bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0212031

Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue
Cited by: 25
Author(s): Christy L. Trejo, Miloš Babić, Elliot Imler, Migdalia Gonzalez, Sergei I. Bibikov, Peter J. Shepard, Harper VanSteenhouse, Joanne M. Yeakley, Bruce Seligmann
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0146636

Genetic Signature of Resistance to White Band Disease in the Caribbean Staghorn Coral Acropora cervicornis
Cited by: 36
Author(s): Silvia Libro, Steven V. Vollmer
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0243178

Gene expression profiles of esophageal squamous cell cancers in Hodgkin lymphoma survivors versus sporadic cases
Cited by: 2
Author(s): Berbel L.M. Ykema, Sanne Hoefnagel, Lisanne S. Rigter, Liudmila L. Kodach, Gerrit A. Meijer, Flora E. van Leeuwen, Hina Khan, Pétur Snæbjörnsson, Berthe M.P. Aleman, Annegien Broeks, Sybren L. Meijer, Kenneth K. Wang, Beatriz Carvalho, Kausilia K. Krishnadath, Monique E. van Leerdam
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0094839

Profiles of Extracellular miRNA in Cerebrospinal Fluid and Serum from Patients with Alzheimer's and Parkinson's Diseases Correlate with Disease Status and Features of Pathology
Cited by: 300
Author(s): Kasandra Burgos, Ivana Malenica, Raghu Metpally, Amanda Courtright, Benjamin Rakela, Thomas G. Beach, Holly A. Shill, Charles H. Adler, Marwan N. Sabbagh, Stephen Villa, Waibhav Tembe, David W. Craig, Kendall Van Keuren‐Jensen
Software Mentions: 1
Published: over 12 years ago

10.7554/eLife.60745

Evolution of fibroblasts in the lung metastatic microenvironment is driven by stage-specific transcriptional plasticity
Cited by: 17
Author(s): Ophir Shani, Yael Raz, Lea Monteran, Ye’ela Scharff, Oshrat Levi-Galibov, Or Megides, Hila Shacham, Noam Cohen, Dana Silverbush, Camilla Avivi, Roded Sharan, Asaf Madi, Ruth Scherz‐Shouval, Iris Barshack, Ilan Tsarfaty, Neta Erez
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0210064

Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms
Cited by: 107
Author(s): Megan R. Sanctuary, Jennifer N. Kain, Shin-Yu Chen, Karen M. Kalanetra, Danielle G. Lemay, Destanie R. Rose, Houa Yang, Daniel J. Tancredi, J. Bruce German, Carolyn M. Slupsky, Paul Ashwood, David A. Mills, Jennifer T. Smilowitz, Kathleen Angkustsiri
Software Mentions: 1
Published: almost 8 years ago

10.7554/eLife.59990

Dot1l interacts with Zc3h10 to activate Ucp1 and other thermogenic genes
Cited by: 9
Author(s): Danielle Yi, Hai P. Nguyen, Jennie Dinh, José A. Viscarra, Ying Xie, Frances Lin, Madeleine Zhu, Jon Dempersmier, Yuhui Wang, Hei Sook Sul
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0223274

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome
Cited by: 34
Author(s): Pablo Arroyo, Brian Ho, Lillian Sau, Scott T. Kelley, Varykina G. Thackray
Software Mentions: 1
Published: about 7 years ago

10.1099/mgen.0.000125

Transcriptomic analysis of aerobic respiratory and anaerobic photosynthetic states in Rhodobacter capsulatus and their modulation by global redox regulators RegA, FnrL and CrtJ
Cited by: 12
Author(s): Joseph E. Kumka, Heidi S. Schindel, Mingxu Fang, Sébastien Zappa, Carl E. Bauer
Software Mentions: 1
Published: about 9 years ago

10.7554/eLife.59850

Genetic timestamping of plasma cells in vivo reveals tissue-specific homeostatic population turnover
Cited by: 16
Author(s): An Xu, Raquel Barbosa, Dinis Pedro Calado
Software Mentions: 1
Published: about 6 years ago

10.3390/nu11040776

Decaffeinated Green Tea Extract Does Not Elicit Hepatotoxic Effects and Modulates the Gut Microbiome in Lean B6C3F1 Mice
Cited by: 15
Author(s): Bill J. Gurley, Isabelle R. Miousse, Intawat Nookaew, Laura Ewing, Charles M. Skinner, Piroon Jenjaroenpun, Thidathip Wongsurawat, Stefanie Kennon-McGill, Bharathi Avula, Ji Yeong Bae, Mitchell R. McGill, David W. Ussery, Ikhlas A. Khan, Igor Koturbash
Software Mentions: 1
Published: over 7 years ago

10.1099/mgen.0.000462

Transcriptomics reveal core activities of the plant growth-promoting bacterium Delftia acidovorans RAY209 during interaction with canola and soybean roots
Cited by: 4
Author(s): Danae M. Suchan, Jordyn Bergsveinson, Lori A. Manzon, Alexa J. Pierce, Yuriy Kryachko, Darren R. Korber, Yifang Tan, Dinah D. Tambalo, Nurul H. Khan, Michael L. Whiting, Christopher K. Yost
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0256112

Characterization of the fecal microbiota of sows and their offspring from German commercial pig farms
Cited by: 8
Author(s): Anja Lührmann, Ksenia Ovadenko, Justinus Hellmich, Christoph Sudendey, Vitaly Belik, Jürgen Zentek, Wilfried Vahjen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0224429

Transcriptional foliar profile of the C3-CAM bromeliad Guzmania monostachia
Cited by: 7
Author(s): Helenice Mercier, Maria Aurineide Rodrigues, Sónia Cristina da Silva Andrade, Luiz Lehmann Coutinho, Bruno Nobuya Katayama Gobara, Alejandra Matiz, Paulo Tamaso Mioto, Ana Zangirólame Gonçalves
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0257417

Oscillating dietary crude protein concentrations increase N retention of calves by affecting urea-N recycling and nitrogen metabolism of rumen bacteria and epithelium
Cited by: 3
Author(s): Ningning Zhang, Zhanwei Teng, Pengtao Li, Tong Fu, Hongxia Lian, Linfeng Wang, Gao Teng-yun
Software Mentions: 1
Published: about 5 years ago

10.1099/mgen.0.000200

Transcriptome analysis of Azospirillum brasilense vegetative and cyst states reveals large-scale alterations in metabolic and replicative gene expression
Cited by: 8
Author(s): Elizabeth A. Malinich, Carl E. Bauer
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.63488

Tendon and motor phenotypes in the Crtap-/- mouse model of recessive osteogenesis imperfecta
Cited by: 10
Author(s): Matthew W. Grol, Nele A Haelterman, Joohyun Lim, Elda Munivez, Marilyn Archer, David M. Hudson, Sara F. Tufa, Douglas R. Keene, Kevin Lei, Dongsu Park, Cole D Kuzawa, Catherine G. Ambrose, David R. Eyre, Brendan Lee
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0234837

A tale of two fish: Comparative transcriptomics of resistant and susceptible steelhead following exposure to Ceratonova shasta highlights differences in parasite recognition
Cited by: 15
Author(s): Damien Barrett, Jerri L. Bartholomew
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0223177

Transcriptome analysis of PK-15 cells in innate immune response to porcine deltacoronavirus infection
Cited by: 18
Author(s): Shan Jiang, Fuqiang Li, Xiuli Li, Lili Wang, Li Zhang, Chao Lu, Zheng Li, Yan Mi
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0137548

Neurotranscriptomics: The Effects of Neonatal Stimulus Deprivation on the Rat Pineal Transcriptome
Cited by: 28
Author(s): Stephen W. Hartley, Steven L. Coon, Luis Savastano, James C. Mullikin, Nisc Comparative Sequencing Program, Cong Fu, David C. Klein
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0205055

Dietary or supplemental fermentable fiber intake reduces the presence of Clostridium XI in mouse intestinal microbiota: The importance of higher fecal bacterial load and density
Cited by: 10
Author(s): Wei Zheng, Kairui Wang, Yijun Sun, Shiu‐Ming Kuo
Software Mentions: 1
Published: about 8 years ago

10.1186/s12967-019-1906-3

A possible role for mitochondrial-derived peptides humanin and MOTS-c in patients with Q fever fatigue syndrome and chronic fatigue syndrome
Cited by: 15
Author(s): Ruud P. H. Raijmakers, Annemarie Jansen, Stephan P. Keijmel, Rob ter Horst, Megan E. Roerink, Boris Novakovic, Leo A. B. Joosten, J.W.M. van der Meer, Mihai G. Netea, Chantal P. Bleeker‐Rovers
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0203160

Identification and comparison of key RNA interference machinery from western corn rootworm, fall armyworm, and southern green stink bug
Cited by: 24
Author(s): Courtney Davis-Vogel, Brandon Van Allen, John L. Van Hemert, Amit Sethi, Mark E. Nelson, Dipali G. Sashital
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0175041

Inositol 1, 4, 5-trisphosphate-dependent nuclear calcium signals regulate angiogenesis and cell motility in triple negative breast cancer
Cited by: 15
Author(s): Erika S. Guimarães, Rosângela Pinheiro Gonçalves Machado, Matheus de Castro Fonseca, Andressa França, Luciana Estefani Drumond de Carvalho, Ana Cândida Araújo e Silva, Brígida Gomes Almeida, Puebla Cassini, Bárbara Hissa, Luciana E. Drumond, Carlos Alberto Gonçalves, Gabriel R. Fernandes, Marina De Brot, Márcio Flávio Dutra Moraes, Lucíola da Silva Barcelos, José Miguel Ortega, André G. Oliveira, M. Fátima Leite
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0202351

Dietary salt levels affect digestibility, intestinal gene expression, and the microbiome, in Nile tilapia (Oreochromis niloticus)
Cited by: 18
Author(s): Eyal Hallali, Fotini Kokou, T.K. Chourasia, Tali Nitzan, Pazit Con, Sheenan Harpaz, Itzhak Mizrahi, Avner Cnaani
Software Mentions: 1
Published: about 8 years ago

10.1264/jsme2.ME16158

Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages
Cited by: 11
Author(s): Takumi Murakami, Tomio Segawa, Roman Dial, Nozomu Takeuchi, Shiro Kohshima, Yuichi Hongoh
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0208344

De novo transcriptome assembly of the Chinese pearl barley, adlay, by full-length isoform and short-read RNA sequencing
Cited by: 9
Author(s): Sang-Ho Kang, Jong-Yeol Lee, Tae‐Ho Lee, Soo-Yun Park, Chang-Kug Kim
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0157828

A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data
Cited by: 8
Author(s): Gregory R. Smith, Marc R. Birtwistle
Software Mentions: 1
Published: over 10 years ago

10.1186/s12934-021-01624-0

Expression of antibody fragments in Saccharomyces cerevisiae strains evolved for enhanced protein secretion
Cited by: 17
Author(s): Yanyan Wang, Xiaowei Li, Xin Chen, Jens Nielsen, Dina Petranović, Verena Siewers
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.47549

A genetic selection reveals functional metastable structures embedded in a toxin-encoding mRNA
Cited by: 12
Author(s): Sara Masachis, Nicolas J. Tourasse, Claire Lays, Marion Faucher, Sandrine Chabas, Isabelle Iost, Fabien Darfeuille
Software Mentions: 1
Published: over 7 years ago

10.1186/s12934-019-1072-6

Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae
Cited by: 22
Author(s): Alexandra Linda Bergman, John Hellgren, Thomas Moritz, Verena Siewers, Jens Nielsen, Yun Chen
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-019-5512-9

Sex differences in gene regulation in the dorsal root ganglion after nerve injury
Cited by: 52
Author(s): K Stephens, Weiqiang Zhou, Zhicheng Ji, Zhiyong Chen, Shaoqiu He, Hongkai Ji, Yun Guan, Sean D. Taverna
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0181101

The nature of the GRE influences the screening for GR-activity enhancing modulators
Cited by: 8
Author(s): Karen Dendoncker, Steven Timmermans, Kelly Van Looveren, Lode De Cauwer, Karolien De Bosscher, Claude Libert
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0240939

Transcriptomic analysis of seed germination improvement of Andrographis paniculata responding to air plasma treatment
Cited by: 4
Author(s): Jiayun Tong, Rui He, Xiaoting Tang, Mingzhi Li, Jie Wan
Software Mentions: 1
Published: about 6 years ago

10.1186/s12934-018-0993-9

Mutational Mtc6p attenuates autophagy and improves secretory expression of heterologous proteins in Kluyveromyces marxianus
Cited by: 12
Author(s): Yang Liu, Wenjuan Mo, Tianfang Shi, Mengzhu Wang, Jungang Zhou, Yao Yu, Wen-Shan Yew, Hong Lü
Software Mentions: 1
Published: about 8 years ago

10.3390/nu12061691

Effect of Exclusive Enteral Nutrition and Corticosteroid Induction Therapy on the Gut Microbiota of Pediatric Patients with Inflammatory Bowel Disease
Cited by: 15
Author(s): Lara Hart, Yasamin Farbod, Jake C. Szamosi, Masato Yamamoto, Philip Britz‐McKibbin, Camilla Halgren, Mary Zachos, Nikhil Pai
Software Mentions: 1
Published: over 6 years ago

10.3390/nu12051464

Maternal Protein Restriction in Rats Alters the Expression of Genes Involved in Mitochondrial Metabolism and Epitranscriptomics in Fetal Hypothalamus
Cited by: 7
Author(s): Morgane Frapin, Simon Guignard, Dimitri Meistermann, Isabelle Grit, Valentine S. Moullé, Vincent Paillé, Patricia Parnet, Valérie Amarger
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21041237

Discrete Hedgehog Factor Expression and Action in the Developing Phallus
Cited by: 5
Author(s): Gerard A. Tarulli, Andrew J Pask, Marilyn B. Renfree
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0213872

Alterations of the MEK/ERK, BMP, and Wnt/β-catenin pathways detected in the blood of individuals with lymphatic malformations
Cited by: 8
Author(s): Tae-Han Kim, E. Tafoya, Malcolm P. Chelliah, Ramrada Lekwuttikarn, Li Jiang, Kavita Y. Sarin, Joyce Teng
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0244364

Response of bitter and sweet Chenopodium quinoa varieties to cucumber mosaic virus: Transcriptome and small RNASeq perspective
Cited by: 2
Author(s): Nourolah Soltani, Margaret Staton, Kimberly D. Gwinn
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21041536

A microRNA Expression Profile as Non-Invasive Biomarker in a Large Arrhythmogenic Cardiomyopathy Cohort
Cited by: 19
Author(s): Maria Bueno Marinas, Rudy Celeghin, Marco Cason, Riccardo Bariani, Anna Chiara Frigo, Joanna Jager, Petros Syrris, Perry Elliott, Barbara Bauce, Gaetano Thiene, Domenico Corrado, Cristina Basso, Kalliopi Pilichou
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0217276

Inhibition of immune checkpoints PD-1, CTLA-4, and IDO1 coordinately induces immune-mediated liver injury in mice
Cited by: 29
Author(s): Timothy Affolter, Heather P. Llewellyn, Derek W. Bartlett, Qing Zong, Shuhua Xia, Vince R. Torti, Changhua Ji
Software Mentions: 1
Published: over 7 years ago

10.1186/s12967-019-1983-3

The circulating exosomal microRNAs related to albuminuria in patients with diabetic nephropathy
Cited by: 48
Author(s): Hyoungnae Kim, Yun-Ui Bae, Jin Seok Jeon, Hyunjin Noh, Hyeong Kyu Park, Dong Won Byun, Dong Cheol Han, Seongho Ryu, Soon Hyo Kwon
Software Mentions: 1
Published: over 7 years ago

10.1111/1751-7915.13343

Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation
Cited by: 11
Author(s): Zongjin Li, Qing Pan, Yunzhu Xiao, Xingxing Fang, Ruoping Shi, Chunxiang Fu, Antoine Danchin, Chenjiang You
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0177928

Serum microRNA signatures as "liquid biopsies" for interrogating hepatotoxic mechanisms and liver pathogenesis in human
Cited by: 38
Author(s): Julian Krauskopf, Theo M. de Kok, Shelli Schomaker, Mark Gosink, Deborah A. Burt, Patricia Chandler, Roscoe L. Warner, Kent J. Johnson, Florian Caiment, Jos Kleinjans, Jiri Aubrecht
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0233646

Gut microbial diversity, inflammation, and oxidative stress are associated with tacrolimus dosing requirements early after heart transplantation
Cited by: 13
Author(s): Douglas L. Jennings, Bruno Bohn, A.M. Zuver, Duygu Onat, M. Gaine, E.A. Royzman, Jonathan Hupf, Danielle L. Brunjes, F. Latif, Susan Restaino, A.R. Garan, V.K. Topkara, Hiroo Takayama, Koji Takeda, Yoshifumi Naka, Maryjane Farr, Renu Nandakumar, Anne Catrin Uhlemann, P.C. Colombo, Ryan T. Demmer, M. Yuzefpolskaya
Software Mentions: 1
Published: over 6 years ago

10.1111/1751-7915.13738

Transcriptional profiling of the stringent response mutant strain E. coli SR reveals enhanced robustness to large‐scale conditions
Cited by: 2
Author(s): Martin Ziegler, Julia Zieringer, Ralf Takors
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0250649

Novel dopamine receptor 3 antagonists inhibit the growth of primary and temozolomide resistant glioblastoma cells
Cited by: 3
Author(s): Sarah Williford, Catherine Libby, Adetokunbo Ayokanmbi, Arphaxad Otamias, Juan Gordillo, Emily R. Gordon, Sara J. Cooper, Matthew Redmann, Yanjie Li, Corinne E. Griguer, Jianhua Zhang, Марек Напиерала, Subramaniam Ananthan, Anita B. Hjelmeland
Software Mentions: 1
Published: over 5 years ago

10.3390/metabo11090601

A Role for Inositol Pyrophosphates in the Metabolic Adaptations to Low Phosphate in Arabidopsis
Cited by: 10
Author(s): Eric Land, Caitlin Cridland, Branch Craige, Anna Dye, Sherry B. Hildreth, Rich F. Helm, Glenda E. Gillaspy, Imara Y. Perera
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0194522

A bi-stable feedback loop between GDNF, EGR1, and ERα contribute to endocrine resistant breast cancer
Cited by: 4
Author(s): Sachi Horibata, Edward J. Rice, Hui Zheng, Chinatsu Mukai, Tinyi Chu, Brooke A. Marks, Scott A. Coonrod, Charles G. Danko
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms21072636

Underlying Ossification Phenotype in a Murine Model of Metastatic Synovial Sarcoma
Cited by: 2
Author(s): Matthew Kirkham, Austen Kalivas, Kaniz Fatema, Sarah Luelling, B Dubanský, Benjamin Dubansky, Kevin B. Jones, Jared J. Barrott
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21072370

Photobiomodulation Mediates Neuroprotection against Blue Light Induced Retinal Photoreceptor Degeneration
Cited by: 27
Author(s): Nora Heinig, Ulrike Schumann, Daniela Calzia, Isabella Panfoli, Marius Ader, Mirko H. H. Schmidt, Richard Funk, Cora Roehlecke
Software Mentions: 1
Published: over 6 years ago

10.3390/nu13031030

Characterization of the Luminal and Mucosa-Associated Microbiome along the Gastrointestinal Tract: Results from Surgically Treated Preterm Infants and a Murine Model
Cited by: 11
Author(s): Ingeborg Klymiuk, Georg Singer, Christoph Castellani, Slave Trajanoski, Beate Obermüller, Holger Till
Software Mentions: 1
Published: over 5 years ago

10.1590/0074-02760200547

Transcriptome comparison of dengue-susceptible and -resistant field derived strains of Colombian Aedes aegypti using RNA-sequencing
Cited by: 3
Author(s): Heather Coatsworth, Paola A. Caicedo, Geoffrey L. Winsor, Fiona S. L. Brinkman, Clara B. Ocampo, Carl Lowenberger
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0177901

The role of the zinc finger protein ZC3H32 in bloodstream-form Trypanosoma brucei
Cited by: 18
Author(s): Claudius Klein, Monica Terrao, Christine Clayton
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms21083009

Human NANOS1 Represses Apoptosis by Downregulating Pro-Apoptotic Genes in the Male Germ Cell Line
Cited by: 5
Author(s): Damian Mikolaj Janecki, Erkut Ilaslan, Maciej Jerzy Smialek, Marcin Sajek, Maciej Kotecki, Barbara Ginter-Matuszewska, Patryk Kraiński, Kamila Kusz-Zamelczyk
Software Mentions: 1
Published: over 6 years ago

10.1007/s12032-021-01572-0

The novel LSD1 inhibitor ZY0511 suppresses diffuse large B-cell lymphoma proliferation by inducing apoptosis and autophagy
Cited by: 6
Author(s): Huan Liu, Jing Wei, Na Sang, Xi Zhong, Xia Zhou, Xinyu Yang, Jing Zhang, Zeping Zuo, Yang Zhou, Shengyong Yang, Jun-Rong Du, Yinglan Zhao
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pgen.1007642

Activating PAX gene family paralogs to complement PAX5 leukemia driver mutations
Cited by: 3
Author(s): Matthew R. Hart, Donovan J. Anderson, Christopher C. Porter, Tobias Neff, Michael Levin, Marshall S. Horwitz
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.1007169

Mutations in THAP1/DYT6 reveal that diverse dystonia genes disrupt similar neuronal pathways and functions
Cited by: 56
Author(s): Zuchra Zakirova, Tomas Fanutza, Justine Bonet, Ben Readhead, Weijia Zhang, Zhengzi Yi, Geneviève Beauvais, Thomas P. Zwaka, Laurie J. Ozelius, Robert D. Blitzer, Pedro Gonzalez‐Alegre, Michelle E. Ehrlich
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1007090

Regulation of transcription elongation in response to osmostress
Cited by: 19
Author(s): Andréa Silva, Santiago Cavero, Victoria Begley, Carme Solé, René Böttcher, Sebastián Chávez, Francesc Posas, Eulàlia de Nadal
Software Mentions: 1
Published: almost 9 years ago

10.1155/2018/4932905

Transcriptome Remodeling of Differentiated Cells during Chronological Ageing of Yeast Colonies: New Insights into Metabolic Differentiation
Cited by: 10
Author(s): Derek Wilkinson, Jana Maršíková, Otakar Hlaváček, Gregor D. Gilfillan, Eva Ježková, Ragnhild Aaløkken, Libuše Váchová, Zdena Palková
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1008732

The transcription and export complex THO/TREX contributes to transcription termination in plants
Cited by: 10
Author(s): Ghazanfar Abbas Khan, Jules Deforges, Rodrigo S. Reis, Yi-Fang Hsieh, Jonatan Montpetit, Wojciech Antosz, Luca Santuari, Christian S. Hardtke, Klaus D. Grasser, Yves Poirier
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21103595

Comparative Transcriptome Analysis of Two Aegilops tauschii with Contrasting Drought Tolerance by RNA-Seq
Cited by: 18
Author(s): Xinpeng Zhao, Shenglong Bai, Lechen Li, Xue Han, Jia-hui Li, Yumeng Zhu, Yuan Fang, Dale Zhang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1009543

Multi-omics approach identifies germline regulatory variants associated with hematopoietic malignancies in retriever dog breeds
Cited by: 9
Author(s): Judith Evans, Heidi G. Parker, Gerard R. Rutteman, Jocelyn Plassais, Guy C. M. Grinwis, Alex C. Harris, Susan E. Lana, Elaine A. Ostrander
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1009821

RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics
Cited by: 14
Author(s): Donghui Choe, Richard Szubin, Saugat Poudel, Anand V. Sastry, Yoseb Song, Yong Jae Lee, Suhyung Cho, Jaehyung Kim, Byung-Kwan Cho
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-021-07785-x

Simultaneous changes in anthocyanin, chlorophyll, and carotenoid contents produce green variegation in pink–leaved ornamental kale
Cited by: 7
Author(s): Yang Liu, Xin Feng, Yuting Zhang, Fuhui Zhou, Pengfang Zhu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-021-07513-5

Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data
Cited by: 3
Author(s): B. E. A. Fantinatti, Érika Stefani Perez, Bruna Tereza Thomazini Zanella, Jéssica Silvino Valente, Tassiana Gutierrez de Paula, Edson Assunção Mareco, Robson Francisco Carvalho, Silvano Piazza, Michela Alessandra Denti, Maeli Dal-Pai-Silva
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1008596

Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types
Cited by: 13
Author(s): Ke Chen, Amitesh Anand, Connor A. Olson, Troy E. Sandberg, Ye Gao, Nathan Mih, Jaehyung Kim
Software Mentions: 1
Published: almost 6 years ago

10.1155/2019/3984906

Suppression of Alzheimer’s Disease-Like Pathology Progression by Mitochondria-Targeted Antioxidant SkQ1: A Transcriptome Profiling Study
Cited by: 24
Author(s): Natalia A. Stefanova, Nikita I. Ershov, N. G. Kolosova
Software Mentions: 1
Published: over 7 years ago

10.1155/2019/1681972

Fusobacterium nucleatumFacilitates Apoptosis, ROS Generation, and Inflammatory Cytokine Production by Activating AKT/MAPK and NF-κB Signaling Pathways in Human Gingival Fibroblasts
Cited by: 48
Author(s): Wenyan Kang, Zhilong Jia, Di Tang, Zhanwei Zhang, Hui Gao, Kunlun He, Qiang Feng
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms21124505

Hub Proteins Involved in RAW 264.7 Macrophages Exposed to Direct Current Electric Field
Cited by: 1
Author(s): Huijuan Li, Shibin Liu, Yongqian Du, Jie Tan, Jiayi Luo, Yu Sun
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21124202

Impaired Expression of Chloroplast HSP90C Chaperone Activates Plant Defense Responses with a Possible Link to a Disease-Symptom-Like Phenotype
Cited by: 9
Author(s): Shaikhul Islam, Sachin Ashok Bhor, Keisuke Tanaka, Hikaru Sakamoto, Takashi Yaeno, Hidetaka Kaya, Kappei Kobayashi
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1005287

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks
Cited by: 35
Author(s): Song-Yao Zhang, Shaowu Zhang, Lian Liu, Jia Meng, Yufei Huang
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pcbi.1007562

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection
Cited by: 10
Author(s): Jinyuan Yan, Henri Estanbouli, Chen Liao, Wook Kim, Jonathan M. Monk, Rayees Rahman, Mini Kamboj, Bernhard Ø. Palsson, Wang Qiu, João B. Xavier
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms21124222

Pleiotropic Functions of FoxN1: Regulating Different Target Genes during Embryogenesis and Nymph Molting in the Brown Planthopper
Cited by: 1
Author(s): Yuxuan Ye, Chuan‐Xi Zhang
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21134615

Integrated RNA-seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots
Cited by: 18
Author(s): Weilong Kong, Chenhao Zhang, Yalin Qiang, Hua Zhong, Gangqing Zhao, Yangsheng Li
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pbio.2006134

KDM5 histone demethylases repress immune response via suppression of STING
Cited by: 89
Author(s): Lizhen Wu, Jian Cao, Wesley L. Cai, Sabine M. Lang, J.R. Horton, Daniel J. Jansen, Zongzhi Z. Liu, Jocelyn F. Chen, Meiling Zhang, Bryan T. Mott, Katherine Pohida, Ganesha Rai, Stephen C. Kales, Mark J. Henderson, Xin Hu, Ajit Jadhav, David J. Maloney, Anton Simeonov, Shu Zhu, Akiko Iwasaki, Matthew D. Hall, Xiaodong Cheng, Gerald S. Shadel, Qin Yan
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pbio.2004328

The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen–encoding var genes
Cited by: 56
Author(s): Gerry Tonkin‐Hill, Leily Trianty, Rintis Noviyanti, Hanh Thi Ngoc Nguyen, Boni F. Sebayang, Daniel A. Lampah, Jutta Marfurt, Simon A. Cobbold, Janavi S. Rambhatla, Malcolm J. McConville, Stephen J. Rogerson, Graham V. Brown, Karen P. Day, Ric N. Price, Nicholas M. Anstey, Anthony T. Papenfuss, Michael Duffy
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pbio.2000949

Pancreas lineage allocation and specification are regulated by sphingosine-1-phosphate signalling
Cited by: 24
Author(s): Ioannis Serafimidis, Eva Rodriguez-Aznar, Mathias Lesche, Kazuaki Yoshioka, Yoh Takuwa, Andreas Dahl, Duojia Pan, Anthony Gavalas
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pbio.1002558

Disruption of an Evolutionarily Novel Synaptic Expression Pattern in Autism
Cited by: 70
Author(s): Xiling Liu, Dingding Han, Mehmet Somel, Xi Jiang, Hai Hu, Patricia Guijarro, Ning Zhang, Amanda Mitchell, Tobias B. Halene, John J. Ely, Chet C. Sherwood, Patrick R. Hof, Zilong Qiu, Svante Pääbo, Schahram Akbarian, Philipp Khaitovich
Software Mentions: 1
Published: about 10 years ago

10.1155/2019/2503924

Transcriptome Analysis and Emerging Driver Identification of CD8+ T Cells in Patients with Vitiligo
Cited by: 7
Author(s): Qiancheng Deng, Jingchao Wei, Puyu Zou, Yangfan Xiao, Zhuotong Zeng, Yaqian Shi, Yi Zhan, Huiming Zhang, Boyu Tang, Qinghai Zeng, Rong Xiao
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms21144823

Distal-Less Homeobox 5 Is a Therapeutic Target for Attenuating Hypertrophy and Apoptosis of Mesenchymal Progenitor Cells
Cited by: 6
Author(s): John Twomey‐Kozak, Salomi Desai, Wenguang Liu, Neill Y. Li, Nicholas J. Lemme, Qian Chen, Brett D. Owens, Chathuraka T. Jayasuriya
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pbio.3000640

MKS-NPHP module proteins control ciliary shedding at the transition zone
Cited by: 25
Author(s): Delphine Gogendeau, Michel Lemullois, P. Le Borgne, Manon Castelli, Anne Aubusson-Fleury, Olivier Arnaiz, Jean Cohen, Christine Vesque, Sylvie Schneider‐Maunoury, Khaled Bouhouche, France Koll, Anne‐Marie Tassin
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21145076

Expression Profiling and Functional Characterization of miR-26a and miR-130a in Regulating Zhongwei Goat Hair Development via the TGF-β/SMAD Pathway
Cited by: 9
Author(s): Yangyang Ding, Xianglan Xue, Zhanfa Liu, Yong Ye, Ping Xiao, Yong‐Jin Pu, Weijun Guan, Joram M. Mwacharo, Yuehui Ma, Qianjun Zhao
Software Mentions: 1
Published: over 6 years ago

10.1186/s12920-021-00957-4

Robust biomarker discovery for hepatocellular carcinoma from high-throughput data by multiple feature selection methods
Cited by: 13
Author(s): Zishuang Zhang, Zhi-Ping Liu
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21155284

Shade Effects on Peanut Yield Associate with Physiological and Expressional Regulation on Photosynthesis and Sucrose Metabolism
Cited by: 18
Author(s): Tingting Chen, Huajian Zhang, Ruier Zeng, Xinyue Wang, Lüping Huang, Leidi Wang, Xuewen Wang, Lei Zhang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pbio.3000287

Placental chemokine compartmentalisation: A novel mammalian molecular control mechanism
Cited by: 16
Author(s): Kit Ming Lee, G. L. Wilson, Marieke Pingen, Ayumi Fukuoka, Christopher A.H. Hansell, Robin Bartolini, Laura Medina-Ruiz, Gerard J. Graham
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pbio.3001097

Nonsense-mediated decay controls the reactivation of the oncogenic herpesviruses EBV and KSHV
Cited by: 7
Author(s): Michiel van Gent, Adrian Reich, Sadanandan E. Velu, Michaela U. Gack
Software Mentions: 1
Published: over 5 years ago

10.1155/2020/7370157

Elevated Glutathione Peroxidase 2 Expression Promotes Cisplatin Resistance in Lung Adenocarcinoma
Cited by: 29
Author(s): Du He, Chen Bi, Nanlin Jiao, Yanhua Liu, Shuai Sun, Youwei Zhang
Software Mentions: 1
Published: over 6 years ago

10.3390/plants9091162

Gene Expression Profiles and Flavonoid Accumulation during Salt Stress in Ginkgo biloba Seedlings
Cited by: 49
Author(s): Ningtao Xu, Sian Liu, Zhaogeng Lu, Siyu Pang, Lu Wang, Li Wang, Weixing Li
Software Mentions: 1
Published: about 6 years ago

10.1155/2020/7895293

Bu-Shen-Yi-Sui Capsule, an Herbal Medicine Formula, Promotes Remyelination by Modulating the Molecular Signals via Exosomes in Mice with Experimental Autoimmune Encephalomyelitis
Cited by: 10
Author(s): Peiyuan Zhao, Jing Ji, Xihong Liu, Hui Zhao, Bin Xue, Liang-Yun Jin, Yongping Fan, Wenjing Zhao, Lei Wang
Software Mentions: 1
Published: over 6 years ago

10.1073/pnas.2026183118

Use of NAD tagSeq II to identify growth phase-dependent alterations in E. coli RNA NAD + capping
Cited by: 14
Author(s): Hailei Zhang, Huan Zhong, Xufeng Wang, Shoudong Zhang, Xiaojian Shao, Hao Hu, Zhi‐Ling Yu, Zongwei Cai, Xuemei Chen, Yiji Xia
Software Mentions: 1
Published: over 5 years ago

10.1073/pnas.1912074117

Methylation-directed glycosylation of chromatin factors represses retrotransposon promoters
Cited by: 21
Author(s): Mathieu Boulard, Sofia Rucli, John Edwards, Timothy H. Bestor
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21176137

Photosystem Disorder Could be the Key Cause for the Formation of Albino Leaf Phenotype in Pecan
Cited by: 2
Author(s): Jiyu Zhang, Tao Wang, Zhemin Jia, Xuehua Zhang, Yongzhi Liu, Gang Wang
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms21176180

Early Molecular Events during Onset of Diapause in Silkworm Eggs Revealed by Transcriptome Analysis
Cited by: 20
Author(s): Jing Gong, Xiaokun Zheng, Shan Zhao, Lingzhen Yang, Xue Zhao, Zhiping Fan, Miao Tang
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms21176376

MBNL1-Associated Mitochondrial Dysfunction and Apoptosis in C2C12 Myotubes and Mouse Skeletal Muscle
Cited by: 6
Author(s): Susumu Yokoyama, Yoshitaka Ohno, Tatsuro Egawa, Kazuya Ohashi, Ryota Ito, Huascar Pedro Ortuste Quiroga, Tomohiro Yamashita, Katsumasa Goto
Software Mentions: 1
Published: about 6 years ago

10.1073/pnas.1811768116

Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain
Cited by: 44
Author(s): Anne L. Sapiro, Anat Shmueli, Gilbert L. Henry, Qin Li, Tali Shalit, Orly Yaron, Yoav Paas, Galit Shohat-Ophir
Software Mentions: 1
Published: almost 8 years ago

10.1007/s13238-020-00811-w

Host metabolism dysregulation and cell tropism identification in human airway and alveolar organoids upon SARS-CoV-2 infection
Cited by: 63
Author(s): Rongjuan Pei, Jianqi Feng, Yecheng Zhang, Hao Sun, Lian Li, Xuejie Yang, Jiangping He, Shuqi Xiao, Ji Xiong, Ying Lin, Kai Wen, Hongwei Zhou, Jiekai Chen, Zhili Rong, Xinwen Chen
Software Mentions: 1
Published: almost 6 years ago

10.3390/plants9081006

Tumorous Stem Development of Brassica Juncea: A Complex Regulatory Network of Stem Formation and Identification of Key Genes in Glucosinolate Biosynthesis
Cited by: 6
Author(s): Mengyao Li, Fangjie Xie, Jie Li, Bo Sun, Yunbo Luo, Yong Zhang, Yan Wang, Fen Zhang, Yunting Zhang, Yuanxiu Lin, Xiaorong Wang, Haoru Tang
Software Mentions: 1
Published: over 6 years ago

10.1093/pcmedi/pbaa037

Vegetarian diets, circulating miRNA expression and healthspan in subjects living in the Blue Zone
Cited by: 9
Author(s): Tiantian Liu, Nicole M. Gatto, Zhong Chen, Hongyu Qiu, Grace Lee, Penelope J. Duerksen-Hughes, Gary E. Fraser, Charles Wang
Software Mentions: 1
Published: about 6 years ago

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