717

Network-directed cis-mediator analysis of normal prostate tissue expression profiles reveals downstream regulatory associations of prostate cancer susceptibility loci
Cited by: 2
Author(s): Nicholas B. Larson, Shannon K. McDonnell, Zachary C. Fogarty, Melissa C. Larson, John C. Cheville, Shaun M. Riska, Saurabh Baheti, Alexandra M. Weber, Asha Nair, Liang Wang, Daniel R. O’Brien, Jaime Davila, Daniel J. Schaid, Stephen N. Thibodeau
Software Mentions: 2
Published: about 7 years ago

10.1155/2018/3057272

Genome-Wide Expression Profiles of Hemp (<i>Cannabis sativa</i> L.) in Response to Drought Stress
Cited by: 20
Author(s): Chunsheng Gao, Chaohua Cheng, Lining Zhao, Yongting Yu, Qing Tang, Pengfei Xin, Touming Liu, Yan Zhen, Yuan Guo, Zang Gonggu
Software Mentions: 2
Published: almost 7 years ago

10.1136/jitc-2020-000832

Skin dendritic cells in melanoma are key for successful checkpoint blockade therapy
Cited by: 18
Author(s): Natasa Prokopi, Christoph H. Tripp, Bart Tummers, Florian Hornsteiner, Sarah Spoeck, Jeremy Chase Crawford, Derek R. Clements, Mirjana Efremova, Katharina Hutter, Lydia Bellmann, Giuseppe Cappellano, Bruno L. Cadilha, Sebastian Kobold, Louis Boon, Daniela Ortner, Zlatko Trajanoski, Suzie Chen, Tanja D. de Gruijl, Juliana Idoyaga, Douglas R. Green, Patrizia Stoitzner
Software Mentions: 2
Published: almost 4 years ago

10.1186/s40425-019-0629-6

Efficient identification of neoantigen-specific T-cell responses in advanced human ovarian cancer
Cited by: 58
Author(s): Song Liu, Junko Matsuzaki, Lei Wei, Takemasa Tsuji, Sebastiano Battaglia, Qiang Hu, Eduardo Cortes, Lai-Ping Wong, Li Yan, Mark D. Long, Anthony Miliotto, Nicholas W. Bateman, Shashikant Lele, Thinle Chodon, Richard C. Koya, Song Yao, Qianqian Zhu, Thomas P. Conrads, Jianmin Wang, G. Larry Maxwell, Amit A. Lugade, Kunle Odunsi
Software Mentions: 2
Published: over 5 years ago

10.1186/s40478-018-0513-5

Cooperative p16 and p21 action protects female astrocytes from transformation
Cited by: 44
Author(s): Najla Kfoury, Tao Sun, Kwanha Yu, Nathan Rockwell, Kelsey L. Tinkum, Zongtai Qi, Nicole M. Warrington, Peter R. McDonald, Anuradha Roy, Scott J. Weir, Carrie A. Mohila, Benjamin Deneen, Joshua B. Rubin
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2164-15-30

Perinatal bisphenol A exposure promotes dose-dependent alterations of the mouse methylome
Cited by: 68
Author(s): Jung Ho Kim, Maureen A. Sartor, Laura S. Rozek, Christopher Faulk, Olivia S. Anderson, Tamara R. Jones, Muna S. Nahar, Dana C. Dolinoy
Software Mentions: 2
Published: almost 11 years ago

10.7554/eLife.54877

Endogenous itaconate is not required for particulate matter-induced NRF2 expression or inflammatory response
Cited by: 29
Author(s): K. Sun, Yan Li, Angelo Y. Meliton, P.S. Woods, Lucas Kimmig, Rengül Cetin-Atalay, Robert B. Hamanaka, Gökhan M. Mutlu
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2020.01429

High-Resolution Profiling of Innate Immune Responses by Porcine Dendritic Cell Subsets in vitro and in vivo
Cited by: 14
Author(s): Gaël Auray, Stephanie C. Talker, Irene Keller, Sylvie Python, Marlène Gerber, Matthias Liniger, Llilianne Ganges, Rémy Bruggmann, Nicolas Ruggli, Artur Summerfield
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2017.01352

Human Primary Macrophages Derived In Vitro from Circulating Monocytes Comprise Adherent and Non-Adherent Subsets with Differential Expression of Siglec-1 and CD4 and Permissiveness to HIV-1 Infection
Cited by: 12
Author(s): Ousman Jobe, Jiae Kim, Eric Tycksen, Sayali Onkar, Nelson L. Michael, Carl R. Alving, Mangala Rao
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2021.705326

Effects of NaCl Concentrations on Growth Patterns, Phenotypes Associated With Virulence, and Energy Metabolism in Escherichia coli BW25113
Cited by: 14
Author(s): Fen Li, Xue-Song Xiong, Yingying Yang, Jun‐Jiao Wang, Mengmeng Wang, Jia-Wei Tang, Qinghua Liu, Liang Wang, Bing Gu
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2021.656548

The Heat Shock Transcription Factor HsfA Is Essential for Thermotolerance and Regulates Cell Wall Integrity in Aspergillus fumigatus
Cited by: 9
Author(s): João Henrique Tadini Marilhano Fabri, Marina Campos Rocha, Caroline Mota Fernandes, Gabriela Félix Persinoti, Laure Nicolas Annick Ries, Anderson Ferreira da Cunha, Gustavo Henrique Goldman, Maurizio Del Poeta, Iran Malavazi
Software Mentions: 2
Published: over 3 years ago

10.3389/fnmol.2017.00279

Dysregulation of Alternative Poly-adenylation as a Potential Player in Autism Spectrum Disorder
Cited by: 14
Author(s): Krzysztof J. Szkop, Peter I. C. Cooke, Joanne A. Humphries, Viktoria Kalna, David S. Moss, Eugene F. Schuster, Irene Nobeli
Software Mentions: 2
Published: about 7 years ago

10.3389/fcell.2021.673374

Identification of TAZ-Dependent Breast Cancer Vulnerabilities Using a Chemical Genomics Screening Approach
Cited by: 4
Author(s): He Shen, Yanmin Chen, Yin Wan, Tao Liu, Jianmin Wang, Yali Zhang, Lei Wei, Qiang Hu, Bo Xu, Mikhail V. Chernov, Costa Frangou, Jianmin Zhang
Software Mentions: 2
Published: over 3 years ago

10.1155/2020/3561235

Transcriptome Analysis Reveals the Effects of Troxerutin and Cerebroprotein Hydrolysate Injection on Injured Spinal Cords in Rats
Cited by: 0
Author(s): Linbang Wang, Hucheng Wang, Ke Tang, Weiyang Zhong, Zhiyu Chen, Zhengxue Quan
Software Mentions: 2
Published: over 4 years ago

10.3389/fphys.2021.650964

Small Conductance Ca2 +-Activated K+ (SK) Channel mRNA Expression in Human Atrial and Ventricular Tissue: Comparison Between Donor, Atrial Fibrillation and Heart Failure Tissue
Cited by: 22
Author(s): Elisa Darkow, Thong Tien Nguyen, Marina Stolina, Fabian A. Kari, Constanze Schmidt, Felix Wiedmann, István Baczkó, Peter Kohl, Sridharan Rajamani, Ursula Ravens, Rémi Peyronnet
Software Mentions: 2
Published: over 3 years ago

10.1242/dmm.036764

Developmental origins for semilunar valve stenosis identified in mice harboring congenital heart disease-associated <i>GATA4</i> mutation
Cited by: 15
Author(s): Stephanie LaHaye, Uddalak Majumdar, Jun Yasuhara, Sara N. Koenig, Adrianna Matos‐Nieves, Rahul Kumar, Vidu Garg
Software Mentions: 2
Published: almost 6 years ago

10.1155/2015/593572

Transcriptomic and Immunohistochemical Profiling of SLC6A14 in Pancreatic Ductal Adenocarcinoma
Cited by: 22
Author(s): Alan R. Penheiter, Sibel Erdoğan, Stephen J. Murphy, Steven N. Hart, Joema Felipe Lima, Fariborz Rakhshan Rohakhtar, Daniel R. O’Brien, William R. Bamlet, Ryan E. Wuertz, Thomas C. Smyrk, Fergus J. Couch, George Vasmatzis, Claire E. Bender, Stephanie K. Carlson
Software Mentions: 2
Published: almost 10 years ago

10.1242/dmm.040816

Zika virus non-structural protein NS4A restricts eye growth in<i>Drosophila</i>through regulation of JAK/STAT signaling
Cited by: 21
Author(s): Sneh Harsh, Yulong Fu, Eric Kenney, Zhe Han, Ioannis Eleftherianos
Software Mentions: 2
Published: almost 5 years ago

10.3389/fpls.2018.00244

Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca2+ Channel Blocker
Cited by: 30
Author(s): Keshi Ma, Wenshuo Shi, Mingang Xu, Jiaxi Liu, Feixiong Zhang
Software Mentions: 2
Published: over 6 years ago

10.3389/fvets.2021.666838

Genomic and Transcriptomic Characterization of Canine Osteosarcoma Cell Lines: A Valuable Resource in Translational Medicine
Cited by: 6
Author(s): Cecilia Gola, Diana Giannuzzi, Andrea Rinaldi, Selina Iussich, Paola Modesto, Emanuela Morello, Paolo Buracco, Luca Aresu, Raffaella De Maria
Software Mentions: 2
Published: over 3 years ago

10.1016/j.dib.2018.03.079

RNA-seq data of invasive ductal carcinoma and adjacent normal tissues from a Korean patient with breast cancer
Cited by: 4
Author(s): Ji Hyung Hong, Yoon Ho Ko, Keunsoo Kang
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-021-01722-0

Efficient manipulation of gene dosage in human iPSCs using CRISPR/Cas9 nickases
Cited by: 4
Author(s): Ye Tao, Yangyang Duan, Hayley W. S. Tsang, He Xu, Yuewen Chen, Han Cao, Yu Chen, Amy Kit Yu Fu, Nancy Y. Ip
Software Mentions: 2
Published: almost 4 years ago

10.1093/g3journal/jkab209

Transcriptomic and photosynthetic responses to grafting of the <i>Nod1</i> gene in nodulated and non-nodulated soybeans
Cited by: 2
Author(s): Qingyuan He, Shihua Xiang, Wubin Wang, Yingjie Shu, Zhengpeng Li, Songhua Wang, Lei Chen, Xiao-Yan Yang, Tuanjie Zhao
Software Mentions: 2
Published: over 3 years ago

10.3390/genes7010001

Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex
Cited by: 22
Author(s): Dovilė Strepetkaitė, Gediminas Alzbutas, Eimantas Astromskas, Aru̅nas Lagunavičius, Rasa Sabaliauskaitė, Кęstutis Arbačiauskas, Juozas R. Lazutka
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12870-017-1217-x

The comparison of alternative splicing among the multiple tissues in cucumber
Cited by: 16
Author(s): Yu Sun, Han Wei Hou, Hongtao Song, Kui Lin, Zhonghua Zhang, Jinglu Hu, Erli Pang
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41419-021-03445-w

Sensing soluble uric acid by Naip1-Nlrp3 platform
Cited by: 14
Author(s): Tárcio Teodoro Braga, Mariana Rodrigues Davanso, Davi Mendes, Tiago Antônio de Souza, Anderson F. Brito, Mário Costa Cruz, Meire Ioshie Hiyane, Dhêmerson Souza de Lima, Vinicius Nunes, Juliana de Fátima Giarola, Dênio Emanuel Pires Souto, Tomasz Próchnicki, Mario A. Lauterbach, Stellee Marcela Petris Biscaia, Rilton Alves de Freitas, Rui Curi, Alessandra Pontillo, Eicke Latz, Niels Olsen Saraiva Câmara
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13059-018-1571-5

Simulation-based benchmarking of isoform quantification in single-cell RNA-seq
Cited by: 23
Author(s): Jennifer Westoby, Marcela Sjöberg-Herrera, Anne C. Ferguson-Smith, Martin Hemberg
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0078480

Unique Transcriptome Patterns of the White and Grey Matter Corroborate Structural and Functional Heterogeneity in the Human Frontal Lobe
Cited by: 39
Author(s): James D. Mills, Tomas Kavanagh, Woojin Scott Kim, Bei Jun Chen, Yoshihiro Kawahara, Glenda M. Halliday, Michael Janitz
Software Mentions: 2
Published: about 11 years ago

10.1186/s12920-018-0424-0

Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma
Cited by: 10
Author(s): Matthew Yen, Zongtai Qi, Xuhua Chen, John A. Cooper, Robi D. Mitra, Michael D. Onken
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0087113

Whole Genome Analyses of a Well-Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements
Cited by: 14
Author(s): Jan B. Egan, Michael T. Barrett, Mia D. Champion, Sumit Middha, Elizabeth Lenkiewicz, Lisa Evers, Princy Francis, Jessica Schmidt, Chao Shi, Scott Van Wier, Sandra K Badar, Gregory Ahmann, K. Martin Kortuem, Nicole J. Boczek, Rafaël Fonseca, David W. Craig, John D. Carpten, Mitesh J. Borad, A. Keith Stewart
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0138347

Effects of Age and Estrogen on Skeletal Gene Expression in Humans as Assessed by RNA Sequencing
Cited by: 58
Author(s): Joshua N. Farr, Matthew M. Roforth, Koji Fujita, Kristy M. Nicks, Julie M. Cunningham, Elizabeth J. Atkinson, Terry M. Therneau, Louise K. McCready, James M. Peterson, Matthew T. Drake, David G. Monroe, Sundeep Khosla
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0148726

Transcriptome Analysis of Chemically-Induced Sensory Neuron Ablation in Zebrafish
Cited by: 5
Author(s): Jane A. Cox, Bo Zhang, Holly M. Pope, Mark M. Voigt
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0220101

Enhanced efficacy of sitravatinib in metastatic models of antiangiogenic therapy resistance
Cited by: 20
Author(s): Melissa Dolan, Michalis Mastri, Amanda Tracz, James G. Christensen, Gurkamal S. Chatta, John M.L. Ebos
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0227522

Expression and function of voltage gated proton channels (Hv1) in MDA-MB-231 cells
Cited by: 12
Author(s): Dan J. Bare, Vladimir V. Cherny, Thomas E. DeCoursey, Abde M. Abukhdeir, Deri Morgan
Software Mentions: 2
Published: over 4 years ago

10.1172/jci.insight.120794

Hepatocyte ALOXE3 is induced during adaptive fasting and enhances insulin sensitivity by activating hepatic PPARγ
Cited by: 19
Author(s): Cassandra B. Higgins, Yiming Zhang, Allyson L. Mayer, Hideji Fujiwara, Alicyn I Stothard, Mark Graham, Benjamin M. Swarts, Brian J. DeBosch
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0204967

Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis
Cited by: 48
Author(s): Shiloh R. Lueschow, Jessica E. Stumphy, Huiyu Gong, Stacy L. Kern, Timothy G. Elgin, Mark A. Underwood, Karen M. Kalanetra, David A. Mills, Melissa H. Wong, David K. Meyerholz, Misty Good, Steven J. McElroy
Software Mentions: 2
Published: about 6 years ago

10.1126/sciadv.abe5671

Ameliorating the hallmarks of cellular senescence in skeletal muscle myogenic progenitors in vitro and in vivo
Cited by: 11
Author(s): Aref Shahini, Nika Rajabian, Debanik Choudhury, Shahryar Shahini, Kalyan Vydiam, T M Nguyen, Joseph Kulczyk, Tyler Santarelli, Izuagie Ikhapoh, Yali Zhang, Jianmin Wang, Song Liu, Aimee Stablewski, Ramkumar Thiyagarajan, Kenneth L. Seldeen, Bruce R. Troen, Jennifer Peirick, Pedro Lei, Stelios T. Andreadis
Software Mentions: 2
Published: about 3 years ago

10.1126/sciadv.abf9975

Memory CD8⁺T cells mediate early pathogen-specific protection via localized delivery of chemokines and IFNγ to clusters of monocytes
Cited by: 5
Author(s): Marie Boutet, Zachary Benet, Erik Guillen, Caroline Koch, Saïdi M. Soudja, Fabien Delahaye, David R. Fooksman, Grégoire Lauvau
Software Mentions: 2
Published: about 3 years ago