bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0210538

Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles
Cited by: 24
Author(s): Antoine Pagé, Julien Tremblay, Luke Masson, Charles W. Greer
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0210586

Contrasting patterns of gene expression indicate differing pyrethroid resistance mechanisms across the range of the New World malaria vector Anopheles albimanus
Cited by: 19
Author(s): Lucy Mackenzie-Impoinvil, Gareth D. Weedall, Juan C. Lol, Jesús Pinto, Lucrecia Vizcaino, Nicole Dzuris, Jacob M. Riveron, Norma Padilla, Charles S. Wondji, Audrey Lenhart
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0186440

Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
Cited by: 13
Author(s): Roberto Orellana, Gina Chaput, Lye Meng Markillie, Hugh D. Mitchell, Matt Gaffrey, Galya Orr, Kristen M. DeAngelis
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0192439

A tale of two mixotrophic chrysophytes: Insights into the metabolisms of two Ochromonas species (Chrysophyceae) through a comparison of gene expression
Cited by: 39
Author(s): Alle A. Y. Lie, Zhenfeng Liu, Ramón Terrado, Avery O. Tatters, Karla B. Heidelberg, David A. Caron
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0147873

Transcriptome Analysis of the SL221 Cells at the Early Stage during Spodoptera litura Nucleopolyhedrovirus Infection
Cited by: 8
Author(s): Yu Qian, Yongqiang Xiong, Jianliang Liu, Dongling Wen, Xiaohui Wu, Hang Yin
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0141398

Deciphering Mineral Homeostasis in Barley Seed Transfer Cells at Transcriptional Level
Cited by: 13
Author(s): Behrooz Darbani, Shahin Noeparvar, Søren Borg
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0111975

17β-Estradiol Modulates Gene Expression in the Female Mouse Cerebral Cortex
Cited by: 17
Author(s): Gwendolyn I. Humphreys, Yvonne Ziegler, Ann M. Nardulli
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0227496

RNA profiling identifies novel, photoperiod-history dependent markers associated with enhanced saltwater performance in juvenile Atlantic salmon
Cited by: 9
Author(s): Marianne Iversen, Teshome Dagne Mulugeta, Børge Gellein Blikeng, Alexander C. West, Even H. Jørgensen, Simen Rød Sandve, David G. Hazlerigg
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0167958

Perigone Lobe Transcriptome Analysis Provides Insights into Rafflesia cantleyi Flower Development
Cited by: 10
Author(s): Xin-Wei Lee, Mohd-Noor Mat-Isa, Nur-Atiqah Mohd-Elias, Mohd Afiq Aizat-Juhari, Hoe-Han Goh, Paul H. Dear, Keng See Chow, Jumaat Adam, Rahmah Mohamed, Mohd Firdaus-Raih, Kiew Lian Wan
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0158317

Chronic Contractile Dysfunction without Hypertrophy Does Not Provoke a Compensatory Transcriptional Response in Mouse Hearts
Cited by: 3
Author(s): Scot J. Matkovich, David R. Grubb, Julie R. McMullen, Elizabeth A. Woodcock
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0197685

Sertoli cell-specific ablation of miR-17-92 cluster significantly alters whole testis transcriptome without apparent phenotypic effects
Cited by: 11
Author(s): Alicia Hurtado, Francisca M. Real, Rogelio Palomino, F. David Carmona, Miguel Burgos, Rafael Jiménez, Francisco Barrionuevo
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0249636

A comparison of shared patterns of differential gene expression and gene ontologies in response to water-stress in roots and leaves of four diverse genotypes of Lolium and Festuca spp. temperate pasture grasses
Cited by: 2
Author(s): Yuan Fu, Ann Thomas, Dagmara Gasior, John A. Harper, Cerys Jones, Matthew Hegarty, Torben Asp, Albert Fradera-Sola, Ian Armstead, Narcís Fernández-Fuentes
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0179411

Differential chromatin profiles partially determine transcription factor binding
Cited by: 4
Author(s): Rujian Chen, David K. Gifford
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0174303

Integrated transcriptomic and proteomic analysis of the molecular cargo of extracellular vesicles derived from porcine adipose tissue-derived mesenchymal stem cells
Cited by: 74
Author(s): Alfonso Eirin, Xiang Yang Zhu, Amrutesh S. Puranik, John R. Woollard, Hui Tang, Surendra Dasari, Amir Lerman, André J. van Wijnen, Lilach O. Lerman
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0177733

Transcriptome-microRNA analysis of Sarcoptes scabiei and host immune response
Cited by: 23
Author(s): Ran He, Xiaobin Gu, Weimin Lai, Xuerong Peng, Guangyou Yang
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0165919

Improving Gene-Set Enrichment Analysis of RNA-Seq Data with Small Replicates
Cited by: 18
Author(s): Susan A. Yoon, Seon‐Young Kim, Dougu Nam
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0067019

ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq
Cited by: 471
Author(s): Andrew D. Fernandes, Jean M. Macklaim, Thomas Linn, Gregor Reid, Gregory B. Gloor
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0224577

Time series experimental design under one-shot sampling: The importance of condition diversity
Cited by: 2
Author(s): Xiaohan Kang, Bruce Hajek, Fen Wu, Yoshie Hanzawa
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0241655

Contact-dependent traits in Pseudomonas syringae B728a
Cited by: 2
Author(s): Monica N. Hernandez, Steven E. Lindow
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0127985

Altered Interactions between the Gut Microbiome and Colonic Mucosa Precede Polyposis in APCMin/+ Mice
Cited by: 45
Author(s): Joshua S. Son, Shanawaj Khair, Donald W. Pettet, Nengtai Ouyang, Xinyu Tian, Yuanhao Zhang, Wei Zhu, Gerardo G. Mackenzie, Charles E. Robertson, Diana Ir, Daniel N. Frank, Basil Rigas, Ellen Li
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0208993

SLC3A2 is a novel endoplasmic reticulum stress-related signaling protein that regulates the unfolded protein response and apoptosis
Cited by: 17
Author(s): Chunlei Liu, Xin Li, Chen Li, Zeyu Zhang, Xiaojian Gao, Zhilong Jia, Haixu Chen, Qian Jia, Xiaojing Zhao, Jixuan Liu, Bohan Liu, Zhihong Xu, Yaping Tian, Kunlun He
Software Mentions: 2
Published: almost 8 years ago

10.3390/cancers12030697

Oxaliplatin-Induced DHX9 Phosphorylation Promotes Oncogenic Circular RNA CCDC66 Expression and Development of Chemoresistance
Cited by: 39
Author(s): Ya-Chi Lin, Ya-Shan Yu, Hongchin Lin, Kuei‐Yang Hsiao
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers11111766

Collagen Induces a More Proliferative, Migratory and Chemoresistant Phenotype in Head and Neck Cancer via DDR1
Cited by: 35
Author(s): Sook Ling Lai, Malcolm Tan, Robert Hollows, Max Robinson, Maha Ibrahim, Sandra Margielewska, Eric Kenneth Parkinson, Anand Ramanathan, Rosnah Binti Zain, Hisham Mehanna, Rachel Spruce, Wenbin Wei, Ivy Chung, Paul G. Murray, Lee Fah Yap, Ian C. Paterson
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41420-021-00649-z

Long noncoding RNA DLGAP1-AS2 facilitates Wnt1 transcription through physically interacting with Six3 and drives the malignancy of gastric cancer
Cited by: 12
Author(s): Jiawei Lu, Ying Xü, Wenjie Xie, Yinbing Tang, Heteng Zhang, Beibei Wang, Ji Mao, Rui Tao, Pengcheng Jiang, Wenbo Zhang
Software Mentions: 2
Published: about 5 years ago

10.1111/cmi.12722

Vps13F links bacterial recognition and intracellular killing inDictyostelium
Cited by: 26
Author(s): Jade Leiba, Ayman Sabra, Romain Bodinier, Anna Marchetti, Wanessa Cristina Lima, Astrid Melotti, Jackie Perrin, Frédéric Burdet, Marco Pagni, Thierry Soldati, Emmanuelle Lelong, Pierre Cosson
Software Mentions: 2
Published: over 9 years ago

10.1007/s00018-018-2842-8

Immune stimuli shape the small non-coding transcriptome of extracellular vesicles released by dendritic cells
Cited by: 49
Author(s): Tom A.P. Driedonks, Susanne G. van der Grein, Yavuz Ariyürek, Henk P.J. Buermans, Henrike Jekel, Wang Ngai Chow, Marca H. M. Wauben, Amy H. Buck, Peter A.C. ’t Hoen, Esther N. M. Nolte‐‘t Hoen
Software Mentions: 2
Published: over 8 years ago

10.1111/cpr.12564

Suppression of long non‐coding RNA TNRC6C‐AS1 protects against thyroid carcinoma through DNA demethylation of STK4 via the Hippo signalling pathway
Cited by: 29
Author(s): Linjie Yang, Jing Wu, Manli Guo, Yong Zhang, Shao-Gang Ma
Software Mentions: 2
Published: over 7 years ago

10.1016/j.celrep.2021.109542

Gli1+ progenitors mediate bone anabolic function of teriparatide via Hh and Igf signaling
Cited by: 12
Author(s): Yu Shi, Xueyang Liao, James Y. Long, Lutian Yao, Jianquan Chen, Bin Yin, Feng Lou, Guangxu He, Ling Ye, Ling Qin, Fanxin Long
Software Mentions: 2
Published: over 5 years ago

10.1007/s12192-018-0910-5

Cellular stress responses to chronic heat shock and shell damage in temperate Mya truncata
Cited by: 18
Author(s): Victoria A. Sleight, Lloyd S. Peck, Elisabeth A. Dyrynda, Valerie J. Smith, Melody S. Clark
Software Mentions: 2
Published: over 8 years ago

10.3390/cells9061371

Intrinsic Abnormalities of Cystic Fibrosis Airway Connective Tissue Revealed by an In Vitro 3D Stromal Model
Cited by: 5
Author(s): Claudia Mazio, Laura S Scognamiglio, Rossella De Cegli, Luis J V Galietta, Diego di Bernardo, Costantino Casale, Francesco Urciuolo, Giorgia Imparato, Paolo Antonio Netti
Software Mentions: 2
Published: over 6 years ago

10.3390/cells10092439

Sexually Dimorphic Transcriptomic Changes of Developing Fetal Brain Reveal Signaling Pathways and Marker Genes of Brain Cells in Domestic Pigs
Cited by: 8
Author(s): Monica Strawn, J.G.N. Moraes, Timothy J. Safranski, Susanta K. Behura
Software Mentions: 2
Published: about 5 years ago

10.3390/cells8111395

Hepatitis C Virus Enhances the Invasiveness of Hepatocellular Carcinoma via EGFR-Mediated Invadopodia Formation and Activation
Cited by: 18
Author(s): Liat Ninio, Abraham Nissani, Tomer Meirson, Tom Domovitz, Alessandro Genna, Shams Twafra, Kannan Srikanth, Roba Dabour, Erez Avraham, Ateret Davidovich, Hava Gil-Henn, Meital Gal-Tanamy
Software Mentions: 2
Published: almost 7 years ago

10.3390/cells10082119

High-Fat Diet Alters the Retinal Transcriptome in the Absence of Gut Microbiota
Cited by: 11
Author(s): David Dao, Bingqing Xie, Urooba Nadeem, Jason Xiao, Asad Movahedan, Mark D’Souza, Vanessa Leone, Seenu M. Hariprasad, Eugene B. Chang, Dinanath Sulakhe, Dimitra Skondra
Software Mentions: 2
Published: about 5 years ago

10.3390/cells9071579

Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments
Cited by: 6
Author(s): Cankut Çubuk, Fatma Ezgi Can, María Peña‐Chilet, Joaquı́n Dopazo
Software Mentions: 2
Published: over 6 years ago

10.3390/cells9092026

Chemical Genetics Approach Identifies Abnormal Inflorescence Meristem 1 as a Putative Target of a Novel Sulfonamide That Protects Catalase2-Deficient Arabidopsis against Photorespiratory Stress
Cited by: 2
Author(s): Tom van der Meer, Arno Verlee, Patrick J. Willems, Francis Impens, Kris Gevaert, Christa Testerink, Christian V. Stevens, Frank Van Breusegem, Pavel Kerchev
Software Mentions: 2
Published: about 6 years ago

10.3390/cells10020200

Phototropin 1 and 2 Influence Photosynthesis, UV-C Induced Photooxidative Stress Responses, and Cell Death
Cited by: 8
Author(s): Anna Rusaczonek, Weronika Czarnocka, Patrick J. Willems, Marzena Sujkowska‐Rybkowska, Frank Van Breusegem, Stanisław Karpiński
Software Mentions: 2
Published: almost 6 years ago

10.3390/cells9030680

Exosomes from Human Adipose Tissue-Derived Mesenchymal Stem Cells Promote Epidermal Barrier Repair by Inducing de Novo Synthesis of Ceramides in Atopic Dermatitis
Cited by: 81
Author(s): Kyong‐Oh Shin, Dong-Soo Ha, Jin Ock Kim, Debra Crumrine, Jason M. Meyer, Joan S. Wakefield, Yerin Lee, Bogyeong Kim, Sungeun Kim, Hyun-Keun Kim, Joon Lee, Hyuck Hoon Kwon, Gyeong-Hun Park, Jun Ho Lee, Jihye Lim, Sejeong Park, Peter M. Elias, Kyungho Park, Yong Weon Yi, Byong Seung Cho
Software Mentions: 2
Published: over 6 years ago

10.3390/cells9040969

Integrative Analysis of Methylome and Transcriptome Reveals the Regulatory Mechanisms of Hair Follicle Morphogenesis in Cashmere Goat
Cited by: 23
Author(s): Shanhe Wang, Fang Li, Jinwang Liu, Yuelang Zhang, Yujie Zheng, Wei Ge, Qu Liu, Xin Wang
Software Mentions: 2
Published: over 6 years ago

10.3390/cells9122690

The PARP Inhibitor Olaparib Modulates the Transcriptional Regulatory Networks of Long Non-Coding RNAs during Vasculogenic Mimicry
Cited by: 5
Author(s): Mónica Fernández-Cortés, Eduardo Andrés-León, F. Javier Oliver
Software Mentions: 2
Published: almost 6 years ago

10.3390/cells9061476

RIG-I Plays a Dominant Role in the Induction of Transcriptional Changes in Zika Virus-Infected Cells, which Protect from Virus-Induced Cell Death
Cited by: 28
Author(s): Mirjam Schilling, Anne Bridgeman, Nicki Gray, Jonny Hertzog, Philip Hublitz, Alain Kohl, Jan Rehwinkel
Software Mentions: 2
Published: over 6 years ago

10.1186/s13148-020-00892-8

Ten-eleven translocation methyl-cytosine dioxygenase 2 deficiency exacerbates renal ischemia-reperfusion injury
Cited by: 5
Author(s): Yan Huang, Li Tan, Yuqi Liu, Ning Huang, Jing Cang, Hao Wang
Software Mentions: 2
Published: over 6 years ago

10.1186/s13148-019-0628-y

Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer
Cited by: 23
Author(s): Simeng Gu, Shujuan Lin, Yichun Ding, Sangni Qian, Danjie Jiang, Xiaocong Zhang, Qilong Li, Jing Yang, Xiaojiang Ying, Zhenjun Li, Mengling Tang, Jianbing Wang, Mingjuan Jin, Kun Chen
Software Mentions: 2
Published: over 7 years ago

10.1186/s13148-021-01109-2

Genome‑wide profiling of DNA methylation and gene expression unravel the epigenetic landscape in diabetes-related hypothyroidism
Cited by: 3
Author(s): Jingyi Luo, Xiaoxia Wang, Yuan Li, Lixin Guo
Software Mentions: 2
Published: over 5 years ago

10.1002/cti2.1082

Immunological observations and transcriptomic analysis of trimester‐specific full‐term placentas from three Zika virus‐infected women
Cited by: 19
Author(s): Fok‐Moon Lum, Vipin Narang, Susan Swee-Shan Hue, Jie Chen, Naomi McGovern, Ravisankar Rajarethinam, Jeslin J. L. Tan, Siti Naqiah Amrun, Yi‐Hao Chan, Cheryl Yi‐Pin Lee, Tze-Kwang Chua, Wearn‐Xin Yee, Nicholas Kim‐Wah Yeo, T. Y. T. Tan, Xuan Liu, Sam Haldenby, Yee‐Sin Leo, Florent Ginhoux, Jerry Ky Chan, Julian A. Hiscox, Chia-Yin Chong, Lisa F. P. Ng
Software Mentions: 2
Published: almost 8 years ago

10.1002/cti2.1334

Expression of CD49f defines subsets of human regulatory T cells with divergent transcriptional landscape and function that correlate with ulcerative colitis disease activity
Cited by: 4
Author(s): Harshi Weerakoon, Jasmin Straube, Katie E. Lineburg, Leanne Cooper, Steven Lane, Corey Smith, Saleh Alabbas, Jakob Begun, John J. Miles, Michelle M. Hill, Ailin Lepletier
Software Mentions: 2
Published: almost 6 years ago

10.1002/ctm2.399

Identification of biomarkers complementary to homologous recombination deficiency for improving the clinical outcome of ovarian serous cystadenocarcinoma
Cited by: 18
Author(s): Zhiwen Shi, Qingguo Zhao, Bin Lv, Xinyu Qu, Xiao Han, Hongyan Wang, Junjun Qiu, Keqin Hua
Software Mentions: 2
Published: over 5 years ago

10.1002/ctm2.328

Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma
Cited by: 20
Author(s): Chuanjie Zhang, Xuan Lu, Jingyi Huang, Hongchao He, Li Chen, Yihan Liu, Haofei Wang, Yu Xu, Siwei Xing, Xiaohao Ruan, Xiaoqun Yang, Lu Chen, Danfeng Xu
Software Mentions: 2
Published: over 5 years ago

10.1007/s12094-021-02621-w

Aberrantly low STAT3 and STAT5 responses are associated with poor outcome and an inflammatory gene expression signature in pediatric acute myeloid leukemia
Cited by: 5
Author(s): Priya Narayanan, Tsz-Kwong Man, Robert B. Gerbing, Rhonda E. Ries, Alexandra M. Stevens, Y.-C. Wang, Xin Long, Alan S. Gamis, Todd M. Cooper, Soheil Meshinchi, Todd A. Alonzo, Michele S. Redell
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-021-02384-8

A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina
Cited by: 18
Author(s): Purushothaman Natarajan, Ashok Kumar Murugesan, Ganesan Govindan, Ayyaru Gopalakrishnan, Ravichandiran Kumar, Purushothaman Duraisamy, Raju Balaji, Tanuja Tanuja, P. Sushree Shyamli, Ajay Parida, Madasamy Parani
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-019-0334-5

Murine osteoclasts secrete serine protease HtrA1 capable of degrading osteoprotegerin in the bone microenvironment
Cited by: 16
Author(s): Nagahiro Ochiai, Yutaka Nakachi, Tomotaka Yokoo, Takahiro Ichihara, Tore Eriksson, Yuki Yonemoto, Takumi Kato, Hitoshi Ogata, Natsuko Fujimoto, Yasuhiro Kobayashi, Nobuyuki Udagawa, Shinsuke Kaku, Tomokazu Ueki, Yasushi Okazaki, Naoyuki Takahashi, Toshio Suda
Software Mentions: 2
Published: over 7 years ago

10.1038/s42003-021-01743-9

Immunoreactive peptide maps of SARS-CoV-2
Cited by: 35
Author(s): Nischay Mishra, Xi Huang, Saurabh Joshi, Cheng Guo, James Ng, Riddhi Thakkar, Yongjian Wu, Dong Xiao, Qianlin Li, Richard S. Pinapati, Eric Sullivan, Adrian Caciula, Rafal Tokarz, Thomas Briese, Jiahai Lu, W. Ian Lipkin
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-021-02295-8

FUT6 deficiency compromises basophil function by selectively abrogating their sialyl-Lewis x expression
Cited by: 6
Author(s): Kia Joo Puan, Boris San Luis, Nurhashikin Yusof, Dilip Kumar, Anand Kumar Andiappan, Wendy Lee, Samanta Cajic, Dragana Vuckovic, Jing De Chan, Tobias Döllner, Han Wei Hou, Yunxuan Jiang, Chao Tian, Erdmann Rapp, Michael Poidinger, De Yun Wang, Nicole Soranzo, Bernett Lee, Olaf Rötzschke
Software Mentions: 2
Published: over 5 years ago

10.1002/embr.201337642

Extensive regulation of the non‐coding transcriptome by hypoxia: role of <scp>HIF</scp> in releasing paused <scp>RNA</scp> pol2
Cited by: 138
Author(s): Hani Choudhry, Johannes Schödel, Spyros Oikonomopoulos, Carme Camps, Steffen Grampp, Adrian L. Harris, Peter J. Ratcliffe, Jiannis Ragoussis, David R. Mole
Software Mentions: 2
Published: almost 13 years ago

10.15252/embr.201847379

<scp>IL</scp> ‐7‐dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti‐tumour response
Cited by: 35
Author(s): Hung-Chang Chen, Nils Eling, Celia P. Martínez-Jiménez, L. M. O'Brien, Valentina Carbonaro, John C. Marioni, Duncan T. Odom
Software Mentions: 2
Published: over 7 years ago

10.15252/embr.201948469

Wnt regulates amino acid transporter Slc7a5 and so constrains the integrated stress response in mouse embryos
Cited by: 21
Author(s): Nadège Poncet, Pamela A. Halley, Christopher Lipina, Marek Gierliński, Alwyn Dady, Gail Singer, Melanie Febrer, Yun‐Bo Shi, Terry P. Yamaguchi, Peter M. Taylor, Kate G. Storey
Software Mentions: 2
Published: almost 7 years ago

10.15252/embr.201948019

The role of Xist ‐mediated Polycomb recruitment in the initiation of X‐chromosome inactivation
Cited by: 72
Author(s): Aurélie Bousard, Ana Raposo, J. Ż̷ylicz, Christel Picard, Vanessa Borges Pires, Yanyan Qi, Cláudia Raquel Estopa Gil, Laurène Syx, Howard Y. Chang, Edith Heard, Simão Teixeira da Rocha
Software Mentions: 2
Published: about 7 years ago

10.1002/ece3.4976

Transcriptomic changes during caste development through social interactions in the termite Zootermopsis nevadensis
Cited by: 15
Author(s): Hajime Yaguchi, Rikako Suzuki, Masatoshi Matsunami, Shuji Shigenobu, Kazuyuki Maekawa
Software Mentions: 2
Published: over 7 years ago

10.1002/ece3.5287

Expression of calcification‐related ion transporters during blue mussel larval development
Cited by: 31
Author(s): Kirti Ramesh, Tejaswi Yarra, Melody S. Clark, Uwe John, Frank Melzner
Software Mentions: 2
Published: over 7 years ago

10.1002/ece3.7083

American lobster postlarvae alter gene regulation in response to ocean warming and acidification
Cited by: 9
Author(s): Maura Niemisto, David M. Fields, Kevin Clark, Jesica D. Waller, Spencer J. Greenwood, Richard A. Wahle
Software Mentions: 2
Published: almost 6 years ago

10.1002/ece3.5724

Differential gene expression in chronic wasting disease‐positive white‐tailed deer (Odocoileus virginianus)
Cited by: 5
Author(s): Emma K. Trone-Launer, Chenghui Wang, Guoqing Lu, Nohra E. Mateus‐Pinilla, Paige R. Zick, James T. Lamer, Paul Shelton, Christopher N. Jacques
Software Mentions: 2
Published: about 7 years ago

10.1002/ece3.7125

Juvenile hormone pathway in honey bee larvae: A source of possible signal molecules for the reproductive behavior ofVarroa destructor
Cited by: 4
Author(s): Cristian M. Aurori, Alexandru-Ioan Giurgiu, Benjamin H. Conlon, Chedly Kastally, Daniel Severus Dezmirean, Jarkko Routtu, Adriana Aurori
Software Mentions: 2
Published: almost 6 years ago

10.1002/ece3.6865

Identification of scavenger receptors and thrombospondin‐type‐1 repeat proteins potentially relevant for plastid recognition in Sacoglossa
Cited by: 12
Author(s): Jenny Melo Clavijo, Silja Frankenbach, Cátia Fidalgo, João Serôdio, Alexander Donath, Angelika Preisfeld, Gregor Christa
Software Mentions: 2
Published: about 6 years ago

10.1093/eep/dvv006

Bisphenol A-associated alterations in genome-wide DNA methylation and gene expression patterns reveal sequence-dependent and non-monotonic effects in human fetal liver
Cited by: 56
Author(s): Christopher Faulk, Jung Ho Kim, Tamara R. Jones, Richard C. McEachin, Muna S. Nahar, Dana C. Dolinoy, Maureen A. Sartor
Software Mentions: 2
Published: almost 12 years ago

10.1186/s40793-020-00368-5

The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania
Cited by: 8
Author(s): Dipti Pitta, Nagaraju Indugu, John D. Toth, Joseph S. Bender, Linda D. Baker, Meagan L. Hennessy, Bonnie Vecchiarelli, Helen Aceto, Zhengxia Dou
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40793-021-00378-x

Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils
Cited by: 2
Author(s): Marian Morales, Vladimir Sentchilo, Noushin Hadadi, Jan Roelof van der Meer
Software Mentions: 2
Published: over 5 years ago

10.1021/acs.est.0c07262

Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon
Cited by: 14
Author(s): Elena Cerro‐Gálvez, Jordi Dachs, Daniel Lundin, María-Carmen Fernández-Pinos, Marta Sebastián, Maria Vila‐Costa
Software Mentions: 2
Published: over 5 years ago

10.1186/1756-8935-6-7

Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development
Cited by: 81
Author(s): Kelly Bush, Benjamin Yuen, Bonnie L. Barrilleaux, John W. Riggs, Henriette O’Geen, Rebecca Cotterman, Paul S. Knoepfler
Software Mentions: 2
Published: over 13 years ago

10.1186/s13072-019-0266-9

Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing
Cited by: 7
Author(s): Jiji T. Kurup, Ion J. Campeanu, Benjamin L. Kidder
Software Mentions: 2
Published: over 7 years ago

10.1155/2017/1676808

Antidepressant Mechanism Research of Acupuncture: Insights from a Genome-Wide Transcriptome Analysis of Frontal Cortex in Rats with Chronic Restraint Stress
Cited by: 19
Author(s): Yu Wang, Huili Jiang, Hong Meng, Jing Rong Li, Xiaojian Yang, Bingcong Zhao, Yang Sun, Ting Bao
Software Mentions: 2
Published: about 9 years ago

10.1155/2020/3561235

Transcriptome Analysis Reveals the Effects of Troxerutin and Cerebroprotein Hydrolysate Injection on Injured Spinal Cords in Rats
Cited by: 0
Author(s): Linbang Wang, Hucheng Wang, Ke Tang, Weiyang Zhong, Zhiyu Chen, Zhengxue Quan
Software Mentions: 2
Published: about 6 years ago

10.1155/2021/8861394

The Pharmacological Activity of the Wenjing Decoction in Recurrent Spontaneous Abortion
Cited by: 6
Author(s): Lixue Cao, Hui Chen, Yanxia Huang, Liudan Chen, Mengru Kang, Jing Liang
Software Mentions: 2
Published: over 5 years ago

10.1111/eva.13054

Transcriptomic divergence between upland and lowland ecotypes contributes to rice adaptation to a drought‐prone agroecosystem
Cited by: 9
Author(s): Zhi Luo, Jie Xiong, Hui Xia, Xiaoyan Ma, Min Gao, Lei Wang, Guolan Liu, Yu Xing, Lijun Luo
Software Mentions: 2
Published: over 6 years ago

10.1111/eva.13166

Incipient resistance to an effective pesticide results from genetic adaptation and the canalization of gene expression
Cited by: 12
Author(s): Xiaoshen Yin, Alexander S. Martinez, Abigail Perkins, Morgan Sparks, Avril M. Harder, Janna R. Willoughby, Marı́a S. Sepúlveda, Mark R. Christie
Software Mentions: 2
Published: almost 6 years ago

10.1002/evl3.220

Experimental evolution supports signatures of sexual selection in genomic divergence
Cited by: 11
Author(s): R. Axel W. Wiberg, Paris Veltsos, Rhonda R. Snook, Michael G. Ritchie
Software Mentions: 2
Published: over 5 years ago

10.1016/j.exphem.2016.11.003

MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation
Cited by: 24
Author(s): Laura Godfrey, Jon Kerry, Ross Thorne, Emmanouela Repapi, James O. J. Davies, Marta Tapia, Erica Ballabio, Jim R. Hughes, Huimin Geng, Marina Konopleva, Thomas A. Milne
Software Mentions: 2
Published: over 9 years ago

10.1186/s40164-021-00226-1

Pan-cancer analysis reveals tumor-associated macrophage communication in the tumor microenvironment
Cited by: 21
Author(s): Linbang Wang, Tao He, Jingkun Liu, Jiaojiao Tai, Bing Wang, Zhiyu Chen, Zhengxue Quan
Software Mentions: 2
Published: over 5 years ago

10.1038/s12276-019-0328-x

Silencing of long noncoding RNA HOXA11-AS inhibits the Wnt signaling pathway via the upregulation of HOXA11 and thereby inhibits the proliferation, invasion, and self-renewal of hepatocellular carcinoma stem cells
Cited by: 33
Author(s): Juncheng Guo, Yijun Yang, Jinfang Zheng, Jianquan Zhang, Min Guo, Yang Xiang, Xiong-Fei Jiang, Xiang Li, You Li, Ping Huang, Lang Zhuo
Software Mentions: 2
Published: almost 7 years ago

10.12688/f1000research.6402.2

The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs
Cited by: 11
Author(s): Jóhannes Guðbrandsson, Ehsan Pashay Ahi, Sigríður Rut Franzdóttir, Kalina H. Kapralova, Bjarni K. Kristjánsson, S. Sophie Steinhaeuser, Valerie H. Maier, Isak M. Johannesson, Sigurður S. Snorrason, Zophonı́as O. Jónsson, Arnar Pálsson
Software Mentions: 2
Published: over 10 years ago

10.1002/2211-5463.12709

Profiling and functional analysis of differentially expressed circular RNAs in high glucose‐induced human umbilical vein endothelial cells
Cited by: 26
Author(s): Guoxi Jin, Qiong Wang, Xiaolei Hu, Xiaoli Li, Xiuying Pei, Erdi Xu, Minglong Li
Software Mentions: 2
Published: about 7 years ago

10.1093/femsle/fnz081

In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae
Cited by: 14
Author(s): Xiaoqian Shi-Kunne, Roger de Pedro Jové, Jasper R L Depotter, Malaika K. Ebert, Michael Seidl, Bart P.H.J. Thomma
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2021.632359

Construction of a circRNA-miRNA-mRNA Regulatory Network Reveals Potential Mechanism and Treatment Options for Osteosarcoma
Cited by: 6
Author(s): Yi He, Haiting Zhou, Wei Wang, Haoran Xu, Hao Cheng
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2018.00365

Comparative Transcriptome Profiling of mRNA and lncRNA Related to Tail Adipose Tissues of Sheep
Cited by: 36
Author(s): Lin Ma, Meng Zhang, Yunjiang Jin, Sarantsetseg Erdenee, Linyong Hu, Hong Chen, Yong Cai, Xianyong Lan
Software Mentions: 2
Published: about 8 years ago

10.3389/fgene.2021.671729

Integrated lncRNA and mRNA Transcriptome Analyses in the Ovary of Cynoglossus semilaevis Reveal Genes and Pathways Potentially Involved in Reproduction
Cited by: 7
Author(s): Yani Dong, Likang Lyu, Daiqiang Zhang, Jing Li, Haishen Wen, Shaowen Bao
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2020.00413

The Prognostic Signature and Potential Target Genes of Six Long Non-coding RNA in Laryngeal Squamous Cell Carcinoma
Cited by: 22
Author(s): Shi-Cai Gong, Meng Xu, Yiyun Zhang, Yijun Shan, Hao Zhang
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2019.00878

Identification of hsa_circ_0001821 as a Novel Diagnostic Biomarker in Gastric Cancer via Comprehensive Circular RNA Profiling
Cited by: 19
Author(s): Shan Kong, Qian Yang, Chenxue Tang, Tianyi Wang, Xianjuan Shen, Shaoqing Ju
Software Mentions: 2
Published: about 7 years ago

10.3389/fgene.2021.626764

Construction of circRNA-Based ceRNA Network to Reveal the Role of circRNAs in the Progression and Prognosis of Hepatocellular Carcinoma
Cited by: 9
Author(s): Rong Deng, Xiaoping Chen, Yulan Dong, Yanqiu Tang, Xuewen Tao, Shuyu Wang, Jincheng Wang, Lin Chen
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2020.565146

Transcriptomes of Different Tissues of Flax (Linum usitatissimum L.) Cultivars With Diverse Characteristics
Cited by: 8
Author(s): Alexey A. Dmitriev, Roman O. Novakovskiy, Elena N. Pushkova, Tatiana A. Rozhmina, А. А. Жученко, Nadezhda L. Bolsheva, А. Д. Бениаминов, Vladimir A. Mitkevich, Liubov V. Povkhova, Ekaterina M. Dvorianinova, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, George S. Krasnov, Nataliya V. Melnikova
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.00913

High Cysteine Membrane Proteins (HCMPs) Are Up-Regulated During Giardia-Host Cell Interactions
Cited by: 14
Author(s): Dimitra Peirasmaki, Showgy Y. Ma’ayeh, Feifei Xu, Marcela Ferella, Sara Campos, Jingyi Liu, Staffan G. Svärd
Software Mentions: 2
Published: about 6 years ago

10.3389/fgene.2020.600227

CDK6 Is a Potential Prognostic Biomarker in Acute Myeloid Leukemia
Cited by: 7
Author(s): Wei Liu, Jin-Mou Yi, Yi Liu, Cong Chen, Kaixuan Zhang, Cheng Zhou, Huien Zhan, Liang Zhao, Stephanie Morales, Xielan Zhao, Hui Zeng
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2018.00369

Multi-Tissue Transcriptome Profiling of North American Derived Atlantic Salmon
Cited by: 11
Author(s): Amin R. Mohamed, Hilary King, Bradley S. Evans, Antônio Reverter, James W. Kijas
Software Mentions: 2
Published: about 8 years ago

10.3389/fgene.2021.709340

Molecular Characteristics of Choledochal Cysts in Children: Transcriptome Sequencing
Cited by: 3
Author(s): Yong Mei Lv, Xiaoyan Xie, Lihui Pu, Qi Wang, Siyu Pu, Chengbo Ai, Yi Liu, Jing Chen, Bo Xiang
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2019.00840

Putative Mitochondrial Sex Determination in the Bivalvia: Insights From a Hybrid Transcriptome Assembly in Freshwater Mussels
Cited by: 17
Author(s): Charlotte Capt, Sébastien Renaut, Donald T. Stewart, Nathan A. Johnson, Sophie Breton
Software Mentions: 2
Published: about 7 years ago

10.3389/fgene.2020.578679

Gene Expression and Co-expression Networks Are Strongly Altered Through Stages in Clear Cell Renal Carcinoma
Cited by: 18
Author(s): José María Zamora-Fuentes, Enrique Hernández‐Lemus, Jesús Espinal-Enríquez
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.556749

Profiling Alternative 3′ Untranslated Regions in Sorghum using RNA-seq Data
Cited by: 4
Author(s): Min Tu, Yin Li
Software Mentions: 2
Published: about 6 years ago

10.3389/fgene.2020.00064

Post-Transcriptional Dysregulation of microRNA and Alternative Polyadenylation in Colorectal Cancer
Cited by: 21
Author(s): Zhanrui Mao, Hui Zhao, Yanmin Qin, Jianming Wei, Jingyong Sun, Weiwei Zhang, Yani Kang
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2016.00164

In Papyro Comparison of TMM (edgeR), RLE (DESeq2), and MRN Normalization Methods for a Simple Two-Conditions-Without-Replicates RNA-Seq Experimental Design
Cited by: 83
Author(s): Élie Maza
Software Mentions: 2
Published: about 10 years ago

10.3389/fgene.2020.00375

Identifying Candida albicans Gene Networks Involved in Pathogenicity
Cited by: 4
Author(s): Graham H. Thomas, Judith M. Bain, Susan Budge, Alistair J. P. Brown, Ryan M. Ames
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2020.00839

Preferential Mapping of Sex-Biased Differentially-Expressed Genes of Larvae to the Sex-Determining Region of Flathead Grey Mullet (Mugil cephalus)
Cited by: 9
Author(s): Lior Dor, Andrey Shirak, Arie Y Curzon, Hanna Rosenfeld, Iris Meiri Ashkenazi, Oriya Nixon, Eyal Seroussi, J. I. Weller, Ron Maymon
Software Mentions: 2
Published: about 6 years ago

10.3389/fgene.2020.00574

Long Non-coding RNA and mRNA Profile of Liver Tissue During Four Developmental Stages in the Chicken
Cited by: 10
Author(s): Chunyou Ning, Tianyuan Ma, Silu Hu, Zhongxian Xu, Pu Zhang, Xiaoling Zhao, Yan Wang, Huadong Yin, Yaodong Hu, Xiaolan Fan, Bo Zeng, Mingyao Yang, Dapeng Yang, Qingyong Ni, Yan Li, Mingwang Zhang, Huailiang Xu, Yongfang Yao, Qing Zhu, Diyan Li
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2020.00153

Identification of 13 Key Genes Correlated With Progression and Prognosis in Hepatocellular Carcinoma by Weighted Gene Co-expression Network Analysis
Cited by: 33
Author(s): Yang Gu, Jun Li, Deliang Guo, Baiyang Chen, Pengpeng Liu, Yusha Xiao, Kuo‐Chung Yang, Zhisu Liu, Quanyan Liu
Software Mentions: 2
Published: over 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568