bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/srep24964

Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection
Cited by: 34
Author(s): Guanxiang Liang, Nilusha Malmuthuge, Yongjuan Guan, Yan Ren, Philip Griebel, Le Luo Guan
Software Mentions: 3
Published: over 10 years ago

10.1038/srep25474

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells
Cited by: 41
Author(s): Pamela Milani, Renan Escalante-Chong, Brandon Shelley, Natasha L. Patel-Murray, Xin X, Miriam Adam, Berhan Mandefro, Dhruv Sareen, Clive N. Svendsen, Ernest Fraenkel
Software Mentions: 3
Published: over 10 years ago

10.1038/srep26114

Comparative analysis of the integument transcriptomes of the black dilute mutant and the wild-type silkworm Bombyx mori
Cited by: 17
Author(s): Songyuan Wu, Xiaoling Tong, Chenxing Peng, Xiong Guan, Kunpeng Lu, Hai Hu, Tan D, Chunlin Li, Minjin Han, Cheng Lü, Fangyin Dai
Software Mentions: 3
Published: over 10 years ago

10.1038/srep27043

Differences in DNA Repair Capacity, Cell Death and Transcriptional Response after Irradiation between a Radiosensitive and a Radioresistant Cell Line
Cited by: 33
Author(s): Mireia Borràs-Fresneda, Joan Francesc Barquinero, Maria Gomolka, Sabine Hornhardt, Ute Rößler, Gemma Armengol, Leonardo Barrios
Software Mentions: 3
Published: about 10 years ago

10.1038/srep28702

Global transcriptome changes in perennial ryegrass during early infection by pink snow mould
Cited by: 12
Author(s): Mallikarjuna Rao Kovi, Mohamed Abdelhalim, Anil Kunapareddy, Åshild Ergon, Anne Marte Tronsmo, May Bente Brurberg, Ingerd Skow Hofgaard, Torben Asp, Odd Arne Rognli
Software Mentions: 3
Published: about 10 years ago

10.1038/srep31150

Schistosome sex matters: a deep view into gonad-specific and pairing-dependent transcriptomes reveals a complex gender interplay
Cited by: 99
Author(s): Zhigang Lu, Florian Sessler, Nancy Holroyd, Steffen Hahnel, Thomas Quack, Matthew Berriman, Christoph G. Grevelding
Software Mentions: 3
Published: about 10 years ago

10.1038/srep33151

De novo Transcriptome Analysis Reveals Distinct Defense Mechanisms by Young and Mature Leaves of Hevea brasiliensis (Para Rubber Tree)
Cited by: 37
Author(s): Yuxiao Fang, Hailiang Mei, Binhui Zhou, Xiaohu Xiao, Meng Yang, Yacheng Huang, Xiangyu Long, Songnian Hu, Chaorong Tang
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep33296

Global analysis of differential gene expression related to long-term sperm storage in oviduct of Chinese Soft-Shelled Turtle Pelodiscus sinensis
Cited by: 23
Author(s): Tengfei Liu, Ping Yang, Hong Chen, Yufei Huang, Yi Liu, Yasir Waqas, Nisar Ahmed, Xia Chu, Qiusheng Chen
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep37536

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle
Cited by: 24
Author(s): Alejandra Rougon‐Cardoso, Mitzi Flores-Ponce, Hilda E. Ramos-Aboites, Christian E. Martínez-Guerrero, Youjin Hao, Luís Cunha, Jonathan Alejandro Rodríguez-Martínez, Cesaré Ovando-Vázquez, José Roberto Bermúdez-Barrientos, Cei Abreu‐Goodger, Noelina Hernández, Nélson Simões, Rafaél Montiel
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep40049

The molecular sensory machinery of a Chagas disease vector: expression changes through imaginal moult and sexually dimorphic features
Cited by: 41
Author(s): José Manuel Latorre-Estivalis, Hugh M. Robertson, Kimberly K. O. Walden, Jerônimo C. Ruiz, Leilane Oliveira Gonçalves, Alessandra A. Guarneri, Marcelo G. Lorenzo
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-018-25430-8

Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat
Cited by: 22
Author(s): Prabin Bajgain, Blake Russell, Mohsen Mohammadi
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-26170-5

Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions
Cited by: 6
Author(s): David Talavera, Christopher J. Kershaw, Joseph L. Costello, Lydia M. Castelli, William Rowe, Paul F. G. Sims, Mark P. Ashe, Chris M. Grant, Graham D. Pavitt, Simon J. Hubbard
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-23514-z

Comparative transcriptomics gives insights into the evolution of parasitism in Strongyloides nematodes at the genus, subclade and species level
Cited by: 22
Author(s): Vicky L. Hunt, Akinori Hino, Akemi Yoshida, Taisei Kikuchi
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-26841-3

Screening and characterisation of sex differentiation-related long non-coding RNAs in Chinese soft-shell turtle (Pelodiscus sinensis)
Cited by: 19
Author(s): Jun Zhang, Peng Yu, Qinyan Zhou, Xilei Li, Shuquan Ding, Shiping Su, Xiaohua Zhang, Xiaoli Yang, Weicheng Zhou, Qing Wan, Jian‐Fang Gui
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-27293-5

Brain Cell Type Specific Gene Expression and Co-expression Network Architectures
Cited by: 283
Author(s): Andrew McKenzie, Minghui Wang, Mads E. Hauberg, John F. Fullard, Alexey Kozlenkov, Alexandra B. Keenan, Yasmin L. Hurd, Stella Dracheva, Patrizia Casaccia, Panos Roussos, Bin Zhang
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-26902-7

Airway brushing as a new experimental methodology to detect airway gene expression signatures in mouse lung squamous cell carcinoma
Cited by: 5
Author(s): Jing Pan, Donghai Xiong, Qi Zhang, Éva Szabó, Mark Steven Miller, Ronald A. Lubet, Yian Wang, Ming You
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-28299-9

Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma
Cited by: 38
Author(s): Jun Han, Meijun Chen, Yihan Wang, Boxuan Gong, Tianwei Zhuang, Lingyu Liang, Hong Qiao
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-29759-y

High Dose Vitamin D supplementation alters faecal microbiome and predisposes mice to more severe colitis
Cited by: 36
Author(s): Simon Ghaly, Nadeem O. Kaakoush, Frances Lloyd, Terence McGonigle, D. Mok, Angela Baird, Borut Klopcic, Lavinia Gordon, Shelley Gorman, Cynthia Forest, Roger Bouillon, Ian C. Lawrance, Prue H. Hart
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-30640-1

PyMT-1099, a versatile murine cell model for EMT in breast cancer
Cited by: 14
Author(s): Mohit Saxena, Ravi Kiran Reddy Kalathur, Melanie Neutzner, Gerhard Christofori
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-32310-8

The m6A-methylase complex recruits TREX and regulates mRNA export
Cited by: 82
Author(s): Simon Lesbirel, Nicolas Viphakone, Matthew T Parker, Jacob Parker, Catherine G. Heath, Ian Sudbery, Stuart A. Wilson
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-32579-9

ADIPOR1 is essential for vision and its RPE expression is lost in the Mfrprd6 mouse
Cited by: 32
Author(s): Valentin M. Sluch, Angela Banks, Hui Li, Maura Crowley, Vanessa Davis, Chuanxi Xiang, Junzheng Yang, John Demirs, Joanna Vrouvlianis, Barrett Leehy, Shawn Hanks, Alexandra M. Hyman, Jorge Aranda, Bo Chang, Chad E. Bigelow, Dennis S. Rice
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-33478-9

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues
Cited by: 54
Author(s): Bryan J. Pavlovic, Lauren E. Blake, Julien Roux, Claudia Chavarria, Yoav Gilad
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-33943-5

Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation
Cited by: 33
Author(s): Erich Hofmann, Rhett M. Rautsaw, Jason L. Strickland, Matthew L. Holding, Michael Hogan, Andrew J. Mason, Darin R. Rokyta, Christopher L. Parkinson
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-33807-y

Characterization of the miRNA regulators of the human ovulatory cascade
Cited by: 23
Author(s): Gil M. Yerushalmi, Mali Salmon‐Divon, Libby Ophir, Yuval Yung, Micha Baum, Giovanni Coticchio, Rubens Fadini, Mario Mignini-Renzini, Mariabeatrice Dal Canto, Ronit Machtinger, Ettie Maman, Ariel Hourvitz
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-34591-5

Brassica yellows virus’ movement protein upregulates anthocyanin accumulation, leading to the development of purple leaf symptoms on Arabidopsis thaliana
Cited by: 18
Author(s): Xiangru Chen, Ying Wang, Hang-Hai Zhao, Xiaoyan Zhang, Xianbing Wang, Dawei Li, Jialin Yu, Chenggui Han
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-34636-9

Gene set enrichment analysis of the bronchial epithelium implicates contribution of cell cycle and tissue repair processes in equine asthma
Cited by: 13
Author(s): Laurence Tessier, Olivier Côté, Mary E. Clark, Laurent Viel, Andrés Diaz-Méndez, Simon Anders, Dorothee Bienzle
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-36059-y

Genome-Wide Transcriptome Landscape of Embryonic Brain-Derived Neural Stem Cells Exposed to Alcohol with Strain-Specific Cross-Examination in BL6 and CD1 Mice
Cited by: 22
Author(s): Wayne Xu, Vichithra R. B. Liyanage, Aaron MacAulay, Romina D. Levy, Kyle Curtis, Carl O. Olson, Robby M. Zachariah, Shayan Amiri, Marjorie Buist, Geoffrey Hicks, James R. Davie, Mojgan Rastegar
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-36866-3

Marine biogenics in sea spray aerosols interact with the mTOR signaling pathway
Cited by: 12
Author(s): Jana Asselman, Emmanuel Van Acker, Maarten De Rijcke, Laurentijn Tilleman, Filip Van Nieuwerburgh, Jan Mees, Karel A.C. De Schamphelaere, Colin R. Janssen
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-37669-2

Molecular evidence for distinct modes of nutrient acquisition between visceral and neurotropic schistosomes of birds
Cited by: 10
Author(s): Roman Leontovyč, Neil D. Young, Pasi K. Korhonen, Ross S. Hall, Jana Bulantová, Veronika Jeřábková, Martin Kašný, Robin B. Gasser, Petr Horák
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-39880-1

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Cited by: 25
Author(s): Bruno Arcà, Alessio Colantoni, Carmine Fiorillo, Francesco Severini, Vladimír Beneš, Marco Di Luca, Raffaele Calogero, Fabrizio Lombardo
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-40016-8

Whole transcriptome targeted gene quantification provides new insights on pulmonary sarcomatoid carcinomas
Cited by: 10
Author(s): Greta Alì, Rossella Bruno, Anello Marcello Poma, Ornella Affinito, Antonella Monticelli, Paolo Piaggi, Sara Ricciardi, Marco Lucchi, Franca Melfi, Antonio Chella, Sérgio Cocozza, Gabriella Fontanini
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-40754-9

Genome analysis of Pseudomonas syringae pv. actinidiae biovar 6, which produces the phytotoxins, phaseolotoxin and coronatine
Cited by: 34
Author(s): Takashi Fujikawa, Hiroyuki Sawada
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-39608-1

Field transcriptome revealed a novel relationship between nitrate transport and flowering in Japanese beech
Cited by: 16
Author(s): Akiko Satake, Kazutaka Kawatsu, Kenjiro Teshima, Daisuke Kabeya, Qingmin Han
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-42680-2

Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts
Cited by: 31
Author(s): Yuanhang Liu, Pritha Chanana, Jaime Davila, Xiaonan Hou, Valentina Zanfagnin, Cordelia D. McGehee, Ellen L. Goode, Eric C. Polley, Paul Haluska, S. John Weroha, Chen Wang
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-43135-4

The transgenerational effects of oocyte mitochondrial supplementation
Cited by: 11
Author(s): Justin C. St. John, Yogeshwar Makanji, Jacqueline L. Johnson, Te-Sha Tsai, Simone Lagondar, Fleur Rodda, Xin Sun, Mulyoto Pangestu, Penny Chen, Peter Temple-Smith
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-43354-9

Analysis by RNA-seq of transcriptomic changes elicited by heat shock in Leishmania major
Cited by: 20
Author(s): Alberto Rastrojo, Laura Corvo, Rodrigo Lombraña, José Carlos Solana, Begoña Aguado, José Marı́a Requena
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-43075-z

A universal transcriptomic signature of age reveals the temporal scaling of Caenorhabditis elegans aging trajectories
Cited by: 35
Author(s): Andrei E. Tarkhov, Ramani Alla, Srinivas Ayyadevara, Mikhail A. Pyatnitskiy, L. I. Men’shikov, Robert J. Shmookler Reis, П. О. Федичев
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-020-63040-5

Circulating RNA Transcriptome of Pregnant Women with TSH Just Above the Trimester-Specific Reference and its Correlation with the Hypertensive Phenotype
Cited by: 2
Author(s): Andréa Harumy de Lima Hirata, Luiz Antônio de Jesus Rocha, Valdelena Alessandra da Silva, Rafael Fernandes Almeida, Lucas dos Santos Bacigalupo, Patrícia Siqueira Varela, Leonardo Martins Silva, João Bosco Pesquero, Humberto Dellê, Cleber Camacho
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-64938-w

Gene expression trajectories during male and female reproductive development in balsam poplar (Populus balsamifera L.)
Cited by: 10
Author(s): Quentin Cronk, Raju Soolanayakanahally, Katharina Bräutigam
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-65947-5

De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress
Cited by: 13
Author(s): Elham Younesi-Melerdi, Ghorbanali Nematzadeh, Ali Pakdin Parizi, Mohammad Reza Bakhtiarizadeh, Seyed Abolfazl Motahari
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-66986-8

ssGSEA score-based Ras dependency indexes derived from gene expression data reveal potential Ras addiction mechanisms with possible clinical implications
Cited by: 100
Author(s): Ming Yi, Dwight V. Nissley, Frank McCormick, Robert M. Stephens
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-67482-9

miRNA–mRNA network regulation in the skeletal muscle fiber phenotype of chickens revealed by integrated analysis of miRNAome and transcriptome
Cited by: 20
Author(s): Yifan Liu, Ming Zhang, Yanju Shan, Gaige Ji, Xiaojun Ju, Yan Tu, Zhongwei Sheng, Jing Xie, Jianmin Zou, Shu JingTing
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-67513-5

Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM
Cited by: 50
Author(s): Marcus Alvarez, Elior Rahmani, Brandon Jew, Kristina M. Garske, Min‐Hua Zong, Jihane N. Benhammou, Chun Jimmie Ye, Joseph R. Pisegna, Kirsi H. Pietiläinen, Eran Halperin, Päivi Pajukanta
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-68187-9

Prostate cancer-derived holoclones: a novel and effective model for evaluating cancer stemness
Cited by: 9
Author(s): Louise Flynn, Martin P. Barr, Anne‐Marie Baird, Paul Smyth, Órla Casey, Gordon Blackshields, John Greene, Stephen R. Pennington, Emily Hams, Padraic G. Fallon, John O’Leary, Orla Sheils, Stephen Finn
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-67588-0

Glomerular endothelial cell heterogeneity in Alport syndrome
Cited by: 8
Author(s): Hasmik Soloyan, Matthew E. Thornton, Valentina Villani, Patrick Khatchadourian, Paolo Cravedi, Andrea Angeletti, Brendan H. Grubbs, Roger De Filippo, Laura Perin, Sargis Sedrakyan
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-71210-8

Exploring the genetic basis of fatty liver development in geese
Cited by: 3
Author(s): Yu Yang, Huiying Wang, Guangquan Li, Yi Liu, Cui Wang, Daqian He
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-71527-4

A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy
Cited by: 17
Author(s): Mukesh Kumar, Elena Papaleo
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-73694-w

Rewiring of gene expression in circulating white blood cells is associated with pregnancy outcome in heifers (Bos taurus)
Cited by: 14
Author(s): Sarah E. Moorey, Bailey N. Walker, Michelle F Elmore, J. Bradford Elmore, Soren P. Rodning, Fernando H. Biase
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-76688-w

Identification of immune-related genes as prognostic factors in bladder cancer
Cited by: 12
Author(s): Jie Zhu, Han Wang, Ting Ma, Yan He, Meng‐Ru Shen, Wei Song, Jingjing Wang, Jianping Shi, Mengyao Wu, Chao Liu, Wenjie Wang, Yongzhen Huang
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-77105-y

Deep phenotyping of myalgic encephalomyelitis/chronic fatigue syndrome in Japanese population
Cited by: 16
Author(s): Toshimori Kitami, Sanae Fukuda, Tamotsu Kato, Kouzi Yamaguti, Yasuhito Nakatomi, Emi Yamano, Yosky Kataoka, Kei Mizuno, Yuuri Tsuboi, Yasushi Kogo, Harukazu Suzuki, Masayoshi Itoh, M. Morioka, Hideya Kawaji, Haruhiko Koseki, Jun Kikuchi, Yoshihide Hayashizaki, Hiroshi Ohno, Hirohiko Kuratsune, Yasuyoshi Watanabe
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-76762-3

Transcriptome and genome sequencing elucidates the molecular basis for the high yield and good quality of the hybrid rice variety Chuanyou6203
Cited by: 7
Author(s): Juansheng Ren, Fan Zhang, Fangyuan Gao, Lihua Zeng, Xianjun Lu, Xiuqin Zhao, Jian Lv, Xiangwen Su, Liping Liu, Mingli Dai, Jianlong Xu, Guangjun Ren
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-77402-6

Mycosporine-like amino acid and aromatic amino acid transcriptome response to UV and far-red light in the cyanobacterium Chlorogloeopsis fritschii PCC 6912
Cited by: 16
Author(s): Carole A. Llewellyn, Carolyn Greig, Alla Silkina, Bethan Kultschar, Matthew D. Hitchings, Garry Farnham
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-80065-y

Transcriptomics analysis for the identification of potential age-related genes and cells associated with three major urogenital cancers
Cited by: 3
Author(s): Jinlong Cao, Jianpeng Li, Xin Yang, Pan Li, Zhiqiang Yao, Dali Han, Lijun Ying, Lijie Wang, Junqiang Tian
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-81085-y

Early stability and late random tumor progression of a HER2-positive primary breast cancer patient-derived xenograft
Cited by: 6
Author(s): Lorena Landuzzi, Arianna Palladini, Claudio Ceccarelli, Sofia Asioli, Giordano Nicoletti, Veronica Giusti, Francesca Ruzzi, Marianna L. Ianzano, Laura Scalambra, Roberta Laranga, Tania Balboni, Maddalena Arigoni, Martina Olivero, Raffaele Calogero, Carla De Giovanni, Massimiliano Dall’Ora, Enrico Di Oto, Donatella Santini, Maria Pia Foschini, M.C. Cucchi, Simone Zanotti, Mario Taffurelli, Patrizia Nanni, Pier‐Luigi Lollini
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-81639-0

Loss of Parkinson’s susceptibility gene LRRK2 promotes carcinogen-induced lung tumorigenesis
Cited by: 21
Author(s): Chandra B. Lebovitz, Nicole Wretham, Maryam Osooly, Katy Milne, Tia Dash, Shelby Thornton, Basile Tessier‐Cloutier, Paalini Sathiyaseelan, Svetlana Bortnik, Nancy E. Go, Elizabeth C. Halvorsen, Rachel A. Cederberg, Norman S. Chow, Nancy Dos Santos, Kevin L. Bennewith, Brad H. Nelson, Marcel B. Bally, Wan L. Lam, Sharon M. Gorski
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-84080-5

Persistent COUP-TFII expression underlies the myopathy and impaired muscle regeneration observed in resistance to thyroid hormone-alpha
Cited by: 1
Author(s): Paola Aguiari, Yanyun Liu, Astgik Petrosyan, Sheue-yann Cheng, Gregory A. Brent, Laura Perin, Anna Milanesi
Software Mentions: 3
Published: over 5 years ago

10.7150/thno.50051

Adenylosuccinate lyase is oncogenic in colorectal cancer by causing mitochondrial dysfunction and independent activation of NRF2 and mTOR-MYC-axis
Cited by: 17
Author(s): Stephanie Taha‐Mehlitz, Gaia Bianco, Mairene Coto‐Llerena, Venkatesh Kancherla, Glenn R. Bantug, John Gallon, Caner Ercan, Federica Panebianco, Serenella Eppenberger‐Castori, M. Strauß, Sebastian M. Staubli, Martin Bolli, Ralph Peterli, Matthias S. Matter, Luigi Terracciano, Markus von Flüe, Charlotte K.Y. Ng, Savas D. Soysal, Otto Kollmar, Salvatore Piscuoglio
Software Mentions: 3
Published: over 5 years ago

10.7150/thno.53737

Intratumor heterogeneity of breast cancer detected by epialleles shows association with hypoxic microenvironment
Cited by: 5
Author(s): Yihan Wang, Yan Zhang, Yan Huang, Chuangeng Chen, Xingda Zhang, Ying Xing, Yue Gu, Mengyan Zhang, Li Cai, Shouping Xu, Baoqing Sun
Software Mentions: 3
Published: over 5 years ago

10.7150/thno.54999

Progressive stretch enhances growth and maturation of 3D stem-cell-derived myocardium
Cited by: 28
Author(s): Kun Lü, Thomas Seidel, Xiaochun Cao-Ehlker, Tatjana Dorn, Aarif M.N. Batcha, Christine Schneider, María Eugenia Aubet Semmler, Tilmann Volk, Alessandra Moretti, Andreas Dendorfer, Roland Tomasi
Software Mentions: 3
Published: over 5 years ago

10.7150/thno.57237

The metabesity factor HMG20A potentiates astrocyte survival and reactive astrogliosis preserving neuronal integrity
Cited by: 14
Author(s): Petra I. Lorenzo, Eugenia Martin Vázquez, Livia López-Noriega, Esther Fuente-Martín, José Manuel Mellado-Gil, Jaime M. Franco, Nadia Cobo-Vuilleumier, José A. Guerrero-Martínez, Silvana Y. Romero-Zerbo, Jesús A Perez-Cabello, Sabrina Rivero, Antonio Campos‐Caro, Christian Claude Lachaud, Alejandra Crespo Barreda, Manuel Aguilar‐Diosdado, Esther Fuentes, Aléjandro Martín-Montalvo, Manuel Álvarez‐Dolado, Franz Martı́n, Gemma Rojo‐Martínez, David Pozo, Francisco Javier Bermúdez‐Silva, Valentine Comaills, José Carlos Castañeda Reyes, Benoît Gauthier
Software Mentions: 3
Published: over 5 years ago

10.3390/toxins9060184

Screening of Deoxynivalenol Producing Strains and Elucidation of Possible Toxigenic Molecular Mechanism
Cited by: 13
Author(s): Xizhong Zheng, Xiaoli Zhang, Lina Zhao, Maurice Tibiru Apaliya, Qiya Yang, Wei Sun, Xiaoyun Zhang, Hongyin Zhang
Software Mentions: 3
Published: about 9 years ago

10.3390/toxins12050290

AFB1 Induced Transcriptional Regulation Related to Apoptosis and Lipid Metabolism in Liver of Chicken
Cited by: 27
Author(s): Xueqin Liu, Suchismita Mishra, Tao Wang, Zhongxian Xu, Xiaoling Zhao, Yan Wang, Huadong Yin, Xiaolan Fan, Bo Zeng, Mingyao Yang, Dapeng Yang, Qingyong Ni, Yan Li, Mingwang Zhang, Qing Zhu, Feng Chen, Diyan Li
Software Mentions: 3
Published: over 6 years ago

10.1186/s40035-018-0135-7

GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis
Cited by: 11
Author(s): William R. Swindell, Krzysztof Bojanowski, Mark S. Kindy, R.M.W. Chau, Dorothy Ko
Software Mentions: 3
Published: over 7 years ago

10.1186/s40035-021-00249-y

Several miRNAs derived from serum extracellular vesicles are potential biomarkers for early diagnosis and progression of Parkinson’s disease
Cited by: 31
Author(s): Shulei He, Lu Huang, Ci Shao, Tiejian Nie, Xia Li, Bozhou Cui, Fangfang Lu, Lin Zhu, Bolin Chen, Qian Yang
Software Mentions: 3
Published: about 5 years ago

10.1038/tp.2016.229

Transcriptome sequencing of the choroid plexus in schizophrenia
Cited by: 42
Author(s): S Kim, Young Sun Hwang, Doheon Lee, Maree J. Webster
Software Mentions: 3
Published: over 9 years ago

10.1038/s41398-018-0355-8

Cell type-specific gene expression patterns associated with posttraumatic stress disorder in World Trade Center responders
Cited by: 79
Author(s): Pei‐Fen Kuan, Xiaohua Yang, Sean Clouston, Ruwei Xu, Roman Kotov, Monika A. Waszczuk, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 3
Published: over 7 years ago

10.1038/s41398-019-0610-7

Protein expression of prenyltransferase subunits in postmortem schizophrenia dorsolateral prefrontal cortex
Cited by: 8
Author(s): Anita Pinner, Toni Mueller, Khaled Alganem, Robert E. McCullumsmith, James H. Meador‐Woodruff
Software Mentions: 3
Published: over 6 years ago

10.1038/s41398-021-01435-2

Convergent and distributed effects of the 3q29 deletion on the human neural transcriptome
Cited by: 8
Author(s): Esra Sefik, Ryan H. Purcell, q Emory, Elaine F. Walker, Gary J. Bassell, Jennifer G. Mullé
Software Mentions: 3
Published: about 5 years ago

10.1186/s13063-021-05442-y

Does intervention with GLP-1 receptor agonist semaglutide modulate perception of sweet taste in women with obesity: study protocol of a randomized, single-blinded, placebo-controlled clinical trial
Cited by: 3
Author(s): Mojca Jensterle, Simona Ferjan, Tadej Battelino, Jernej Kovač, Saba Battelino, Dušan Šuput, Andrej Vovk, Andrej Janež
Software Mentions: 3
Published: about 5 years ago

10.1101/2021.01.19.427194

BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2
Cited by: 7
Author(s): Ruilin Tian, Avi J. Samelson, Veronica V. Rezelj, Merissa Chen, Gokul N. Ramadoss, Xiaoyan Guo, Alice Mac Kain, Quang Tran, Shion A. Lim, Irene Lui, James K. Nuñez, Sarah J. Rockwood, Na Liu, Jared Carlson-Stevermer, Jennifer Oki, Travis J. Maures, Kevin Holden, Jonathan S. Weissman, James A. Wells, Bruce R. Conklin, Marco Vignuzzi, Martin Kampmann
Software Mentions: 3
Published: over 5 years ago

10.1101/2021.01.19.426885

Rapid protection from COVID-19 in nonhuman primates vaccinated intramuscularly but not intranasally with a single dose of a recombinant vaccine
Cited by: 14
Author(s): Wakako Furuyama, Kyle Shifflett, Amanda N Pinksi, Amanda Griffin, Friederike Feldmann, Atsushi Okumura, Tylisha Gourdine, Allen Jankeel, Jamie Lovaglio, Patrick W. Hanley, Tina Thomas, Chad S. Clancy, Ilhem Messaoudi, Andrea Marzi
Software Mentions: 3
Published: over 5 years ago

10.1101/2021.07.11.451964

Pathogenic and transcriptomic differences of emerging SARS-CoV-2 variants in the Syrian golden hamster model
Cited by: 3
Author(s): Kyle L. O’Donnell, Amanda N. Pinski, Chad S. Clancy, Tylisha Gourdine, Kyle Shifflett, Paige Fletcher, Ilhem Messaoudi, Andrea Marzi
Software Mentions: 3
Published: about 5 years ago

10.1128/mBio.00813-16

Effect of Shear Stress on Pseudomonas aeruginosa Isolated from the Cystic Fibrosis Lung
Cited by: 24
Author(s): Jozef Dingemans, Pieter Monsieurs, Sung-Huan Yu, Aurélie Crabbé, Konrad U. Förstner, Anne Malfroot, Pierre Cornélis, Rob Van Houdt
Software Mentions: 3
Published: almost 10 years ago

10.1128/mBio.01950-18

Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery
Cited by: 8
Author(s): James T. Van Leuven, Meng Mao, Denghui Xing, Gordon M. Bennett, John P. McCutcheon
Software Mentions: 3
Published: about 7 years ago

10.1128/mBio.00215-20

Norovirus Replication in Human Intestinal Epithelial Cells Is Restricted by the Interferon-Induced JAK/STAT Signaling Pathway and RNA Polymerase II-Mediated Transcriptional Responses
Cited by: 56
Author(s): Myra Hosmillo, Yasmin Chaudhry, Komal Nayak, Frédéric Sorgeloos, Bon‐Kyoung Koo, Alessandra Merenda, Reidun Lillestøl, Lydia N Drumright, Matthias Zilbauer, Ian Goodfellow
Software Mentions: 3
Published: over 6 years ago

10.1128/mBio.01628-20

Pathogenesis of Human Papillomaviruses Requires the ATR/p62 Autophagy-Related Pathway
Cited by: 11
Author(s): Siqi Hong, Yan Li, Paul J. Kaminski, Jorge Andrade, Laimonis A. Laimins
Software Mentions: 3
Published: about 6 years ago

10.1128/mBio.03533-20

<i>In Vivo</i> Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses
Cited by: 23
Author(s): Carl J. Yeoman, Christopher J. Fields, Pascale Lepercq, Philippe Ruiz, Evelyne Forano, Bryan A. White, Pascale Mosoni
Software Mentions: 3
Published: over 5 years ago

10.1128/mSphere.00378-19

Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats
Cited by: 15
Author(s): Julia M. McGonigle, Jeremiah A. Bernau, Brenda B. Bowen, William J. Brazelton
Software Mentions: 3
Published: about 7 years ago

10.1128/mSphere.00065-20

Convergence between Regulation of Carbon Utilization and Catabolic Repression in Xanthophyllomyces dendrorhous
Cited by: 3
Author(s): Pilar Martínez-Moya, Sebastián Campusano, Pamela Córdova, Alberto Paradela, Dionisia Sepúlveda, Jennifer Alcaı́no, Marcelo Baeza, Víctor Cifuentes
Software Mentions: 3
Published: over 6 years ago

10.1128/mSphere.00659-20

MARTX Toxin-Stimulated Interplay between Human Cells and Vibrio vulnificus
Cited by: 8
Author(s): Byoung Sik Kim, Jong-Hwan Kim, Sunghee Choi, Shinhye Park, Eun-Young Lee, Sung-Cheol Koh, Choong‐Min Ryu, Seon‐Young Kim, Myung Hee Kim
Software Mentions: 3
Published: about 6 years ago

10.1128/mSystems.00216-19

Dual RNA-seq in Streptococcus pneumoniae Infection Reveals Compartmentalized Neutrophil Responses in Lung and Pleural Space
Cited by: 19
Author(s): Neil D. Ritchie, Tom Evans
Software Mentions: 3
Published: about 7 years ago

10.1128/mSystems.00416-19

Genomewide Analysis of Mode of Action of the <i>S</i> -Adenosylmethionine Analogue Sinefungin in Leishmania infantum
Cited by: 13
Author(s): Arijit Bhattacharya, Meenakshi Sharma, Charles Packianathan, Barry P. Rosen, Philippe Leprohon, Marc Ouellette
Software Mentions: 3
Published: almost 7 years ago

10.1128/mSystems.00451-19

Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer
Cited by: 24
Author(s): Sarah Tomkovich, Raad Z. Gharaibeh, Christine M. Dejea, Jillian L. Pope, Jinmai Jiang, Kathryn Winglee, Josée Gauthier, Rachel C. Newsome, Ye Yang, Anthony A. Fodor, Thomas D. Schmittgen, Cynthia L. Sears, Christian Jobin
Software Mentions: 3
Published: over 6 years ago

10.1128/mSystems.00358-21

Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments
Cited by: 16
Author(s): Sean Ting-Shyang Wei, Yi Lung Chen, Yu Wei Wu, Tien Yu Wu, Yi Li Lai, Po Hsiang Wang, Wael Ismail, Tzong‐Huei Lee, Yin-Ru Chiang
Software Mentions: 3
Published: about 5 years ago

10.1186/s40246-019-0199-1

Transcriptome-wide analysis of differentially expressed chemokine receptors, SNPs, and SSRs in the age-related macular degeneration
Cited by: 22
Author(s): Madhu Sudhana Saddala, Anton Lennikov, Anthony Mukwaya, Lijuan Fan, Zhengmao Hu, Huang Hu
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.10809

An aspartyl protease defines a novel pathway for export of Toxoplasma proteins into the host cell
Cited by: 93
Author(s): Michael Coffey, Brad E. Sleebs, Alessandro D. Uboldi, Alexandra L. Garnham, Magdalena Franco, Nicole D. Marino, Michael W. Panas, David J. P. Ferguson, Marta Enciso, Matthew T O'Neill, Sash Lopaticki, Rebecca J. Stewart, Grant Dewson, Gordon K. Smyth, Brian J. Smith, Seth L. Masters, John C. Boothroyd, Justin A Boddey, Christopher J. Tonkin
Software Mentions: 3
Published: almost 11 years ago

10.7554/eLife.50705

Cardiac mitochondrial function depends on BUD23 mediated ribosome programming
Cited by: 10
Author(s): Matthew Baxter, Maria Voronkov, Toryn Poolman, Gina L. J. Galli, Christian Pinali, Laurence Goosey, Abigail Knight, Karolina Krakowiak, Robert Maidstone, Mudassar Iqbal, Min Zi, Sukhpal Prehar, Elizabeth J. Cartwright, Julie Gibbs, Laura Matthews, Antony Adamson, Neil Humphreys, Pedro Rebelo-Guiomar, Michal Minczuk, David A. Bechtold, A. S. I. Loudon, David Ray
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.63731

CEP78 functions downstream of CEP350 to control biogenesis of primary cilia by negatively regulating CP110 levels
Cited by: 24
Author(s): André Gonçalves, Sarah Kirstine Hasselbalch, Beinta Biskopstø Joensen, Sebastian Patzke, Pernille Martens, Signe Krogh Ohlsen, Mathieu Quinodoz, Konstantinos Nikopoulos, Reem Suleiman, Magnus Per Damsø Jeppesen, Catja Weiss, Søren Tvorup Christensen, Carlo Rivolta, Jens S. Andersen, Pietro Farinelli, Lotte B. Pedersen
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.47866

Elevating acetyl-CoA levels reduces aspects of brain aging
Cited by: 72
Author(s): António Currais, Ling Huang, Joshua Goldberg, Michael Petrascheck, Gamze Ates, António Pinto-Duarte, Maxim N. Shokhirev, David Schubert, Pamela Maher
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.34970

SET-9 and SET-26 are H3K4me3 readers and play critical roles in germline development and longevity
Cited by: 17
Author(s): Wenke Wang, Amaresh Chaturbedi, Minghui Wang, Serim An, Velayudhan Satheeja Santhi, Siu Sylvia Lee
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.58836

Gene autoregulation by 3’ UTR-derived bacterial small RNAs
Cited by: 32
Author(s): Mona Hoyos, Michaela Huber, Konrad U. Förstner, Kai Papenfort
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.48718

Receptor-specific interactome as a hub for rapid cue-induced selective translation in axons
Cited by: 40
Author(s): Max Koppers, Roberta Cagnetta, Toshiaki Shigeoka, Lucia Cs Wunderlich, Pedro P. Vallejo Ramirez, Julie Qiaojin Lin, Sixian Zhao, Maximilian Ah Jakobs, Asha Dwivedy, Michael S. Minett, Anaïs Bellon, Clemens F. Kaminski, William A. Harris, John G. Flanagan, Christine E. Holt
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.31362

A tissue-specific, Gata6-driven transcriptional program instructs remodeling of the mature arterial tree
Cited by: 11
Author(s): Marta Losa, Víctor Latorre, Munazah Andrabi, Franck Ladam, Charles G. Sagerström, Ana Nóvoa, Peyman Zarrineh, Laure Bridoux, Neil A. Hanley, Bernard Malissen, Nicoletta Bobola
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.52563

Linker histone H1.2 and H1.4 affect the neutrophil lineage determination
Cited by: 9
Author(s): Gabriel Sollberger, Robert Streeck, Falko Apel, Brian E. Caffrey, Arthur I. Skoultchi, Arturo Zychlinsky
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.63997

Quantitative glycoproteomics reveals cellular substrate selectivity of the ER protein quality control sensors UGGT1 and UGGT2
Cited by: 23
Author(s): Benjamin M. Adams, Nathan P Canniff, Kevin P Guay, Ida Signe Bohse Larsen, Daniel N. Hebert
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.50845

A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols
Cited by: 34
Author(s): Vayu Maini Rekdal, Paola Nol Bernadino, Michael U. Luescher, Sina Kiamehr, Cuong H. Le, Jordan E. Bisanz, Peter J. Turnbaugh, Elizabeth N. Bess, Emily P. Balskus
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.65331

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast
Cited by: 2
Author(s): Rachael Emily Turner, Paul F. Harrison, Angavai Swaminathan, Calvin A. Kraupner-Taylor, Belinda J. Goldie, Michael See, Amanda L. Peterson, Ralf B. Schittenhelm, David Powell, Darren J. Creek, Bernhard Dichtl, Traude H. Beilharz
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.01439

Coordinated genomic control of ciliogenesis and cell movement by RFX2
Cited by: 115
Author(s): Mei I. Chung, Taejoon Kwon, Fan Tu, Eric Brooks, Ritu Gupta, Matthew D. Meyer, Julie C. Baker, Edward M. Marcotte, John B. Wallingford
Software Mentions: 3
Published: over 12 years ago

10.7554/eLife.29518

Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naïve state
Cited by: 32
Author(s): Yixuan Wang, Chengchen Zhao, Zhenzhen Hou, Yuanyuan Yang, Yan Bi, Hong Wang, Yong Zhang, Shaorong Gao
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.49816

Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment
Cited by: 16
Author(s): Jordan G. Okie, Amisha T. Poret-Peterson, Zarraz M.-P. Lee, Alexander Richter, Luis David Alcaraz, Luis E. Eguiarte, Janet L. Siefert, Valeria Souza, Chris L. Dupont, James J. Elser
Software Mentions: 3
Published: over 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568