bioconductor: cummeRbund | Projects

10.1186/s12859-020-03846-2

ARPIR: automatic RNA-Seq pipelines with interactive report
Cited by: 10
Author(s): Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini, Maria Paola Martelli
Software Mentions: 11
Published: almost 4 years ago

10.1186/s13059-019-1647-x

Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma
Cited by: 48
Author(s): Domenico Alessandro Silvestris, Ernesto Picardi, Valeriana Cesarini, Bruno Fosso, Nicolò Mangraviti, Luca Massimi, Maurizio Martini, Graziano Pesole, Franco Locatelli, Angela Gallo
Software Mentions: 10
Published: over 5 years ago

10.1093/database/bay027

Maser: one-stop platform for NGS big data from analysis to visualization
Cited by: 38
Author(s): Sonoko Kinjo, Norikazu Monma, Sadahiko Misu, Norikazu Kitamura, Junichi Imoto, Kazutoshi Yoshitake, Takashi Gojobori, Kazuho Ikeo
Software Mentions: 10
Published: almost 7 years ago

10.1038/s41598-019-50642-x

Transcriptome Sequencing of Peripheral Blood Mononuclear Cells from Elite Controller-Long Term Non Progressors
Cited by: 11
Author(s): Francisco Díez-Fuertes, Humberto Erick De La Torre Tarazona, Esther Calonge, María Pernas, María del Mar Alonso-Socas, Laura Capa, Javier García-Pérez, Anavaj Sakuntabhai, José Alcamı́
Software Mentions: 8
Published: about 5 years ago

10.1186/1471-2105-16-S11-S4

Epiviz: a view inside the design of an integrated visual analysis software for genomics
Cited by: 3
Author(s): Florin Chelaru, Héctor Corrada Bravo
Software Mentions: 7
Published: about 9 years ago

10.1371/journal.pone.0123380

Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1)
Cited by: 41
Author(s): Christopher Terranova, Sridhar T. Narla, Yu Wei Lee, Jonathan Bard, Abhirath Parikh, Ewa K. Stachowiak, Emmanuel S. Tzanakakis, Michael Buck, Barbara Birkaya, Michal K. Stachowiak
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pbio.3000365

Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis
Cited by: 95
Author(s): Yuqiong Hu, Xiaoye Wang, Boqiang Hu, Yunuo Mao, Yidong Chen, Liying Yan, Jun Yong, Ji Dong, Wei Yuan, Wei Wang, Lu Wen, Jie Qiao, Fuchou Tang
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2021.683681

Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant (Solanum melongena)
Cited by: 9
Author(s): Saad Serfraz, Vikas Sharma, Florian Maumus, Xavier Aubriot, Andrew D. W. Geering, Pierre‐Yves Teycheney
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0245487

Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh)
Cited by: 5
Author(s): Chris Gottschalk, Songwen Zhang, Phil Schwallier, Sean M. Rogers, Martin J. Bukovac, Steve van Nocker
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.56474

A divergent cyclin/cyclin-dependent kinase complex controls the atypical replication of a malaria parasite during gametogony and transmission
Cited by: 42
Author(s): Aurélia C. Balestra, Mohammad Zeeshan, Edward Rea, Carla Pasquarello, Lorenzo Brusini, Tobias Mourier, Amit Kumar Subudhi, Natacha Klages, Patrizia Arboit, Rajan Kumar Pandey, Declan Brady, Sue Vaughan, Anthony A. Holder, Arnab Pain, David Ferguson, Alexandre Hainard, Rita Tewari, Mathieu Brochet
Software Mentions: 5
Published: over 4 years ago

10.1186/s13075-015-0544-2

Transcriptome analysis of ageing in uninjured human Achilles tendon
Cited by: 61
Author(s): Mandy J. Peffers, Yongxiang Fang, Kathleen Cheung, Tim Koh Jia Wei, Peter Clegg, Helen L. Birch
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0158936

LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome
Cited by: 91
Author(s): Alaguraj Veluchamy, Teddy Jégu, Federico Ariel, David Latrasse, Kadarkaraisamy Mariappan, Soon-Kap Kim, Martín Crespi, Heribert Hirt, Catherine Bergounioux, Cécile Raynaud, Moussa Benhamed
Software Mentions: 4
Published: over 8 years ago

10.1186/s12870-017-1037-z

Proanthocyanidin accumulation and transcriptional responses in the seed coat of cranberry beans (Phaseolus vulgaris L.) with different susceptibility to postharvest darkening
Cited by: 30
Author(s): José A. Freixas Coutin, Seth Munholland, Anjali Silva, Sanjeena Subedi, Lewis Lukens, William L. Crosby, K. Peter Pauls, Gale G. Bozzo
Software Mentions: 4
Published: over 7 years ago

10.7150/ijms.36255

Transcriptome Profiling Reveals Distinct Phenotype of Human Bone Marrow Mesenchymal Stem Cell-derived Hepatocyte-like cells
Cited by: 9
Author(s): Dongyan Shi, Jiaojiao Xin, Yingyan Lu, Wenchao Ding, Jing Jiang, Qian Zhou, Suwan Sun, Beibei Guo, Xingping Zhou, Li Jun
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12896-015-0207-z

A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq
Cited by: 22
Author(s): Kevin Lambirth, Adam M. Whaley, Ivory C. Blakley, Jessica A. Schlueter, Kenneth L. Bost, Ann E. Loraine, Kenneth J. Piller
Software Mentions: 4
Published: about 9 years ago

10.1186/s12985-016-0659-3

Derivation of chicken induced pluripotent stem cells tolerant to Newcastle disease virus-induced lysis through multiple rounds of infection
Cited by: 7
Author(s): Leonardo Susta, Ying He, Jessica M. Hutcheson, Yangqing Lu, Franklin D. West, Steven L. Stice, Ping Yu, Zaid Abdo, Claudio L. Afonso
Software Mentions: 4
Published: almost 8 years ago

10.1186/1471-2164-15-845

Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data
Cited by: 66
Author(s): Kunshan Zhang, Kefei Huang, Yuan Luo, Siguang Li
Software Mentions: 4
Published: about 10 years ago

10.1186/1471-2164-15-636

In depth annotation of the Anopheles gambiae mosquito midgut transcriptome
Cited by: 30
Author(s): Alejandro Padrón, Alvaro Molina-Cruz, Mariam Quiñones, José M. C. Ribeiro, Urvashi N. Ramphul, Janneth Rodrigues, Kui Shen, Ashley Haile, José L. Ramirez, Carolina Barillas‐Mury
Software Mentions: 4
Published: over 10 years ago

10.1111/cmi.12397

The co‐transcriptome of uropathogenic<scp>E</scp>scherichia coli‐infected mouse macrophages reveals new insights into host–pathogen interactions
Cited by: 62
Author(s): Charalampos Harris Mavromatis, Nilesh J. Bokil, Makrina Totsika, Asha Kakkanat, Kolja Schaale, Carlo Vittorio Cannistraci, Tae Woo Ryu, Scott A. Beatson, Glen C. Ulett, Mark A. Schembri, Matthew J. Sweet, Timothy Ravasi
Software Mentions: 4
Published: almost 10 years ago

10.3389/fcimb.2017.00227

Transcriptomic Profiling of High-Density Giardia Foci Encysting in the Murine Proximal Intestine
Cited by: 32
Author(s): Jonathan K Pham, Christopher Nosala, Elaine P. Scott, Kristofer Nguyen, Kari D. Hagen, Hannah Starcevich, Scott C. Dawson
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2016.01245

Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica
Cited by: 20
Author(s): Lulu Xie, Fēi Li, Shifan Zhang, Hui Zhang, Wei Qian, Pei-Rong Li, Shujiang Zhang, Rifei Sun
Software Mentions: 4
Published: about 8 years ago

10.3390/genes8020068

Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts
Cited by: 34
Author(s): Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Masaru Tomita, Kumiko Ui-Tei
Software Mentions: 4
Published: over 7 years ago

10.1186/gb-2013-14-4-r31

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
Cited by: 368
Author(s): Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D. Uno, Takeshi Imai, Hiroki R. Ueda
Software Mentions: 4
Published: over 11 years ago

10.1038/srep15041

DDX3Y gene rescue of a Y chromosome AZFa deletion restores germ cell formation and transcriptional programs
Cited by: 57
Author(s): Cyril Ramathal, Benjamin Angulo, Meena Sukhwani, Jun Cui, Jens Durruthy-Durruthy, Fang Fang, Paula Schanes, Paul J. Turek, Kyle E. Orwig, Renee A. Reijo Pera
Software Mentions: 4
Published: about 9 years ago

10.1038/srep20759

Comparative transcriptome analysis of peripheral blood mononuclear cells in hepatitis B-related acute-on-chronic liver failure
Cited by: 10
Author(s): Qian Zhou, Wenchao Ding, Liangliang Jiang, Jiaojiao Xin, Tianzhou Wu, Dongyan Shi, Jing Jiang, Cao H, Lanjuan Li, Jun Li
Software Mentions: 4
Published: over 8 years ago

10.1186/s40478-019-0712-8

Inhibition of mitochondrial respiration prevents BRAF-mutant melanoma brain metastasis
Cited by: 30
Author(s): Terje Sundstrøm, Lars Prestegarden, Francisco Azuaje, Synnøve Nymark Aasen, Gro Vatne Røsland, Jobin K. Varughese, Marzieh Bahador, Simon Bernatz, Yannick Braun, Patrick N. Harter, Kai Ove Skaftnesmo, Elizabeth S. Ingham, Lisa M. Mahakian, Sarah Tam, Clifford G. Tepper, Kjell Petersen, Katherine W. Ferrara, Karl Johan Tronstad, Morten Lund‐Johansen, Rudi Beschorner, Rolf Bjerkvig, Frits Thorsen
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1007273

Ethylene induced plant stress tolerance by Enterobacter sp. SA187 is mediated by 2‐keto‐4‐methylthiobutyric acid production
Cited by: 80
Author(s): Axel de Zélicourt, Lukáš Synek, Maged M. Saad, Hanin S. Alzubaidy, Rewaa S. Jalal, Yakun Xie, Cristina Andrés‐Barrao, Eleonora Rolli, Florence Guérard, Kadarkaraisamy Mariappan, İhsanullah Daur, Jean Colcombet, Moussa Benhamed, Thomas Depaepe, Dominique Van Der Straeten, Heribert Hirt
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-11379-7

RNA-seq analysis of the kidneys of broiler chickens fed diets containing different concentrations of calcium
Cited by: 12
Author(s): Woncheoul Park, Deivendran Rengaraj, Dong Yong Kil, Heebal Kim, Hak-Kyo Lee, Ki Duk Song
Software Mentions: 3
Published: about 7 years ago

10.18632/aging.101446

Common and unique transcriptional responses to dietary restriction and loss of insulin receptor substrate 1 (IRS1) in mice
Cited by: 7
Author(s): Melissa M. Page, Eugene F. Schuster, Manikhandan Mudaliar, Paweł Herzyk, Dominic J. Withers, Colin Selman
Software Mentions: 3
Published: over 6 years ago

10.1242/dev.116996

Gene activation-associated long noncoding RNAs function in mouse preimplantation development
Cited by: 71
Author(s): Nobuhiko Hamazaki, Masahiro Uesaka, Kinichi Nakashima, Kiyokazu Agata, Takuya Imamura
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.ppat.1005273

Plasmodium P-Type Cyclin CYC3 Modulates Endomitotic Growth during Oocyst Development in Mosquitoes
Cited by: 60
Author(s): Magali Roques, Richard J. Wall, Alexander P. Douglass, Abhinay Ramaprasad, David Ferguson, Mbinda L. Kaindama, Lorenzo Brusini, Joshi Nimitray, Zineb Rchiad, Declan Brady, David S. Guttery, Sally P. Wheatley, Hiroyuki Yamano, Anthony A. Holder, Arnab Pain, Bill Wickstead, Rita Tewari
Software Mentions: 3
Published: almost 9 years ago

10.1080/19336896.2019.1615197

Rodent models allow BSE discrimination of goat prions and reveal geographical differences in the biological properties of scrapie
Cited by: 4
Author(s): Laura Pirisinu, Olivier Andréoletti, Frédéric Lantier, Pier Luigi Acutis, S. Acin, Wilfred Goldmann, Theodoros Sklaviadis, Loukia Ekateriniadou, Christine Fast, Penelope Papasavva-Stylianou, Stéphanie Simon, J. Spiropoulol, Umberto Agrimi, J.G. Jacobs, Alex Bossers, Lucien van Keulen, Maria Mazza, Romolo Nonno, J.P.M. Langeveld
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.26851

Molecular architecture underlying fluid absorption by the developing inner ear
Cited by: 35
Author(s): Keiji Honda, Sung Huhn Kim, Michael C. Kelly, J. C. Burns, Laura A. Constance, Xiangming Li, Fei Zhou, Michael Hoa, Matthew W. Kelley, Philine Wangemann, Robert J. Morell, Andrew J. Griffith
Software Mentions: 3
Published: about 7 years ago

10.7554/eLife.10870

ETS family transcriptional regulators drive chromatin dynamics and malignancy in squamous cell carcinomas
Cited by: 69
Author(s): Hanseul Yang, Daniel Schramek, René Adam, Brice E. Keyes, Ping Wang, Deyou Zheng, Elaine Fuchs
Software Mentions: 3
Published: almost 9 years ago

10.1128/mBio.00768-21

Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans
Cited by: 7
Author(s): Joel T Steyer, Damien J. Downes, Cameron C. Hunter, Pierre Migeon, Richard B. Todd
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms21061993

Time-Course Transcriptome Study Reveals Mode of bZIP Transcription Factors on Light Exposure in Arabidopsis
Cited by: 15
Author(s): Y. Kurihara, Yuko Makita, Haruka Shimohira, Minami Matsui
Software Mentions: 3
Published: over 4 years ago

10.18632/oncotarget.13104

Identification of KLK10 as a therapeutic target to reverse trastuzumab resistance in breast cancer
Cited by: 15
Author(s): Zhuo Wang, Beihong Ruan, Y. Jin, Yulong Zhang, Jiaqiu Li, Liyuan Zhu, Wenxia Xu, Lifeng Feng, Hongchuan Jin, Xian Wang
Software Mentions: 3
Published: about 8 years ago

10.1186/s13567-019-0622-6

Transcriptome analysis unraveled potential mechanisms of resistance to Haemonchus contortus infection in Merino sheep populations bred for parasite resistance
Cited by: 27
Author(s): Runfeng Zhang, Fang Liu, Peter W. Hunt, Congjun Li, Lichun Zhang, Aaron Ingham, Robert W. Li
Software Mentions: 3
Published: almost 6 years ago

10.1186/gb-2012-13-11-r104

InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor
Cited by: 41
Author(s): Alain Coletta, Colin Molter, Robin Duqué, David Steenhoff, Jonatan Taminau, Virginie de Schaetzen, Stijn Meganck, Cosmin Lazar, David Venet, Vincent Detours, Ann Nowé, Hugues Bersini, David Solis
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-018-20458-2

SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses
Cited by: 10
Author(s): Dominik Dornfeld, Alexandra H. Dudek, Thibaut Vausselin, Sira C. Günther, Judd F. Hultquist, Sebastian Giese, Daria Khokhlova-Cubberley, Yap Ching Chew, Lars Pache, Nevan J. Krogan, Adolfo Garcı́a-Sastre, Martin Schwemmle, Megan L. Shaw
Software Mentions: 3
Published: almost 7 years ago

10.1016/j.dib.2016.04.033

RNA-sequencing data analysis of uterus in ovariectomized rats fed with soy protein isolate, 17β-estradiol and casein
Cited by: 0
Author(s): Martin J. J. Ronis, Horacio Gómez-Acevedo, Michael L. Blackburn, Mario A. Cleves, Ritu Singhal, Thomas M. Badger
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-019-50710-2

Otoferlin Depletion Results in Abnormal Synaptic Ribbons and Altered Intracellular Calcium Levels in Zebrafish
Cited by: 7
Author(s): Aayushi Manchanda, Paroma Chatterjee, Josephine A. Bonventre, Derik E. Haggard, Katie S. Kindt, Robert L. Tanguay, Colin P. Johnson
Software Mentions: 2
Published: about 5 years ago

10.1016/j.devcel.2016.12.023

Non-Canonical and Sexually Dimorphic X Dosage Compensation States in the Mouse and Human Germline
Cited by: 72
Author(s): Mahesh N. Sangrithi, Hélène Royo, Shantha K. Mahadevaiah, Obah A. Ojarikre, Leena Bhaw, Abdul Karim Sesay, Antoine H.F.M. Peters, Michael Stadler, James M. A. Turner
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.54304

Progenitors oppositely polarize WNT activators and inhibitors to orchestrate tissue development
Cited by: 16
Author(s): Irina Matos, Amma Asare, John Levorse, Tamara Ouspenskaia, June de la Cruz-Racelis, Laura-Nadine Schuhmacher, Elaine Fuchs
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-015-2210-0

Transcriptomics of diapause in an isogenic self-fertilizing vertebrate
Cited by: 12
Author(s): Felix Mesak, Andrey Tatarenkov, John C. Avise
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-016-2689-z

Comparative transcriptome analysis revealing dormant conidia and germination associated genes in Aspergillus species: an essential role for AtfA in conidial dormancy
Cited by: 64
Author(s): Daisuke Hagiwara, Hiroki Takahashi, Yoko Kusuya, Susumu Kawamoto, Katsuhiko Kamei, Tohru Gonoi
Software Mentions: 2
Published: over 8 years ago

10.3389/fimmu.2020.609456

Innovation in Nucleotide-Binding Oligomerization-Like Receptor and Toll-Like Receptor Sensing Drives the Major Histocompatibility Complex-II Free Atlantic Cod Immune System
Cited by: 5
Author(s): Xing‐Kun Jin, Bernat Morro, Ole K. Tørresen, Visila Moiche, Monica Hongrø Solbakken, Kjetill S. Jakobsen, Sissel Jentoft, Simon Mackenzie
Software Mentions: 2
Published: almost 4 years ago

10.3389/fnmol.2014.00087

Defining the nociceptor transcriptome
Cited by: 102
Author(s): Matthew Thakur, Megan Crow, Natalie Richards, Gareth I. J. Davey, Emma Levine, Jayne H. Kelleher, Chibeza C. Agley, Franziska Denk, Sdr Harridge, Stephen B. McMahon
Software Mentions: 2
Published: almost 10 years ago

10.3389/fpls.2019.01639

The Lamin-Like LITTLE NUCLEI 1 (LINC1) Regulates Pattern-Triggered Immunity and Jasmonic Acid Signaling
Cited by: 18
Author(s): Mai Jarad, Kadarkaraisamy Mariappan, Marília Almeida-Trapp, Michael Florian Mette, Axel Mithöfer, Naganand Rayapuram, Heribert Hirt
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-020-07326-y

Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver
Cited by: 25
Author(s): Krystyna Cwiklinski, Mark W. Robinson, Sheila Donnelly, John P. Dalton
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1004920

Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage
Cited by: 130
Author(s): Jörg Hagmann, Claude Becker, Jonas V. Müller, Oliver Stegle, Rhonda C. Meyer, George Wang, Korbinian Schneeberger, Joffrey Fitz, Thomas Altmann, Joy Bergelson, Karsten Borgwardt, Detlef Weigel
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12870-017-1124-1

Metabolic pathways and genes identified by RNA-seq analysis of barley near-isogenic lines differing by allelic state of the Black lemma and pericarp (Blp) gene
Cited by: 19
Author(s): Anastasiya Y. Glagoleva, Nikolay A. Shmakov, O. Y. Shoeva, Gennady V. Vasiliev, Natalia V. Shatskaya, Andreas Börner, D. A. Afonnikov, Elena K. Khlestkina
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0189664

Transcriptome profiling identifies regulators of pathogenesis in collagen VI related muscular dystrophy
Cited by: 15
Author(s): Russell J. Butterfield, Diane M. Dunn, Ying Hu, Kory R. Johnson, Carsten G. Bönnemann, Robert B. Weiss
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12870-015-0680-5

Hairy Canola (Brasssica napus) re-visited: Down-regulating TTG1 in an AtGL3-enhanced hairy leaf background improves growth, leaf trichome coverage, and metabolite gene expression diversity
Cited by: 13
Author(s): Ushan Alahakoon, Ali Taheri, Naghabushana K. Nayidu, D. J. Epp, Min Yu, Isobel A. P. Parkin, Dwayne D. Hegedus, Peta C. Bonham‐Smith, Margaret Y. Gruber
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12918-018-0608-4

The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells
Cited by: 10
Author(s): Kimberly C. Olney, David B. Nyer, Daniel A. Vargas, Melissa A. Wilson Sayres, Karmella A. Haynes
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-019-50959-7

RNA sequencing for ligature induced periodontitis in mice revealed important role of S100A8 and S100A9 for periodontal destruction
Cited by: 18
Author(s): Shogo Maekawa, Satoru Onizuka, Seiji Katagiri, Masahiro Hatasa, Yujin Ohsugi, Naoki Sasaki, Kouichi Watanabe, Anri Ohtsu, Rina Komazaki, Kohei Ogura, Tohru Miyoshi‐Akiyama, Takanori Iwata, Hiroshi Nitta, Yuichi Izumi
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-39141-1

Transcriptomic profiles of retinal ganglion cells are defined by the magnitude of intraocular pressure elevation in adult mice
Cited by: 16
Author(s): Yong H. Park, Joshua D. Snook, Edwin J. Ostrin, Sangbae Kim, Rui Chen, Benjamin J. Frankfort
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0191492

Differential DNA methylation and transcription profiles in date palm roots exposed to salinity
Cited by: 37
Author(s): Ibtisam Al-Harrasi, Rashid Al-Yahyai, Mahmoud W. Yaish
Software Mentions: 2
Published: almost 7 years ago

10.1534/g3.116.034389

Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis
Cited by: 7
Author(s): Igor Zeman, Martina Neboháčová, Gabriela Gérecová, Kornélia Katonová, Eva Jánošíková, Michaela Jakúbková, Ivana Centárová, Ivana Dunčková, Ľubomír Tomáška, Leszek P. Pryszcz, Toni Gabaldón, Jozef Nosek
Software Mentions: 2
Published: almost 8 years ago

10.3390/ani10030469

Reconstruction and Analysis of Cattle Metabolic Networks in Normal and Acidosis Rumen Tissue
Cited by: 14
Author(s): Masoumeh Gholizadeh, Jamal Fayazi, Yazdan Asgari, Hakimeh Zali, Lars Kaderali
Software Mentions: 2
Published: over 4 years ago

10.1093/icb/icz096

Immediate Transcriptional Response to a Temperature Pulse under a Fluctuating Thermal Regime
Cited by: 4
Author(s): Dacotah Melicher, Alex S. Torson, Tanner J. Anderson, George D. Yocum, Joseph P. Rinehart, Julia H. Bowsher
Software Mentions: 2
Published: over 5 years ago

10.3390/cells10010076

Identification of Targets from LRRK2 Rescue Phenotypes
Cited by: 3
Author(s): Joanne Toh, Ling Ling Chua, Patrick Ho, Edwin Sandanaraj, Carol Tang, Hongyan Wang, Eng King Tan
Software Mentions: 2
Published: almost 4 years ago

10.3390/cells9122590

MRE11 Is Crucial for Malaria Parasite Transmission and Its Absence Affects Expression of Interconnected Networks of Key Genes Essential for Life
Cited by: 2
Author(s): David S. Guttery, Abhinay Ramaprasad, David J. P. Ferguson, Mohammad Zeeshan, Rajan Kumar Pandey, Declan Brady, Anthony A. Holder, Arnab Pain, Rita Tewari
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-99030-4

Iron homeostasis in the absence of ferricrocin and its consequences in fungal development and insect virulence in Beauveria bassiana
Cited by: 2
Author(s): Jiraporn Jirakkakul, Nuchnudda Wichienchote, Somsak Likhitrattanapisal, Supawadee Ingsriswang, Thippawan Yoocha, Sithichoke Tangphatsornruang, Rudsamee Wasuwan, Supapon Cheevadhanarak, Morakot Tanticharoen, Alongkorn Amnuaykanjanasin
Software Mentions: 1
Published: about 3 years ago

10.1186/s12864-015-1989-z

Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis
Cited by: 30
Author(s): Andrew K. Watson, Tom A. Williams, Bryony A. P. Williams, Karen Moore, Robert P. Hirt, T. Martin Embley
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-017-4357-3

Identification of Sertoli cell-specific transcripts in the mouse testis and the role of FSH and androgen in the control of Sertoli cell activity
Cited by: 30
Author(s): Ugo Soffientini, Diane Rebourcet, M. H. Abel, S Lee, Graham Hamilton, Paul A. Fowler, Lee B. Smith, Peter J. O’Shaughnessy
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12881-020-01088-w

Gene expression profiling of fibroblasts in a family with LMNA-related cardiomyopathy reveals molecular pathways implicated in disease pathogenesis
Cited by: 4
Author(s): Halida P. Widyastuti, Trina M. Norden-Krichmar, Anna Grosberg, Michael V. Zaragoza
Software Mentions: 1
Published: over 4 years ago

10.3390/biology7040047

A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways
Cited by: 10
Author(s): Abdalla Elbialy, Shuichi Asakawa, Shugo Watabe, Shigeharu Kinoshita
Software Mentions: 1
Published: about 6 years ago

10.3390/microorganisms8081253

Host–Pathogen Interactions between Xanthomonas fragariae and Its Host Fragaria × ananassa Investigated with a Dual RNA-Seq Analysis
Cited by: 8
Author(s): Michael Gétaz, Joanna Puławska, Theo H. M. Smits, Joël F. Pothier
Software Mentions: 1
Published: about 4 years ago

10.3390/microorganisms9071447

HrpL Regulon of Bacterial Pathogen of Woody Host Pseudomonas savastanoi pv. savastanoi NCPPB 3335
Cited by: 3
Author(s): Alba Moreno‐Pérez, Cayo Ramos, Luis Rodríguez‐Moreno
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1007338

TGFβ signaling related genes are involved in hormonal mediation during termite soldier differentiation
Cited by: 21
Author(s): Yudai Masuoka, Hajime Yaguchi, Kouhei Toga, Shuji Shigenobu, Kazuyuki Maekawa
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1006100

The Gene Expression Program for the Formation of Wing Cuticle in Drosophila
Cited by: 51
Author(s): L.F. Sobala, Paul N. Adler
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0220441

Effects of long-term feeding of rapeseed meal on skeletal muscle transcriptome, production efficiency and meat quality traits in Norwegian Landrace growing-finishing pigs
Cited by: 17
Author(s): Adrijana Škugor, Nils Petter Kjos, Arvind Sundaram, Liv Torunn Mydland, Ragnhild Ånestad, Anne‐Helene Tauson, Margareth Øverland
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0154412

A Mutation in LTBP2 Causes Congenital Glaucoma in Domestic Cats (Felis catus)
Cited by: 24
Author(s): Markus H. Kuehn, Koren A. Lipsett, Marilyn Menotti‐Raymond, S. Scott Whitmore, Todd E. Scheetz, Victor A. David, Stephen J. O’Brien, Zhongyuan Zhao, Jackie K. Jens, Elizabeth M. Snella, N. Matthew Ellinwood, Gillian J. McLellan
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0176333

A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms
Cited by: 15
Author(s): Christiane Noronha Fernandes-Brum, Pâmela Marinho Rezende, Thales Henrique Cherubino Ribeiro, Raphael Ricon de Oliveira, Thaís Cunha de Sousa Cardoso, Laurence Rodrigues do Amaral, Matheus de Souza Gomes, Antônio Chalfun-Júnior
Software Mentions: 1
Published: over 7 years ago

10.3389/fcimb.2017.00032

PerC Manipulates Metabolism and Surface Antigens in Enteropathogenic Escherichia coli
Cited by: 7
Author(s): Jay L. Mellies, Amy Platenkamp, Jossef F. Osborn, Lily Ben‐Avi
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep34341

Increased nicotine response in iPSC-derived human neurons carrying the CHRNA5 N398 allele
Cited by: 30
Author(s): Eileen N. Oni, Apoorva Halikere, Guohui Li, Alana J. Toro-Ramos, Mavis R. Swerdel, Jessica L. Verpeut, Jennifer C. Moore, Nicholas T. Bello, Laura J. Bierut, Alison M. Goate, Jay A. Tischfield, Zhiping P. Pang, Ronald P. Hart
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-017-07222-8

Mechanism of biofilm-mediated stress resistance and lifespan extension in C. elegans
Cited by: 38
Author(s): О. А. Смоленцева, Ivan Gusarov, Laurent Gautier, Ilya Shamovsky, Alicia S. DeFrancesco, Richard Losick, Evgeny Nudler
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-46445-9

High Fat Diet Triggers a Reduction in Body Fat Mass in Female Mice Deficient for Utx demethylase
Cited by: 8
Author(s): Kyoko Ota, Akiyoshi Komuro, Hideharu Amano, Akinori Kanai, Kai Ge, Takeshi Ueda, Hitoshi Okada
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-49725-6

Transcriptome analysis of Globodera pallida from the susceptible host Solanum tuberosum or the resistant plant Solanum sisymbriifolium
Cited by: 13
Author(s): Rinu Kooliyottil, Louise‐Marie Dandurand, Joseph C. Kuhl, Allan Caplan, Fangming Xiao, Benjamin Mimee, Joël Lafond-Lapalme
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-60187-z

Genome-wide transcriptome and physiological analyses provide new insights into peanut drought response mechanisms
Cited by: 18
Author(s): Sailaja Bhogireddy, Abishek Xavier, Vanika Garg, Nancy Layland, Renée S. Arias, Paxton Payton, Spurthi N. Nayak, Manish K. Pandey, Naveen Puppala, Rajeev K. Varshney
Software Mentions: 1
Published: over 4 years ago

10.7150/thno.46143

M2 macrophage-derived exosomes promote the c-KIT phenotype of vascular smooth muscle cells during vascular tissue repair after intravascular stent implantation
Cited by: 48
Author(s): Wenhua Yan, Tianhan Li, Tieying Yin, Zhengjun Hou, Kai Qu, Nan Wang, Colm Durkan, Lingqing Dong, Juhui Qiu, Hans Gregersen, Guixue Wang
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms18112326

Whole Blood mRNA Expression-Based Prognosis of Metastatic Renal Cell Carcinoma
Cited by: 13
Author(s): Karthik V. Giridhar, Carlos Sosa, David W. Hillman, Cristobal T. Sanhueza, Candace Lee Dalpiaz, Brian A. Costello, Fernando Quevedo, Henry C. Pitot, Roxana S. Dronca, Donna Ertz, John C. Cheville, Krishna Vanaja Donkena, Manish Kohli
Software Mentions: 1
Published: about 7 years ago

Projects: bioconductor: cummeRbund

Papers Mentioning cummeRbund 83