bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-50357-z

A ribosomal protein S5 isoform is essential for oogenesis and interacts with distinct RNAs in Drosophila melanogaster
Cited by: 25
Author(s): Jian Kong, Hong Han, Julie Bergalet, Louis Philip Benoit Bouvrette, Greco Hernández, Nam Sung Moon, Hojatollah Vali, Éric Lécuyer, Paul Lasko
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-50388-6

Direct conversion of fibroblasts into urothelial cells that may be recruited to regenerating mucosa of injured urinary bladder
Cited by: 10
Author(s): Yuta Inoue, Tsunao Kishida, Shin-ichiro Kotani, Mika Akiyoshi, Hideto Taga, Makoto Seki, Osamu Ukimura, Osam Mazda
Software Mentions: 2
Published: about 7 years ago

10.15252/emmm.201911917

Zinc inhibits lethal inflammatory shock by preventing microbe‐induced interferon signature in intestinal epithelium
Cited by: 11
Author(s): Jolien Souffriau, Steven Timmermans, Tineke Vanderhaeghen, Charlotte Wallaeys, Kelly Van Looveren, Lindsy Aelbrecht, Sylviane Dewaele, Jolien Vandewalle, Evy Goossens, Serge Verbanck, Filip Boyen, Melanie Eggermont, Lindsey De Commer, Riet De Rycke, Michiel De Bruyne, Raúl Y. Tito, Marlies Ballegeer, Sofie Vandevyver, Tiago Velho, Luís F. Moita, Tino Hochepied, Karolien De Bosscher, Jeroen Raes, Filip Van Immerseel, Rudi Beyaert, Claude Libert
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0235962

Comparative transcriptome analysis provides insights into the molecular mechanism underlying double fertilization between self-crossed Solanum melongena and that hybridized with Solanum aethiopicum
Cited by: 4
Author(s): Dandan Li, Siqi Li, Wenjia Li, Ake Liu, Yaqin Jiang, Guiyun Gan, Weiliu Li, Xuyu Liang, Yu Ning, Riyuan Chen, Yikui Wang
Software Mentions: 2
Published: over 6 years ago

10.15252/emmm.202114323

Very‐low‐carbohydrate diet enhances human T‐cell immunity through immunometabolic reprogramming
Cited by: 39
Author(s): Simon Hirschberger, Gabriele Strauß, David Effinger, Xaver Marstaller, Alicia Ferstl, Martin B. Müller, Tingting Wu, Max Hübner, Tim Rahmel, Hannah Mascolo, Nicole Exner, Julia Heß, Friedrich W. Kreth, Kristian Unger, Simone Kreth
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-50970-y

Static magnetic field regulates Arabidopsis root growth via auxin signaling
Cited by: 26
Author(s): Yue Jin, Wei Guo, Xupeng Hu, Mengmeng Liu, Xiang Xu, Fenhong Hu, Yiheng Lan, Chenkai Lv, Yanwen Fang, Mengyu Liu, Tieliu Shi, Shisong Ma, Zhicai Fang, Jirong Huang
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-50298-7

CD138 plasma cells may predict brain metastasis recurrence following resection and stereotactic radiosurgery
Cited by: 3
Author(s): M. Soike, Jennifer Logue, Shadi Qasem, Ryan T. Hughes, E. McTyre, Jing Su, Pierre L. Triozzi, Maurizio Bendandi, Hui-Wen Lo, Tamjeed Ahmed, Stacey S. O’Neill, Waldemar Debinski, Boris Pasche, Kounosuke Watabe, Lance D. Miller, Michael D. Chan, Jimmy Ruiz
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.23670

DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids
Cited by: 101
Author(s): Sebastián Cánovas, Elena Ivanova, Raquel Romar, Soledad García-Martínez, Cristina Soriano‐Úbeda, Francisco Alberto García–Vázquez, Heba Saadeh, Simon Andrews, Gavin Kelsey, Pilar Coy
Software Mentions: 2
Published: almost 10 years ago

10.15252/emmm.201506111

Peroxisome proliferator‐activated receptor gamma (PPARγ) is central to the initiation and propagation of human angiomyolipoma, suggesting its potential as a therapeutic target
Cited by: 10
Author(s): Oren Pleniceanu, Racheli Shukrun, Dorit Omer, Einav Vax, Itamar Kanter, Klaudyna Dziedzic, Naomi Pode‐Shakked, Michal Mark‐Daniei, Sara Pri‐Chen, Yehudit Gnatek, Hadas Alfandary, Nira Varda‐Bloom, Dekel D. Bar-Lev, Naomi Bollag, Rachel Shtainfeld, Leah Armon, Achia Urbach, Tomer Kalisky, Arnon Nagler, Orit Harari‐Steinberg, Jack L. Arbiser, Benjamin Dekel
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-019-52268-5

Gene expression profile of Aedes aegypti females in courtship and mating
Cited by: 11
Author(s): Diego Peres Alonso, Melina Campos, Heitor Troca, Rafael Kunii, Frédéric Tripet, Paulo Eduardo Martins Ribolla
Software Mentions: 2
Published: about 7 years ago

10.15252/emmm.201708736

Deficiency in intestinal epithelial O‐GlcNAcylation predisposes to gut inflammation
Cited by: 45
Author(s): Mingli Zhao, Xin Xiong, Kai Ren, Bing Xu, Meng Cheng, Chinmayi S Sahu, Kaichun Wu, Yongzhan Nie, Zan Huang, Richard S. Blumberg, Xiaonan Han, Hai Bin Ruan
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0179531

Combining 'omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut
Cited by: 96
Author(s): Angela Kruse, Somayeh Fattah-Hosseini, Surya Saha, Richard S. Johnson, EricaRose Warwick, Kasie Sturgeon, Lukas A. Mueller, Michael J. MacCoss, Robert G. Shatters, Michelle Heck
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-019-52648-x

Temporal and spatial dynamics of Bacteria, Archaea and protists in equatorial coastal waters
Cited by: 30
Author(s): Caroline Chénard, Winona Wijaya, Daniel Vaulot, Adriana Lopes dos Santos, Patrick Martin, Avneet Kaur, Federico M. Lauro
Software Mentions: 2
Published: about 7 years ago

10.1016/j.dib.2021.107111

RNA sequencing data for gamma radiation response in the extremotolerant tardigrade Ramazzottius varieornatus
Cited by: 3
Author(s): Yuki Yoshida, Daiki D. Horikawa, Tetsuya Sakashita, Yuichiro Yokota, Yasuhiko Kobayashi, Masaru Tomita, Kazuharu Arakawa
Software Mentions: 2
Published: over 5 years ago

10.1016/j.dib.2020.105562

Transcriptomic data indicating differential expressed genes between HIV-1 Associated Nephropathy (HIVAN) mouse model (Tg26) and wildtype mice
Cited by: 2
Author(s): V. Praveen Chakravarthi, Sireesha Yerrathota, Priyanka S. Radadiya, Clark Bloomer, Sumedha Gunewardhana, Madhulika Sharma
Software Mentions: 2
Published: over 6 years ago

10.1016/j.dib.2020.106008

Dataset for transcriptome analysis of Salmonella enterica subsp. enterica serovar Typhimurium strain 14028S response to starvation
Cited by: 1
Author(s): Natalia Gogoleva, С. В. Черкасов, Alexander S. Balkin, А. О. Плотников, Elena Shagimardanova, A.M. Subbot, С. В. Черкасов, Alexander A. Kamnev
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-53391-z

A human expression system based on HEK293 for the stable production of recombinant erythropoietin
Cited by: 32
Author(s): Christine Lin Chin, Justin B. Goh, Harini Srinivasan, Kaiwen Ivy Liu, Gowher Ali, Raghuvaran Shanmugam, Hsueh Lee Lim, Matthew S F Choo, Wen Qin Tang, Andy Hee-Meng Tan, Terry Nguyen-Khuong, Meng How Tan, Say Kong Ng
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0218352

Fall armyworm (Spodoptera frugiperda Smith) feeding elicits differential defense responses in upland and lowland switchgrass
Cited by: 15
Author(s): Nathan A. Palmer, Saumik Basu, Tiffany Heng-Moss, Jeffrey D. Bradshaw, Gautam Sarath, Joe Louis
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-53504-8

Treatment with etanercept and low monocyte concentration contribute to the risk of invasive aspergillosis in patients post allogeneic stem cell transplantation
Cited by: 5
Author(s): Tamara Zoran, Michael Weber, Jan Springer, P. Lewis White, Joachim Bauer, Annika Schober, Claudia Löffler, Bastian Seelbinder, Kerstin Hünniger, Oliver Kurzai, André Scherag, Sascha Schäuble, Oliver Morton, Hermann Einsele, Jörg Linde, Jürgen Löffler
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-54083-4

Peripheral blood mononuclear cell transcriptomes reveal an over-representation of down-regulated genes associated with immunity in HIV-exposed uninfected infants
Cited by: 7
Author(s): Zaneta D. Musimbi, Martin K. Rono, James R. Otieno, Nelson Kibinge, Lynette Isabella Ochola‐Oyier, Etienne P. de Villiers, Eunice Nduati
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-54845-0

Transcriptome-wide Profiling of Cerebral Cavernous Malformations Patients Reveal Important Long noncoding RNA molecular signatures
Cited by: 13
Author(s): Santhilal Subhash, Norman Kalmbach, Florian Wegner, Susanne Petri, Torsten Glomb, Oliver Dittrich–Breiholz, Can Huang, Kiran Kumar Bali, Wolfram S. Kunz, Amir Samii, Helmut Bertalanffy, Chandrasekhar Kanduri, Souvik Kar
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-54545-9

Carcinoembryonic antigen cell adhesion molecule 6 (CEACAM6) in Pancreatic Ductal Adenocarcinoma (PDA): An integrative analysis of a novel therapeutic target
Cited by: 29
Author(s): Ritu Pandey, Muhan Zhou, Sameer Islam, Baowei Chen, Nelson W. Barker, Paul Langlais, Anup Srivastava, Moulun Luo, Laurence Cooke, Eric Weterings, Daruka Mahadevan
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-54055-8

Changes in meta-transcriptome of rumen epimural microbial community and liver transcriptome in young calves with feed induced acidosis
Cited by: 5
Author(s): Wenli Li, S.L. Gelsinger, Andrea Edwards, Christina Riehle, Daniel C. Koch
Software Mentions: 2
Published: almost 7 years ago

10.1093/dnares/dsv014

Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in<i>Paramecium tetraurelia</i>
Cited by: 18
Author(s): Miriam Cheaib, Azim Dehghani Amirabad, Karl Nordström, Marcel H. Schulz, Martín Simón
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-019-55734-2

Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups
Cited by: 18
Author(s): Nobuto Yamamoto, Yanran Wang, Runmao Lin, Yueyang Liang, Yao Liu, Jun Zhu, Lingxia Wang, Shiquan Wang, Huainian Liu, Qi Deng, Shuangcheng Li, Ping Li, Anqi Zheng
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-56509-5

Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research
Cited by: 6
Author(s): Susann Haehnel, Kristin Reiche, Dennis Loeffler, Andreas Horn, Conny Blumert, Sven-Holger Puppel, Nicole Kaiser, Felicitas Rapp, Michael Rade, Friedemann Horn, Juergen Meixensberger, Ingo Bechmann, Frank Gaunitz, Karsten Winter
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.67250

Cardiac pathologies in mouse loss of imprinting models are due to misexpression of H19 long noncoding RNA
Cited by: 6
Author(s): Ki-Sun Park, Beenish Rahat, Hyung Chul Lee, Zu‐Xi Yu, Jacob Noeker, Apratim Mitra, Connor M. Kean, Russell H. Knutsen, Danielle Springer, Claudia Gebert, Beth A. Kozel, Karl Pfeifer
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-56908-8

Nervous system-wide profiling of presynaptic mRNAs reveals regulators of associative memory
Cited by: 9
Author(s): Rachel N. Arey, Rachel Kaletsky, Coleen T. Murphy
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.dnarep.2019.06.006

The roles of the human SETMAR (Metnase) protein in illegitimate DNA recombination and non-homologous end joining repair
Cited by: 14
Author(s): Michael Tellier, Ronald Chalmers
Software Mentions: 2
Published: over 7 years ago

10.1016/j.crbiot.2019.09.001

Increased mAb production in amplified CHO cell lines is associated with increased interaction of CREB1 with transgene promoter
Cited by: 10
Author(s): Hussain Dahodwala, Prashant Kaushik, Vijay Tejwani, Chih‐Chung Kuo, Patrice Ménard, Michael Henry, Bjørn Gunnar Voldborg, Nathan E. Lewis, Paula Meleady, Susan T. Sharfstein
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-020-59067-3

Enhanced pre-pubertal nutrition upregulates mitochondrial function in testes and sperm of post-pubertal Holstein bulls
Cited by: 9
Author(s): Chinju Johnson, Alysha Dance, Igor Kovalchuk, John P. Kastelic, Jacob C. Thundathil
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-59284-w

The Adipocyte Acquires a Fibroblast-Like Transcriptional Signature in Response to a High Fat Diet
Cited by: 48
Author(s): Juli E. Jones, Nabil Rabhi, Joseph Orofino, Ramya Gamini, Valentina Perissi, Cécile Vernochet, Stephen R. Farmer
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.66921

Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction
Cited by: 16
Author(s): Muhammad Arif, Martina Klevstig, Rui Benfeitas, Stephen Doran, Hasan Türkez, Mathias Uhlén, Maryam Clausen, Johannes Wikström, Damla Etal, Cheng Cheng Zhang, Malin Levin, Adil Mardinoğlu, Jan Borén
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-59535-w

A Microbial Signature Identifies Advanced Fibrosis in Patients with Chronic Liver Disease Mainly Due to NAFLD
Cited by: 34
Author(s): Tien S. Dong, William Katzka, Venu Lagishetty, Kayti Luu, Meg Hauer, Joseph R. Pisegna, Jonathan P. Jacobs
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.63595

Foxc1 establishes enhancer accessibility for craniofacial cartilage differentiation
Cited by: 21
Author(s): Pengfei Xu, Haoze V Yu, Kuo-Chang Tseng, Mackenzie Flath, Péter Fábián, Neil Segil, J. Gage Crump
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-60133-z

MicroRNA sequencing of rat hippocampus and human biofluids identifies acute, chronic, focal and diffuse traumatic brain injuries
Cited by: 15
Author(s): Harris A. Weisz, Deborah Kennedy, Steven G. Widen, Heidi Spratt, Stacy L. Sell, Christine Bailey, Melinda Sheffield‐Moore, Douglas S. DeWitt, Donald S. Prough, Harvey S. Levin, Claudia S. Robertson, Helen L. Hellmich
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-60210-3

Increased mitochondrial and lipid metabolism is a conserved effect of Insulin/PI3K pathway downregulation in adipose tissue
Cited by: 6
Author(s): Lucia Bettedi, Anqi Yan, Eugene F. Schuster, Nazif Alic, Lazaros C. Foukas
Software Mentions: 2
Published: over 6 years ago

10.1016/j.cub.2020.12.014

femaleless Controls Sex Determination and Dosage Compensation Pathways in Females of Anopheles Mosquitoes
Cited by: 24
Author(s): Elzbieta Krzywińska, Luca Ferretti, Jianwei Li, Jian-Chiuan Li, Chun Hong Chen, Jaroslaw Krzywinski
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-61208-7

Evolutionary and Molecular Characterization of liver-enriched gene 1
Cited by: 3
Author(s): Yanna Dang, Jinyang Wang, Chen Liu, Kun Zhang, Jinrong Peng, Jin He
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-61236-3

MicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma
Cited by: 9
Author(s): Christopher B. Lietz, Cassandra Garbutt, William T. Barry, Vikram Deshpande, Yen‐Lin Chen, Santiago Lozano-Calderón, Yao‐Yu Wang, Brian Lawney, David Ebb, Gregory M. Coté, Zhenfeng Duan, Francis J. Hornicek, Edwin Choy, G. Petur Nielsen, Benjamin Haibe‐Kains, John Quackenbush, Dimitrios Spentzos
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-61758-w

Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress
Cited by: 17
Author(s): Tim S. Crawford, Fazeelat Karamat, Nóra Lehotai, Matilda Rentoft, Jeanette Blomberg, Åsa Strand, Stefan Björklund
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-62174-w

CYP2J2 Modulates Diverse Transcriptional Programs in Adult Human Cardiomyocytes
Cited by: 16
Author(s): Eric A. Evangelista, Theresa Aliwarga, Nona Sotoodehnia, Paul N. Jensen, Barbara McKnight, Rozenn N. Lemaître, Rheem A. Totah, Sina A. Gharib
Software Mentions: 2
Published: over 6 years ago

10.1186/s13054-018-2242-3

Identification of a transcriptome profile associated with improvement of organ function in septic shock patients after early supportive therapy
Cited by: 14
Author(s): Matteo Barcella, Bernardo Bollen Pinto, Daniele Braga, Francesca D’Avila, Federico Tagliaferri, Marie-Angélique Cazalis, Guillaume Monneret, Antoine Herpain, Karim Bendjelid, Cristina Barlassina
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.17290

Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62
Cited by: 114
Author(s): Rowena DeJesus, Francesca Moretti, Gregory McAllister, Zuncai Wang, Philip S. Bergman, Shanming Liu, Elizabeth Frias, John Alford, John S. Reece‐Hoyes, Alicia Lindeman, Jennifer Kelliher, Carsten Russ, Judith Knehr, Walter Carbone, Martin Beibel, Guglielmo Roma, Aylwin Ng, John A. Tallarico, Jeffery A. Porter, Ramnik J. Xavier, Craig Mickanin, Leon O. Murphy, Gregory R. Hoffman, Beat Nyfeler
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-020-62456-3

Blood flow-restricted resistance exercise alters the surface profile, miRNA cargo and functional impact of circulating extracellular vesicles
Cited by: 32
Author(s): Jesper Just, Yan Yan, Jean Farup, Peter Sieljacks, Mette Sloth, Morten T. Venø, Tingting Gu, Frank Vincenzo de Paoli, Jens Randel Nyengaard, Rikke Bæk, Maléne Møller Jørgensen, Jørgen Kjems, Kristian Vissing, Kim Ryun Drasbek
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-62853-8

Network-based metabolic characterization of renal cell carcinoma
Cited by: 48
Author(s): Nishtha Pandey, Vinay Lanke, P. K. Vinod
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-63357-1

Neuronal LXR Regulates Neuregulin 1 Expression and Sciatic Nerve-Associated Cell Signaling in Western Diet-fed Rodents
Cited by: 6
Author(s): Chaitanya K. Gavini, Raiza Bonomo, Virginie Mansuy‐Aubert
Software Mentions: 2
Published: over 6 years ago

10.1186/s13054-019-2670-8

A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock
Cited by: 17
Author(s): Daniele Braga, Matteo Barcella, Antoine Herpain, Federico Aletti, Erik B. Kistler, Bernardo Bollen Pinto, Karim Bendjelid, Cristina Barlassina
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-63230-1

Dysregulated miRNA in a cancer-prone environment: A study of gastric non-neoplastic mucosa
Cited by: 3
Author(s): Binnari Kim, Jiryeon Jang, You Jeong Heo, So Young Kang, Heejin Yoo, Insuk Sohn, Byung Hoon Min, Kyoung Mee Kim
Software Mentions: 2
Published: over 6 years ago

10.1016/j.csbj.2020.07.014

Transcriptome and proteome analyses reveal the regulatory networks and metabolite biosynthesis pathways during the development of Tolypocladium guangdongense
Cited by: 12
Author(s): Jinjie Wang, Min Li, Chenghua Zhang, Huijiao Cheng, Yu Gao, Wang-Qiu Deng, Tai‐Hui Li
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-64498-z

Homeostatic maintenance and age-related functional decline in the Drosophila ear
Cited by: 15
Author(s): Alyona Keder, Camille Tardieu, Liza Malong, Anastasia Filia, Assel Kashkenbayeva, Fay Newton, Marcos Georgiades, Jonathan E. Gale, Michael Lovett, Andrew P. Jarman, Joerg T. Albert
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.40532

Downsizing the molecular spring of the giant protein titin reveals that skeletal muscle titin determines passive stiffness and drives longitudinal hypertrophy
Cited by: 55
Author(s): Ambjorn Brynnel, Yaeren Hernandez, Balázs Kiss, Johan Lindqvist, Maya Adler, Justin Kolb, Robbert van der Pijl, Jochen Gohlke, Joshua Strom, John E. Smith, Coen A.C. Ottenheijm, Henk Granzier
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0212229

A novel polyketide synthase gene cluster in the plant pathogenic fungus Pseudocercospora fijiensis
Cited by: 7
Author(s): Roslyn D. Noar, Elizabeth Thomas, Margaret E. Daub
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.44795

A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis
Cited by: 47
Author(s): Ritu Gupta, Adhish Walvekar, Shun Liang, Zeenat Rashida, Premal Shah, Sunil Laxman
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-020-66455-2

EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells
Cited by: 17
Author(s): Seiko Yoshino, Yusuke Matsui, Yoshikazu Fukui, Masahide Seki, Kiyoshi Yamaguchi, Akane Kanamori, Yurika Saitoh, Teppei Shimamura, Yutaka Suzuki, Yoichi Furukawa, Shuichi Kaneko, Motoharu Seiki, Yoshinori Murakami, Jun‐ichiro Inoue, Takeharu Sakamoto
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0241698

Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation
Cited by: 25
Author(s): Bo Yu, Naresh Doni Jayavelu, Stephanie L. Battle, Jessica C. Mar, Timothy Schimmel, Jacques Cohen, R. David Hawkins
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-66598-2

Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study
Cited by: 31
Author(s): Mohammad Tahseen Al Bataineh, Nihar Ranjan Dash, Pierre Bel Lassen, Bayan Hassan Banimfreg, Aml Mohamed Nada, Eugeni Belda, Karine Clément
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-66286-1

A new brilliantly blue-emitting luciferin-luciferase system from Orfelia fultoni and Keroplatinae (Diptera)
Cited by: 16
Author(s): Vadim R. Viviani, Jaqueline R. Silva, Danilo T. Amaral, Vanessa R. Bevilaqua, Fábio Camargo Abdalla, Bruce R. Branchini, Carl Hirschie Johnson
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-66735-x

RNA sequencing of corneas from two keratoconus patient groups identifies potential biomarkers and decreased NRF2-antioxidant responses
Cited by: 29
Author(s): Vaibhav Shinde, Nan Hu, Alka Mahale, George Maiti, Yassine J. Daoud, Charles G. Eberhart, Azza Maktabi, Albert S. Jun, Samar A Al-Swailem, Shukti Chakravarti
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.57858

Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen
Cited by: 21
Author(s): Hao Zhang, Yang Zhang, Xinyue Zhou, Shaela Wright, Judith Hyle, Lianzhong Zhao, Jie An, Xujie Zhao, Ying Shao, Beisi Xu, Hyeong-Min Lee, Taosheng Chen, Yang Zhou, Xiang Chen, Rui Lu, Chunliang Li
Software Mentions: 2
Published: about 6 years ago

10.1038/s42003-018-0215-3

Sox9 regulates cell state and activity of embryonic mouse mammary progenitor cells
Cited by: 11
Author(s): Naoko Kogata, Philip Bland, Mandy Tsang, Erik Oliemuller, Anne Lowe, Beatrice A. Howard
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-020-67389-5

Blast-induced hearing impairment in rats is associated with structural and molecular changes of the inner ear
Cited by: 9
Author(s): Ying Wang, Rodrigo Urioste, Yanling Wei, Donna M. Wilder, Peethambaran Arun, Venkata Siva Sai Sujith Sajja, Irene D. Gist, Tracy S. Fitzgerald, Weise Chang, Matthew W. Kelley, Joseph B. Long
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 6 years ago

10.1038/s42003-020-01297-2

Redundant type II cadherins define neuroepithelial cell states for cytoarchitectonic robustness
Cited by: 9
Author(s): Kou Hiraga, Yukiko Inoue, Junko Asami, Mayuko Hotta, Yuki Morimoto, Shoji Tatsumoto, Mikio Hoshino, Yasuhiro Go, Tohru Inoue
Software Mentions: 2
Published: about 6 years ago

10.1038/s42003-021-02272-1

Genome-wide CRISPR screen identifies protein pathways modulating tau protein levels in neurons
Cited by: 12
Author(s): Carlos Sanchez, Christopher M. Acker, Audrey Gray, Malini Varadarajan, Chun-Yan Song, Nadire Cochran, Steven Paula, Alicia Lindeman, Shaojian An, Gregory McAllister, John Alford, John S. Reece‐Hoyes, Carsten Russ, Lucas Craig, Ketthsy Capre, Christian Doherty, Gregory R. Hoffman, Sarah J. Luchansky, Manuela Polydoro, Ricardo E. Dolmetsch, Fiona Elwood
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-68098-9

Irradiation dependent inflammatory response may enhance satellite cell engraftment
Cited by: 8
Author(s): Bruno Doreste, Silvia Torelli, Jennifer E. Morgan
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-68235-4

Involvement of Arabidopsis BIG protein in cell death mediated by Myo-inositol homeostasis
Cited by: 3
Author(s): Quentin Bruggeman, Florence Piron‐Prunier, Frédérique Tellier, Jean-Denis Faure, David Latrasse, Deborah Manza‐Mianza, Christelle Mazubert, Sylvie Citerne, Stéphanie Boutet-Mercey, Raphaël Lugan, Catherine Bergounioux, Cécile Raynaud, Moussa Benhamed, Marianne Delarue
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-68040-z

Klf9 is a key feedforward regulator of the transcriptomic response to glucocorticoid receptor activity
Cited by: 20
Author(s): Ian M. Gans, Ellen I. Hartig, Shusen Zhu, Andrea R. Tilden, Lucie N. Hutchins, Nathaniel J. Maki, Joel H. Graber, James A. Coffman
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-021-02516-0

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli
Cited by: 11
Author(s): Irina A. Rodionova, Ye Gao, Anand V. Sastry, Ying Hefner, Hyun Gyu Lim, Dmitry A. Rodionov, Milton H. Saier, Jaehyung Kim
Software Mentions: 2
Published: about 5 years ago

10.1038/s42003-021-02073-6

Mitofusin-2 boosts innate immunity through the maintenance of aerobic glycolysis and activation of xenophagy in mice
Cited by: 15
Author(s): Prashanta Silwal, Jin‐Kyung Kim, Soyeon Jeon, June-Young Lee, Young Jae Kim, Yi Sak Kim, Yeji Seo, Jihye Kim, Soo Yeon Kim, Min Joung Lee, Jun Young Heo, Myeong Ho Jung, Hyun Sik Kim, Dong-Wook Hyun, Jeong Eun Han, Jake Whang, Yang Hoon Huh, Sang‐Hee Lee, Won Do Heo, Jin Man Kim, Jin-Woo Bae, Eun‐Kyeong Jo
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-80859-0

Differences in the bacteriome of swab, saliva, and tissue biopsies in oral cancer
Cited by: 25
Author(s): Divya Gopinath, Rohit Kunnath Menon, Chun Wie Chong, Moinak Banerjee, Swagatika Panda, Deviprasad Mandal, Paresh Kumar Behera, Susanta Roychoudhury, Supriya Kheur, MG Botelho, Newell W. Johnson
Software Mentions: 2
Published: almost 6 years ago

10.1038/s42003-021-02514-2

Moisture modulates soil reservoirs of active DNA and RNA viruses
Cited by: 30
Author(s): Ruonan Wu, Michelle Davison, Yuqian Gao, Carrie Nicora, Jason McDermott, Kristin Burnum-Johnson, Kirsten Hofmockel, Janet K. Jansson
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-80278-1

Neonatal intensive care unit (NICU) exposures exert a sustained influence on the progression of gut microbiota and metabolome in the first year of life
Cited by: 9
Author(s): Polly Soo Xi Yap, Chun Wie Chong, Azanna Ahmad Kamar, Ivan Kok Seng Yap, Yao Mun Choo, Nai Ming Lai, Cindy Shuan Ju Teh
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.11275

Comparative analysis of viral RNA signatures on different RIG-I-like receptors
Cited by: 79
Author(s): Raul Y. Sanchez David, Chantal Combredet, Odile Sismeiro, Marie‐Agnès Dillies, Bernd Jagla, Jean‐Yves Coppée, Marie Mura, Mathilde Guerbois Galla, Philippe Desprès, Frédéric Tangy, Anastassia V. Komarova
Software Mentions: 2
Published: over 10 years ago

10.1038/s42003-020-01264-x

FUBP1 and FUBP2 enforce distinct epigenetic setpoints for MYC expression in primary single murine cells
Cited by: 7
Author(s): Ying Zheng, Wendy Dubois, Craig J. Benham, Eric Batchelor, David Levens
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-021-81226-3

A genome-wide transcriptomic analysis of embryos fathered by obese males in a murine model of diet-induced obesity
Cited by: 6
Author(s): Laura Bernhardt, Marcus Dittrich, Rabih El‐Merahbi, Antoine‐Emmanuel Saliba, Tobias Müller, Grzegorz Sumara, Jörg Vogel, Stefanie Nichols-Burns, Megan Mitchell, Thomas Haaf, Nady El Hajj
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-81387-1

Analysis of ovarian transcriptomes reveals thousands of novel genes in the insect vector Rhodnius prolixus
Cited by: 17
Author(s): Vitor Lima Coelho, Tarcísio Fontenele de Brito, Ingrid Alexandre de Abreu Brito, Maira Arruda Cardoso, Mateus Berni, Helena Araujo, Michael Sammeth, Andrea Pane
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-81790-8

Pre- and postmenopausal women have different core urinary microbiota
Cited by: 19
Author(s): Nadia Ammitzbøll, Benedikt Bau, Caspar Bundgaard‐Nielsen, Annemarie Brusen Villadsen, Ann Maria Jensen, Peter Leutscher, Karin Glavind, Søren Hagstrøm, Louise Thomsen Schmidt Arenholt, Susanne Sørensen
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.70948

Inducible and reversible inhibition of miRNA-mediated gene repression in vivo
Cited by: 17
Author(s): Gaspare La Rocca, Bryan King, Bing Shui, Xiaohua Li, Minsi Zhang, Kemal M. Akat, Paul Ogrodowski, Chiara Mastroleo, Kevin Chen, Vincenzo Cavalieri, Yilun Ma, Viviana Anelli, Doron Betel, Joana A. Vidigal, Thomas Tuschl, Gunter Meister, Craig B. Thompson, Tullia Lindsten, Kevin M. Haigis, Andrea Ventura
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-81888-z

Weighted gene co-expression network analysis identifies modules and functionally enriched pathways in the lactation process
Cited by: 28
Author(s): Mohammad Farhadian, S. A. Rafat, Bahman Panahi, Christopher Mayack
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-81843-y

Low-dose Drosera rotundifolia induces gene expression changes in 16HBE human bronchial epithelial cells
Cited by: 4
Author(s): Fábio Arruda-Silva, Paolo Bellavite, Marta Marzotto
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-81340-2

Screening for potential targets to reduce stenosis in bioprosthetic heart valves
Cited by: 3
Author(s): Rudi Foth, Orr Shomroni, Matthias Sigler, Jürgen Hörer, Julie Cleuziou, Thomas Paul, Katja Eildermann
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-82051-4

Signalling pathways and mechanistic cues highlighted by transcriptomic analysis of primordial, primary, and secondary ovarian follicles in domestic cat
Cited by: 6
Author(s): Shauna Kehoe, Katarina Jewgenow, Paul R. Johnston, Susan Mbedi, Beate C. Braun
Software Mentions: 2
Published: almost 6 years ago

10.1038/s42003-021-02495-2

Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses
Cited by: 1
Author(s): Swetha Rajasekaran, Jalal K. Siddiqui, Jessica Rakijas, Brandon Nicolay, Chen‐Yu Lin, Eshan Khan, Rahi Patel, Robert T. Morris, Emanuel Wyler, Myriam Boukhali, Jayashree Balasubramanyam, Ranjith Kumar, Capucine Van Rechem, Christine Vogel, Sailaja Elchuri, Markus Landthaler, Benedikt Obermayer, Wilhelm Haas, Nicholas J. Dyson, Wayne Miles
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-82726-y

Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota
Cited by: 169
Author(s): Francesco Durazzi, Claudia Sala, Gastone Castellani, Gerardo Manfreda, Daniel Remondini, Alessandra De Cesare
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0210371

Long live the queen, the king and the commoner? Transcript expression differences between old and young in the termite Cryptotermes secundus
Cited by: 20
Author(s): José Manuel Monroy Kuhn, Karen Meusemann, Judith Korb
Software Mentions: 2
Published: almost 8 years ago

10.1038/s42003-021-02339-z

Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus
Cited by: 15
Author(s): Henrique Machado, Yara Seif, George Sakoulas, Connor A. Olson, Ying Hefner, Amitesh Anand, Ying Jones, Richard Szubin, Jaehyung Kim, Victor Nizet, Adam M. Feist
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-020-01353-x

Single-cell analysis of AIMP2 splice variants informs on drug sensitivity and prognosis in hematologic cancer
Cited by: 5
Author(s): Jayoung Ku, Ryul Kim, Dongchan Kim, Daeyoon Kim, Seulki Song, Keonyong Lee, Namseok Lee, Min A Kim, Sung Soo Yoon, Nam Hoon Kwon, Sung Hoon Kim, Yoosik Kim, Youngil Koh
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-69395-z

Developmental transcriptome profiling uncovered carbon signaling genes associated with almond fruit drop
Cited by: 5
Author(s): Chen Guo, Wei Yu, Bo Yang, Mubarek Ayup, Ning Li, Jun Li, Kang Liao, Huan Wang
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1006978

Crosstalk between the tricarboxylic acid cycle and peptidoglycan synthesis in Caulobacter crescentus through the homeostatic control of α-ketoglutarate
Cited by: 51
Author(s): Irnov Irnov, Zhe Wang, Nicholas Jannetty, Julián Bustamante, Kyu Y. Rhee, Christine Jacobs‐Wagner
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-021-82931-9

Direct reprogramming of oligodendrocyte precursor cells into GABAergic inhibitory neurons by a single homeodomain transcription factor Dlx2
Cited by: 9
Author(s): Linda L. Boshans, Heun Soh, William M. Wood, Timothy M. Nolan, Ion Mǎndoiu, Yuchio Yanagawa, Anastasios V. Tzingounis, Akiko Nishiyama
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-82202-7

RNAseq shows an all-pervasive day-night rhythm in the transcriptome of the pacemaker of the heart
Cited by: 7
Author(s): Yanwen Wang, Cali Anderson, Halina Dobrzynski, George Hart, Alicia D’Souza, Mark R. Boyett
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-83380-0

The acute transcriptional responses to dietary methionine restriction are triggered by inhibition of ternary complex formation and linked to Erk1/2, mTOR, and ATF4
Cited by: 15
Author(s): Kirsten P. Stone, Sujoy Ghosh, Jean Paul Kovalik, Manda Orgeron, Desiree Wanders, Landon C. Sims, Thomas W. Gettys
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-82551-3

Arsenic hexoxide has differential effects on cell proliferation and genome-wide gene expression in human primary mammary epithelial and MCF7 cells
Cited by: 8
Author(s): Donguk Kim, Na Yeon Park, Keunsoo Kang, Stuart K. Calderwood, Dong‐Hyung Cho, Ill Ju Bae, Heeyoun Bunch
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1009603

Loss of zebrafish atp6v1e1b, encoding a subunit of vacuolar ATPase, recapitulates human ARCL type 2C syndrome and identifies multiple pathobiological signatures
Cited by: 1
Author(s): Lore Pottie, Wouter Van Gool, Michiel Vanhooydonck, Franz‐Georg Hanisch, Geert Goeminne, Andreja Rajković, Paul Coucke, Patrick Sips, Bert Callewaert
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-020-01456-5

Lysine demethylase 7a regulates murine anterior-posterior development by modulating the transcription of Hox gene cluster
Cited by: 5
Author(s): Yoshiki Higashijima, Naomi Nagai, Masamichi Yamamoto, Takatoshi Kitazawa, Yuuki Kawamura, Azuma Taguchi, Natsuko Nakada, Masaomi Nangaku, Tetsushi Furukawa, Hiroyuki Aburatani, Hiroki Kurihara, Youichiro Wada, Yasuharu Kanki
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-83215-y

Modulating the unfolded protein response with ONC201 to impact on radiation response in prostate cancer cells
Cited by: 7
Author(s): Francesca Amoroso, Kimberley Glass, Reema Singh, Francisco Liberal, R.E. Steele, Sarah Maguire, Rohinton S. Tarapore, Joshua E. Allen, Sandra Van Schaeybroeck, Karl T. Butterworth, Kevin M. Prise, Joe M. O’Sullivan, Suneil Jain, David J. Waugh, Ian G. Mills
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-83752-6

Allelopathic effect of Artemisia argyi on the germination and growth of various weeds
Cited by: 29
Author(s): Jinxin Li, Le Chen, Qiaohuan Chen, Yuhuan Miao, Peng Zheng, Bisheng Huang, Lan-Ping Guo, Dahui Liu, Hongzhi Du
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-83932-4

Melanocortin receptor activation alleviates amyloid pathology and glial reactivity in an Alzheimer’s disease transgenic mouse model
Cited by: 10
Author(s): Jackie K Y Lau, Min Tian, Yang Shen, Shun-Fat Lau, Wing‐Yu Fu, Amy Kit Yu Fu, Nancy Y. Ip
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-83846-1

High abundance of sugar metabolisers in saliva of children with caries
Cited by: 10
Author(s): Muhammed A.P. Manzoor, Sohvi Lommi, Jussi Furuholm, Catharina Sarkkola, Elina Engberg, Sajan C. Raju, Heli Viljakainen
Software Mentions: 2
Published: over 5 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

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Papers Mentioning DESeq2 9,583