bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fphys.2019.00101

Characterization of Endothelial and Smooth Muscle Cells From Different Canine Vessels
Cited by: 19
Author(s): Loes A. Oosterhoff, Hedwig S. Kruitwagen, Monique E. van Wolferen, Bas W. M. van Balkom, Michal Mokrý, Nico Lansu, Noortje A.M. van den Dungen, Louis C. Penning, Talitha C.F. Spanjersberg, Johannes W. de Graaf, Tomas Veenendaal, Flin Zomerdijk, Joost O. Fledderus, Bart Spee, Frank G. van Steenbeek
Software Mentions: 3
Published: over 7 years ago

10.3389/fphys.2021.658518

Mechanisms of Impaired Lung Development and Ciliation in Mannosidase-1-Alpha-2 (Man1a2) Mutants
Cited by: 2
Author(s): Mylarappa Ningappa, Morayooluwa Adenuga, Kim A. Ngo, Nada Mohamed, Tejaswini Narayanan, Krishna Prasadan, Chethan Ashokkumar, Jishnu Das, Lori Schmitt, Hannah Hartman, Anuradha Sehrawat, Cláudia Salgado, Miguel Reyes‐Múgica, George K. Gittes, Cecilia Lo, Shankar Subramaniam, Rakesh Sindhi
Software Mentions: 3
Published: about 5 years ago

10.3389/fphys.2020.587358

Transcriptional Programs Driving Shear Stress-Induced Differentiation of Kidney Proximal Tubule Cells in Culture
Cited by: 18
Author(s): Hyun Jung Park, Zhenjiang Fan, Yinge Bai, Qidong Ren, Youssef Rbaibi, Kimberly R. Long, Megan L. Gliozzi, Natalie Rittenhouse, Joseph Locker, Amanda C. Poholek, Ora A. Weisz
Software Mentions: 3
Published: almost 6 years ago

10.3389/fphys.2019.00214

Understanding Molecular Mechanisms of the Brain Through Transcriptomics
Cited by: 14
Author(s): Wei Wang, Guang-Zhong Wang
Software Mentions: 3
Published: over 7 years ago

10.3389/fphys.2020.588450

Transcriptome Analysis and Knockdown of the Juvenile Hormone Esterase Gene Reveal Abnormal Feeding Behavior in the Sugarcane Giant Borer
Cited by: 5
Author(s): Daniel D. Noriega, Fabrício Barbosa Monteiro Arraes, José Dijair Antonino, Leonardo Lima Pepino Macedo, Fernando Fonseca, Roberto Coiti Togawa, Priscila Grynberg, Maria C. M. Silva, A. S. Negrisoli, Maria Fátima Grossi-de-Sá
Software Mentions: 3
Published: almost 6 years ago

10.3389/fpls.2016.01934

De novo Sequencing and Comparative Transcriptomics of Floral Development of the Distylous Species Lithospermum multiflorum
Cited by: 14
Author(s): James I. Cohen
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2016.01255

Photosynthate Regulation of the Root System Architecture Mediated by the Heterotrimeric G Protein Complex in Arabidopsis
Cited by: 28
Author(s): Yashwanti Mudgil, Abhijit Karve, Paulo José Pereira Lima Teixeira, Kun Jiang, Meral Tunc‐Ozdemir, Alan M. Jones
Software Mentions: 3
Published: about 10 years ago

10.3389/fpls.2019.01772

Coexpression of PalbHLH1 and PalMYB90 Genes From Populus alba Enhances Pathogen Resistance in Poplar by Increasing the Flavonoid Content
Cited by: 33
Author(s): Qiuxian Bai, Bingbing Duan, Jianchao Ma, Yannan Fen, Shujiao Sun, Qiming Long, Jiaojiao Lv, Dongshi Wan
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2016.00682

Transcriptomic Analysis Identifies Differentially Expressed Genes (DEGs) Associated with Bolting and Flowering in Radish (Raphanus sativus L.)
Cited by: 17
Author(s): Shaoping Nie, Chao Li, Yan Wang, Liang Xu, Everlyne M. Muleke, Mingjia Tang, Xiaochuan Sun, Liwang Liu
Software Mentions: 3
Published: over 10 years ago

10.3390/genes12040545

A Complex Gene Network Mediated by Ethylene Signal Transduction TFs Defines the Flower Induction and Differentiation in Olea europaea L.
Cited by: 2
Author(s): Amelia Salimonti, Ivano Forgione, Tiziana Maria Sirangelo, Guglielmo Puccio, Antonio Mauceri, Francesco Mercati, Francesco Sunseri, Fabrizio Carbone
Software Mentions: 3
Published: over 5 years ago

10.3390/genes12091374

Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods
Cited by: 5
Author(s): Yibing Liu, Ying Yu, Ai Hong, Fengxia Zhang, Xitong Zhao, Huatao Liu, Yong Shi, Kai Xing, Chuduan Wang
Software Mentions: 3
Published: almost 5 years ago

10.1590/1678-4685-GMB-2016-0101

A comprehensive transcriptome analysis of skeletal muscles in two Polish pig breeds differing in fat and meat quality traits
Cited by: 32
Author(s): Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Ropka‐Molik, M. Tyra, Artur Gurgul
Software Mentions: 3
Published: over 8 years ago

10.1534/genetics.120.303155

Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif
Cited by: 11
Author(s): Robin L. Armstrong, Souradip Das, Christina A. Hill, Robert J. Duronio, Jared Nordman
Software Mentions: 3
Published: over 6 years ago

10.1016/j.gdata.2015.12.027

Transcriptional profiling of the epigenetic regulator Smchd1
Cited by: 12
Author(s): Ruijie Liu, Kelan Chen, Natasha Jansz, Marnie E. Blewitt, Matthew E. Ritchie
Software Mentions: 3
Published: over 10 years ago

10.1186/gb-2010-11-10-r106

Differential expression analysis for sequence count data
Cited by: 12,645
Author(s): Simon Anders, Wolfgang Huber
Software Mentions: 3
Published: almost 16 years ago

10.1186/gb-2012-13-11-r102

Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs
Cited by: 63
Author(s): Ana C. Marques, Jennifer Y. Tan, Sheena Lee, Lesheng Kong, Andreas Heger, Chris P. Ponting
Software Mentions: 3
Published: over 14 years ago

10.1186/gb-2013-14-8-r89

The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus
Cited by: 191
Author(s): Erich M. Schwarz, Pasi K. Korhonen, Bronwyn E. Campbell, Neil D. Young, Aaron R. Jex, Abdul Jabbar, Ross S. Hall, Alinda Mondal, Adina Howe, Jason Pell, Andreas Hofmann, Peter R. Boag, Xing‐Quan Zhu, T. Ryan Gregory, Alex Loukas, Brian A. Williams, Igor Antoshechkin, C. Titus Brown, Paul W. Sternberg, Robin B. Gasser
Software Mentions: 3
Published: over 13 years ago

10.1186/s13059-014-0567-z

The draft genome of Primula veris yields insights into the molecular basis of heterostyly
Cited by: 90
Author(s): Michael Nowak, Giancarlo Russo, Ralph Schlapbach, Cuong Nguyen Huu, Michael Lenhard, Elena Conti
Software Mentions: 3
Published: over 11 years ago

10.1186/s13059-016-0883-6

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
Cited by: 156
Author(s): Anna Vlasova, Salvador Capella-Gutiérrez, Martha Rendón-Anaya, Miguel Ángel Hernández‐Oñate, André E. Minoche, Ionas Erb, Francisco Câmara, Pablo Prieto Barja, André Corvelo, Walter Sanseverino, Gastón Westergaard, Juliane C. Dohm, George J. Pappas, Soledad Saburido-Álvarez, Darek Kedra, Irene González González, Luca Cozzuto, Jèssica Gómez-Garrido, María A. Aguilar-Morón, Núria Andreu, O. Mario Aguilar, Jordi García-Más, Maik Zehnsdorf, Martı́n Vázquez, Alfonso Delgado‐Salinas, Luis Delaye, Ernesto Lowy, Alejandro Mentaberry, Rosana Pereira Vianello-Brondani, José Luis Garcı́a, Tyler Alioto, Federico Sánchez, Heinz Himmelbauer, Marta Santalla, Cédric Notredame, Toni Gabaldón, Alfredo Herrera-Estrella, Roderic Guigó
Software Mentions: 3
Published: over 10 years ago

10.1186/s13059-017-1222-2

Translational contributions to tissue specificity in rhythmic and constitutive gene expression
Cited by: 49
Author(s): Violeta Castelo-Szekely, Alaaddin Bulak Arpat, Peggy Janich, David Gatfield
Software Mentions: 3
Published: about 9 years ago

10.1186/s13059-017-1301-4

Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis
Cited by: 60
Author(s): Jacki Heraud-Farlow, Alistair M. Chalk, Sandra Linder, Qin Li, Scott Taylor, Joshua M. White, Lokman Pang, Brian Liddicoat, Ankita Gupte, Carl R. Walkley
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13059-018-1531-0

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops
Cited by: 54
Author(s): Yu Guo, Andrew A. Perez, Dennis J. Hazelett, Gerhard A. Coetzee, Suhn Kyong Rhie, Peggy J. Farnham
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13059-019-1873-2

The majority of A-to-I RNA editing is not required for mammalian homeostasis
Cited by: 55
Author(s): Alistair M. Chalk, Scott Taylor, Jacki Heraud-Farlow, Carl R. Walkley
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-019-1876-z

Non-coding RNAs underlie genetic predisposition to breast cancer
Cited by: 18
Author(s): Mahdi Moradi Marjaneh, Jonathan Beesley, Tracy A. O’Mara, Pamela Mukhopadhyay, Lambros T. Koufariotis, Stephen H. Kazakoff, Nehal Hussein, Laura Fachal, Nenad Bartoniček, Kristine M. Hillman, Susanne Kaufmann, Haran Sivakumaran, Chanel E. Smart, Amy E. McCart Reed, Kaltin Ferguson, Jodi M. Saunus, Sunil R. Lakhani, Daniel R. Barnes, Antonis C. Antoniou, Marcel E. Dinger, Nicola Waddell, Douglas F. Easton, Alison M. Dunning, Georgia Chenevix-Trench, Stacey L. Edwards, Juliet D. French
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-020-01972-x

A benchmark of algorithms for the analysis of pooled CRISPR screens
Cited by: 38
Author(s): Sunil Bodapati, Timothy Daley, Xueqiu Lin, James Zou, Lei Qi
Software Mentions: 3
Published: over 6 years ago

10.1038/sdata.2017.20

Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells
Cited by: 11
Author(s): Stephen J. Pettitt, Dragomir B. Krastev, Helen Pemberton, Yari Fontebasso, Jessica Frankum, Farah L. Rehman, Rachel Brough, Feifei Song, Ilirjana Bajrami, Rumana Rafiq, Fredrik Wållberg, Iwanka Kozarewa, Kerry Fenwick, Javier Armisen-Garrido, Amanda Swain, Aditi Gulati, James Campbell, Alan Ashworth, Christopher J. Lord
Software Mentions: 3
Published: over 9 years ago

10.1038/sdata.2017.118

A gene expression atlas of adult Schistosoma mansoni and their gonads
Cited by: 44
Author(s): Zhigang Lu, Florian Sessler, Nancy Holroyd, Steffen Hahnel, Thomas Quack, Matthew Berriman, Christoph G. Grevelding
Software Mentions: 3
Published: about 9 years ago

10.1038/sdata.2017.163

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system
Cited by: 4
Author(s): Margherita Francescatto, Marina Lizio, Ingrid H.C.H.M. Philippens, Luba M. Pardo, Ronald E. Bontrop, Mizuho Sakai, Shoko Watanabe, Masayoshi Itoh, Akira Hasegawa, Timo Lassmann, Jessica Severin, Jayson Harshbarger, Imad Abugessaisa, Takeya Kasukawa, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Hideya Kawaji, Patrizia Rizzu, Peter Heutink
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41597-019-0117-3

Metagenomics and transcriptomics data from human colorectal cancer
Cited by: 5
Author(s): Tina Visnovska, Patrick J. Biggs, Frank Frizelle, Rachel Purcell
Software Mentions: 3
Published: about 7 years ago

10.1038/s41597-020-00628-6

Consensus transcriptional regulatory networks of coronavirus-infected human cells
Cited by: 23
Author(s): Scott A. Ochsner, Rudolf T. Pillich, Neil J. McKenna
Software Mentions: 3
Published: almost 6 years ago

10.1038/srep02898

Soft truncation thresholding for gene set analysis of RNA-seq data: Application to a vaccine study
Cited by: 15
Author(s): Brooke L. Fridley, Gregory D. Jenkins, Diane E. Grill, Richard B. Kennedy, Gregory A. Poland, Ann L. Oberg
Software Mentions: 3
Published: almost 13 years ago

10.1038/srep13456

TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability
Cited by: 15
Author(s): Lamiaa Bahnassawy, Thanneer M. Perumal, Laura González-Cano, Anna-Lena Hillje, Leila Taher, Wojciech Makałowski, Yutaka Suzuki, Georg Fuellen, Antonio del Sol, Jens Christian Schwamborn
Software Mentions: 3
Published: about 11 years ago

10.1038/srep18399

Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing
Cited by: 56
Author(s): Aroa Suárez-Vega, Christophe Klopp, Christèle Robert-Granié, Gwenola Tosser‐Klopp, Juan José Arranz
Software Mentions: 3
Published: over 10 years ago

10.1038/srep20837

Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model
Cited by: 15
Author(s): Els Willems, Carlos Guerrero-Bosagna, Eddy Decuypere, Steven Janssens, Johan Buyse, Nadine Buys, Per Jensen, Nadia Everaert
Software Mentions: 3
Published: over 10 years ago

10.1038/srep24061

Empirical insights into the stochasticity of small RNA sequencing
Cited by: 5
Author(s): Li‐Xuan Qin, Thomas Tuschl, Samuel Singer
Software Mentions: 3
Published: over 10 years ago

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/s41598-019-43862-8

CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genes
Cited by: 53
Author(s): Alex K. Datsomor, Nikola Zic, Keshuai Li, Rolf Erik Olsen, Yang Jin, Jon Olav Vik, Rolf B. Edvardsen, Fabian Grammes, Anna Wargelius, Per Winge
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-43935-8

GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data
Cited by: 105
Author(s): Naim Al Mahi, Mehdi Fazel Najafabadi, Marcin Pilarczyk, Michal Kouril, Mario Medvedovic
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-44944-3

Detection of novel biomarkers for early detection of Non-Muscle-Invasive Bladder Cancer using Competing Endogenous RNA network analysis
Cited by: 35
Author(s): Morteza Kouhsar, Sadegh Azimzadeh Jamalkandi, Ali Moeini, Ali Masoudi‐Nejad
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-44924-7

Whole-blood transcriptomic signatures induced during immunization by chloroquine prophylaxis and Plasmodium falciparum sporozoites
Cited by: 23
Author(s): Tuan M. Tran, Else M. Bijker, Mariëlle C. Haks, Tom H. M. Ottenhoff, Leo G. Visser, Remko Schats, Pratap Venepally, Hernán Lorenzi, Peter D. Crompton, Robert W. Sauerwein
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-44600-w

Genome-wide identification and characterization of long non-coding RNAs expressed during sheep fetal and postnatal hair follicle development
Cited by: 27
Author(s): Ablat Sulayman, Kechuan Tian, Xixia Huang, Yuezhen Tian, Xinming Xu, Xuefeng Fu, Bi Zhao, Weiwei Wu, Dan Wang, Aynur Yasin, Hanikezi Tulafu
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-45665-3

Deep transcriptome analysis using RNA-Seq suggests novel insights into molecular aspects of fat-tail metabolism in sheep
Cited by: 32
Author(s): Mohammad Reza Bakhtiarizadeh, Abdolreza Salehi, Ali A. Alamouti, Rostam Abdollahi-Arpanahi, Seyed Alireza Salami
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-45528-x

Loss of MafA and MafB expression promotes islet inflammation
Cited by: 13
Author(s): Tania Singh, Jesper K. Colberg, Luis Sarmiento, Patrícia Chaves, Lars Bolvig Hansen, Sara Bsharat, Luis Rodrigo Cataldo, Monika Dudenhöffer-Pfeifer, Malin Fex, David Bryder, Dan Holmberg, Ewa Sitnicka, Corrado Cilio, Rashmi B. Prasad, Isabella Artner
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-45821-9

Skeletal muscle in MuRF1 null mice is not spared in low-gravity conditions, indicating atrophy proceeds by unique mechanisms in space
Cited by: 39
Author(s): Samuel M. Cadena, Yunyu Zhang, Jian Fang, Sophie Brachat, Pia Kuss, E. Giorgetti, Louis S. Stodieck, Michaela Kneissel, David J. Glass
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-46473-5

Differential expression of individual transcript variants of PD-1 and PD-L2 genes on Th-1/Th-2 status is guaranteed for prognosis prediction in PCNSL
Cited by: 22
Author(s): Yasuo Takashima, Atsushı Kawaguchi, Ryuichi Sato, Kenichi Yoshida, Azusa Hayano, Jumpei Homma, Junya Fukai, Yasuo Iwadate, Koji Kajiwara, Shin Ishizawa, Hiroaki Hondoh, Masakazu Nakano, Seishi Ogawa, Kei Tashiro
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-47389-w

Electrical stimulation shifts healing/scarring towards regeneration in a rat limb amputation model
Cited by: 30
Author(s): Karla Mychellyne Costa Oliveira, John H. Barker, Eugène Berezikov, Lukas Pindur, S Kynigopoulos, Maria Eischen-Loges, Zhongchao Han, Mit Balvantray Bhavsar, Dirk Henrich, Liudmila Leppik
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-48741-w

SerpinB2 inhibits migration and promotes a resolution phase signature in large peritoneal macrophages
Cited by: 24
Author(s): Wayne A. Schroder, Thiago Dominguez Crespo Hirata, Thuy T. Le, Joy Gardner, Glen M. Boyle, Jonathan Ellis, Eri Nakayama, Dilan Pathirana, Helder I. Nakaya, Andreas Suhrbier
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-49440-2

Transgenerational Self-Reconstruction of Disrupted Chromatin Organization After Exposure To An Environmental Stressor in Mice
Cited by: 23
Author(s): Carlos Díaz-Castillo, Raquel Chamorro-García, Toshihiro Shioda, Bruce Blumberg
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-49647-3

Comparative transcriptome analysis of the human endocervix and ectocervix during the proliferative and secretory phases of the menstrual cycle
Cited by: 7
Author(s): Sampurna Mukhopadhyay, Yupu Liang, Hong Hur, G. Villegas, Giulia Calenda, Alexandra Reis, Lily Millen, Patrick Barnable, Lisa Mamkina, Narender Kumar, Tamara Kalir, Rhoda Sperling, Natalia Teleshova
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-50229-6

Model-based clustering for identifying disease-associated SNPs in case-control genome-wide association studies
Cited by: 8
Author(s): Yan Xu, Li Xing, Jessica Su, Xuekui Zhang, Weiliang Qiu
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-50310-0

Comparative transcriptomics between species attributes reactogenicity pathways induced by the capsular group B meningococcal vaccine, 4CMenB, to the membrane-bound endotoxin of its outer membrane vesicle component
Cited by: 9
Author(s): Dylan Sheerin, Daniel O’Connor, Christina Dold, Elizabeth A. Clutterbuck, Moustafa Attar, Christine S. Rollier, Manish Sadarangani, Andrew J. Pollard
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-50718-8

The role of extracellular matrix in mouse and human corneal neovascularization
Cited by: 19
Author(s): Marco Barbariga, F. Vallone, Ettore Mosca, Fabio Bignami, Cinzia Magagnotti, Phillippe Fonteyne, Federica Chiappori, Luciano Milanesi, Paolo Rama, Annapaola Andolfo, Giulio Ferrari
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-52375-3

A New Strategy for Identifying Mechanisms of Drug-drug Interaction Using Transcriptome Analysis: Compound Kushen Injection as a Proof of Principle
Cited by: 4
Author(s): Hao Shen, Zhibo Qu, Yuka Harata-Lee, Jingang Cui, Thazin Nwe Aung, Wei Wang, R. Daniel Kortschak, David L. Adelson
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-52559-x

Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma
Cited by: 35
Author(s): Xia Tang, Delong Feng, Min Li, Jinxue Zhou, Xiaoyuan Li, Dachun Zhao, Bingtao Hao, Dewei Li, Keyue Ding
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-54180-4

A framework for identification of on- and off-target transcriptional responses to drug treatment
Cited by: 23
Author(s): Yi Huang, Masaaki Furuno, Takahiro Arakawa, Satoshi Takizawa, Michiel de Hoon, Harukazu Suzuki, Erik Arner
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-55132-8

Tissue-type plasminogen activator-primed human iPSC-derived neural progenitor cells promote motor recovery after severe spinal cord injury
Cited by: 7
Author(s): Yasuhiro Shiga, Akina Shiga, Pinar Mesci, HyoJun Kwon, Coralie Brifault, Jung Hyun Kim, Jacob Jeziorski, Chanond A. Nasamran, Seiji Ohtori, Alysson R. Muotri, Steven L. Gonias, W. Marie Campana
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-55896-z

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster
Cited by: 7
Author(s): Julia Bespyatykh, Egor Shitikov, Andrei Guliaev, Alexander Smolyakov, Ksenia M. Klimina, Vladimir A. Veselovsky, М В Малахова, Georgij Arapidi, Marine Dogonadze, Olga Manicheva, Dmitry Bespiatykh, Igor Mokrousov, Viacheslav Zhuravlev, Elena N. Ilina, Vadim M. Govorun
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-56790-4

Fetal androgen exposure is a determinant of adult male metabolic health
Cited by: 16
Author(s): Katarzyna Siemienowicz, Panagiotis Filis, Sophie Shaw, Alex Douglas, Jessica Thomas, Sally Mulroy, Forbes Howie, Paul A. Fowler, W. Colin Duncan, Michael T. Rae
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-58709-w

Nanocatalytic activity of clean-surfaced, faceted nanocrystalline gold enhances remyelination in animal models of multiple sclerosis
Cited by: 44
Author(s): Andrew P. Robinson, Joanne Zhongyan Zhang, Haley E. Titus, Molly Karl, Mikhail Merzliakov, Adam R. Dorfman, Stephen J. Karlik, Michael G. Stewart, Richard K. Watt, Benjin D. Facer, Jon D. Facer, Noah D. Christian, Karen S. Ho, Michael T. Hotchkin, Mark G. Mortenson, Robert H. Miller, Stephen D. Miller
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-61420-5

Eosinophil accumulation in postnatal lung is specific to the primary septation phase of development
Cited by: 17
Author(s): Lucas F. Loffredo, Mackenzie E. Coden, Brian M. Jeong, Matthew T. Walker, Kishore R. Anekalla, Ton C. Doan, Raul I. Rodriguez, M.J. Browning, Ki-Won Nam, James J. Lee, Hiam Abdala‐Valencia, Sergejs Berdnikovs
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-61857-8

De novo transcriptome assembly and analysis of Phragmites karka, an invasive halophyte, to study the mechanism of salinity stress tolerance
Cited by: 18
Author(s): Soumya Shree Nayak, Seema Pradhan, Dinabandhu Sahoo, Ajay Parida
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-63263-6

Circulating MicroRNA Profiling in Non-ST Elevated Coronary Artery Syndrome Highlights Genomic Associations with Serial Platelet Reactivity Measurements
Cited by: 14
Author(s): Kristian C. Becker, Lydia Coulter Kwee, Megan L. Neely, Elizabeth Grass, Joseph A. Jakubowski, Keith Fox, Harvey D. White, Simon Gregory, Paul A. Gurbel, Leonardo de Pinto Carvalho, Richard C. Becker, E. Magnus Ohman, Matthew T. Roe, Svati H. Shah, Mark Y. Chan
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-62286-3

Fabrication of Perfusable Vascular Channels and Capillaries in 3D Liver-like Tissue
Cited by: 20
Author(s): Nobuhito Mori, Yuka Akagi, Yukiko Imai, Yoichiro Takayama, Yasuyuki S. Kida
Software Mentions: 3
Published: over 6 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: almost 10 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

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568