bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/1471-2164-15-155

Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses
Cited by: 36
Author(s): Xin Luo, Minho Chae, Raga Krishnakumar, Charles G. Danko, W. Lee Kraus
Software Mentions: 4
Published: over 12 years ago

10.3389/fmolb.2021.608369

Identification of a DNA Repair Gene Signature and Establishment of a Prognostic Nomogram Predicting Biochemical-Recurrence-Free Survival of Prostate Cancer
Cited by: 9
Author(s): Gongwei Long, Wei Ouyang, Yucong Zhang, Guoliang Sun, Jiahua Gan, Zhiquan Hu, Heng Li
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.45310

A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development
Cited by: 45
Author(s): Christopher I. Cazzonelli, Xin Hou, Yağiz Alagöz, John Rivers, Namraj Dhami, Jiwon Lee, Shashikanth Marri, Barry J. Pogson
Software Mentions: 4
Published: over 6 years ago

10.1097/MIB.0000000000001131

Azathioprine with Allopurinol
Cited by: 7
Author(s): Sally A. Coulthard, Phil Berry, Sarah McGarrity, Simon D. McLaughlin, Azhar Ansari, Christopher P.F. Redfern
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.67740

Bacterial–fungal interactions in the neonatal gut influence asthma outcomes later in life
Cited by: 16
Author(s): Rozlyn C.T. Boutin, Charisse Petersen, Sarah E. Woodward, Antonio Serapio-Palacios, Tahereh Bozorgmehr, Rachelle Loo, Alina Chalanuchpong, Mihai Cirstea, Bernard C. Lo, Kelsey E. Huus, Weronika Barcik, Meghan B. Azad, Allan B. Becker, Piush J. Mandhane, Theo J. Moraes, Malcolm R. Sears, Padmaja Subbarao, Kelly M. McNagny, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 4
Published: over 5 years ago

10.1186/s40659-018-0188-1

Identification of key genes and miRNAs markers of papillary thyroid cancer
Cited by: 31
Author(s): Jie Qiu, Wenwei Zhang, Chuanshan Zang, Xiaomin Liu, Fuxue Liu, Ruifeng Ge, Yan Sun, Qingsheng Xia
Software Mentions: 4
Published: almost 8 years ago

10.3390/insects11010004

Comparative Transcriptome Analysis of Thitarodes Armoricanus in Response to the Entomopathogenic Fungi Paecilomyces Hepiali and Ophiocordyceps Sinensis
Cited by: 7
Author(s): Zhongchen Rao, Li Cao, Hua Wu, Xuehong Qiu, Guiqing Liu, Richou Han
Software Mentions: 4
Published: over 6 years ago

10.3389/fnmol.2018.00178

Stable STIM1 Knockdown in Self-Renewing Human Neural Precursors Promotes Premature Neural Differentiation
Cited by: 21
Author(s): Renjitha Gopurappilly, Bipan Kumar Deb, Pragnya Chakraborty, Gaiti Hasan
Software Mentions: 4
Published: about 8 years ago

10.3389/fimmu.2021.672168

Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy
Cited by: 18
Author(s): Sandra Hellberg, Johanna Raffetseder, Olof Rundquist, Rasmus Magnusson, Georgia Papapavlou, Maria C. Jenmalm, Jan Ernerudh, Mika Gustafsson
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.64204

Single-PanIN-seq unveils that ARID1A deficiency promotes pancreatic tumorigenesis by attenuating KRAS-induced senescence
Cited by: 5
Author(s): Shou Liu, Wenjian Cao, Yichi Niu, Jiayi Luo, Yanhua Zhao, Zheng Hu, Chenghang Zong
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0169648

The Smc5/6 Complex Restricts HBV when Localized to ND10 without Inducing an Innate Immune Response and Is Counteracted by the HBV X Protein Shortly after Infection
Cited by: 107
Author(s): Congrong Niu, Christine M. Livingston, Li Li, Rudolf K. F. Beran, Stéphane Daffis, Dhivya Ramakrishnan, Dara Burdette, Leanne Peiser, Eduardo Salas, Hilario J. Ramos, Mei Yu, Guofeng Cheng, Michel Strubin, William E. Delaney, Simon P. Fletcher
Software Mentions: 4
Published: over 9 years ago

10.1039/c8mo00042e

Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data
Cited by: 78
Author(s): Benjamin Alexander-Dann, Lavinia Lorena Pruteanu, Erin Oerton, Naomi L. Sharma, Ioana Berindan‐Neagoe, Dezső Módos
Software Mentions: 4
Published: over 8 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0071462

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Cited by: 163
Author(s): Yan Guo, Quanhu Sheng, Li Jiang, Fei Ye, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: about 13 years ago

10.3389/fnmol.2018.00288

Dysregulation of MicroRNAs and Target Genes Networks in Peripheral Blood of Patients With Sporadic Amyotrophic Lateral Sclerosis
Cited by: 84
Author(s): Maria Liguori, Nicoletta Nuzziello, Alessandro Introna, Arianna Consiglio, Flavio Licciulli, Eustachio D’Errico, Antonio Scarafino, Eugenio Distaso, Isabella Laura Simone
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0211491

A five-gene signature predicts overall survival of patients with papillary renal cell carcinoma
Cited by: 29
Author(s): Zhe Gao, Dong Zhang, Yi Duan, Lei Yan, Yi‐Ming Fan, Zhiqing Fang, Zhaoxu Liu
Software Mentions: 4
Published: over 7 years ago

10.1186/s13024-018-0303-3

Inhibition of monocyte-like cell extravasation protects from neurodegeneration in DBA/2J glaucoma
Cited by: 44
Author(s): Pete A. Williams, Catherine E. Braine, Krishnakumar Kizhatil, Nicole E. Foxworth, Nicholas G. Tolman, Jeffrey M. Harder, R. Scott, Gregory L. Sousa, Alyssa Panitch, Gareth R. Howell, Simon W. M. John
Software Mentions: 4
Published: over 7 years ago

10.1016/j.immuni.2021.05.016

A PGE2-MEF2A axis enables context-dependent control of inflammatory gene expression
Cited by: 22
Author(s): Francesco Cilenti, Giulia Barbiera, Nicoletta Caronni, Dario Iodice, Elisa Montaldo, Simona Barresi, Eleonora Lusito, Vincenzo Cuzzola, Francesco Maria Vittoria, Luca Mezzanzanica, Paolo Miotto, Pietro Di Lucia, Dejan Lazarevic, Daniela María Cirillo, Matteo Iannacone, Marco Genua, Renato Ostuni
Software Mentions: 4
Published: about 5 years ago

10.1186/s13024-020-00394-4

Trem2 deficiency differentially affects phenotype and transcriptome of human APOE3 and APOE4 mice
Cited by: 40
Author(s): Nicholas F. Fitz, Cody M. Wolfe, Brittany E. Playso, Richard J. Biedrzycki, Yi Lü, Kyong Nyon Nam, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0214559

DNA methylation, microRNA expression profiles and their relationships with transcriptome in grass-fed and grain-fed Angus cattle rumen tissue
Cited by: 9
Author(s): Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Jianan Liu, Zan Liu, Jiuzhou Song
Software Mentions: 4
Published: almost 7 years ago

10.1200/CCI.19.00118

Statistical Assessment of Depth Normalization for Small RNA Sequencing
Cited by: 7
Author(s): Li‐Xuan Qin, Jian Zou, Jiejun Shi, Ann Lee, Aleksandra Mihailović, Thalia A. Farazi, Thomas Tuschl, Samuel Singer
Software Mentions: 4
Published: almost 6 years ago

10.1093/jxb/eraa036

The contribution of cis- and trans-acting variants to gene regulation in wild and domesticated barley under cold stress and control conditions
Cited by: 14
Author(s): Matthew Haas, Axel Himmelbach, Martin Mascher
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0093846

The SLE Transcriptome Exhibits Evidence of Chronic Endotoxin Exposure and Has Widespread Dysregulation of Non-Coding and Coding RNAs
Cited by: 104
Author(s): Lei Shi, Zhe Zhang, Angela M Yu, Wei Wang, Zhi Wei, Ehtisham Akhter, Kelly Maurer, Patrícia Costa-Reis, Li Song, Michelle Petri, Kathleen E. Sullivan
Software Mentions: 4
Published: over 12 years ago

10.1111/mmi.12977

<scp>K</scp>dm<scp>A</scp>, a histone<scp>H</scp>3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in<scp>A</scp>spergillus nidulans
Cited by: 41
Author(s): Agnieszka Gacek‐Matthews, Luke M. Noble, Clemens Gruber, Harald Berger, Michael Sulyok, Ana T. Marcos, Joseph Strauss, Alex Andrianopoulos
Software Mentions: 4
Published: over 11 years ago

10.1186/s13059-019-1880-3

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications
Cited by: 17
Author(s): Jingwen Fang, Qing Ma, Constance R. Chu, Beibei Huang, Lingjie Li, Pengfei Cai, Pedro J. Batista, Karen Tolentino, Jin Xu, Rui Li, Pengcheng Du, Kun Qu, Howard Y. Chang
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.29750

cAMP signaling regulates DNA hydroxymethylation by augmenting the intracellular labile ferrous iron pool
Cited by: 29
Author(s): Vladimir Camarena, David W. Sant, Tyler C. Huff, Sushmita Mustafi, Ryan K Muir, Allegra T. Aron, Christopher J. Chang, Adam R. Renslo, Paula V. Monje, Gaofeng Wang
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.21221

Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice
Cited by: 45
Author(s): Jeroen Overman, Frank Fontaine, Mehdi Moustaqil, Deepak Mittal, Emma Sierecki, Natalia Sacilotto, Johannes Zuegg, Avril A. B. Robertson, Kelly A. Holmes, Angela A. Salim, Sreeman K. Mamidyala, Mark S. Butler, Ashley Robinson, Emmanuelle Lesieur, Wayne A. Johnston, Kirill Alexandrov, Brian L. Black, Benjamin M. Hogan, Sarah De Val, Robert J. Capon, Jason S. Carroll, Timothy L. Bailey, Peter Koopman, Ralf Jauch, Mark J. Smyth, Matthew A. Cooper, Yann Gambin, Mathias François
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.63556

Deficient spermiogenesis in mice lacking Rlim
Cited by: 7
Author(s): Feng Wang, María Gracia Gervasi, Ana Bošković, Fengyun Sun, Vera D. Rinaldi, Jun Yu, Mary C. Wallingford, Darya A Tourzani, Jesse Mager, Lihua Julie Zhu, Oliver J. Rando, Pablo E. Visconti, Lara Strittmatter, Ingolf Bach
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.21052

Embryonic origin of adult stem cells required for tissue homeostasis and regeneration
Cited by: 66
Author(s): Erin L. Davies, Kai Y. Lei, Christopher Seidel, Amanda E Kroesen, Sean A. McKinney, Longhua Guo, Sofia Robb, E. J. Ross, Kirsten Gotting, Alejandro Sánchez Alvarado
Software Mentions: 4
Published: over 9 years ago

10.1093/hmg/ddab140

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles
Cited by: 15
Author(s): Andrew P. Voigt, Nathaniel K. Mullin, S. Scott Whitmore, Adam P. DeLuca, Erin R Burnight, Xiuying Liu, Budd A. Tucker, Todd E. Scheetz, Edwin M Stone, Robert F. Mullins
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0145257

Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation
Cited by: 73
Author(s): Dandan Feng, Qi Li, Hong Yu, Xuelin Zhao, Lingfeng Kong
Software Mentions: 4
Published: over 10 years ago

10.1007/s00438-020-01735-0

Major latex protein-like encoding genes contribute to Rhizoctonia solani defense responses in sugar beet
Cited by: 16
Author(s): Louise Holmquist, Fredrik Dölfors, Johan Fogelqvist, Jonathan Cohn, Thomas Kraft, Christina Dixelius
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13059-018-1575-1

VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies
Cited by: 92
Author(s): Mengjie Chen, Xiang Zhou
Software Mentions: 4
Published: almost 8 years ago

10.1128/mSystems.00215-21

Time-Resolved Proteome Analysis of Listeria monocytogenes during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation
Cited by: 5
Author(s): Marlène S Birk, Rina Ahmed-Begrich, Stefan Tran, Alexander K. W. Elsholz, Christian K. Frese, Emmanuelle Charpentier
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.55102

The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway
Cited by: 17
Author(s): Qinyu Hao, Xinying Zong, Qinyu Sun, Yo Chuen Lin, You Shang, Seyedsasan Hashemikhabir, Rosaline Y.C. Hsu, Mohammad Kamran, Ritu Chaudhary, Vidisha Tripathi, Deepak Kumar Singh, Arindam Chakraborty, Xiao Ling Li, Yoonjung Kim, Arturo V. Orjalo, Maria Polycarpou‐Schwarz, Branden S. Moriarity, Lisa M. Miller Jenkins, Hans Johansson, Yuelin J. Zhu, Sven Diederichs, Anindya Bagchi, Tae Hoon Kim, Sarath Chandra Janga, Ashish Lal, Supriya G. Prasanth, Kannanganattu V. Prasanth
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13059-018-1503-4

A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila
Cited by: 61
Author(s): François Mallard, Viola Nolte, Raymond Tobler, Martin Kapun, Christian Schlötterer
Software Mentions: 4
Published: about 8 years ago

10.1186/s13059-017-1328-6

Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS
Cited by: 49
Author(s): Hung‐Ying Lin, Qiang Liu, Li Xiao, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-016-3219-8

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans
Cited by: 21
Author(s): J.R. Peterson, Sheng Shee Thor, Lars Köhler, Petra R. A. Kohler, William W. Metcalf, Zaida Luthey‐Schulten
Software Mentions: 4
Published: almost 10 years ago

10.1128/mSystems.00596-19

Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics
Cited by: 7
Author(s): Matthew Chung, Laura Teigen, Silvia Libro, Robin E. Bromley, Dustin Olley, Nikhil Kumar, Lisa Sadzewicz, Luke J. Tallon, Anup Mahurkar, Jeremy M. Foster, Michelle L. Michalski, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-017-1277-0

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
Cited by: 72
Author(s): Koen Van den Berge, Charlotte Soneson, Mark D. Robinson
Software Mentions: 4
Published: about 9 years ago

10.3390/molecules21111431

Comparative Transcriptomic Analysis of Grape Berry in Response to Root Restriction during Developmental Stages
Cited by: 20
Author(s): Lu Feng, Qiong Lin, Di Wu, Shiping Wang, Dengliang Wang, Chongde Sun
Software Mentions: 4
Published: almost 10 years ago

10.1128/mSystems.00284-18

Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis : Implications for Isoprenoid Production
Cited by: 22
Author(s): Julia Martien, Alexander S. Hebert, David Stevenson, Matthew Regner, Daven B. Khana, Joshua J. Coon, Daniel Amador‐Noguez
Software Mentions: 4
Published: over 7 years ago

10.1016/j.celrep.2021.109032

Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome
Cited by: 17
Author(s): Alejandro Brenes, Harunori Yoshikawa, Dalila Bensaddek, Bogdan Mirauta, Daniel D Seaton, Jens Hukelmann, Hao Jiang, Oliver Stegle, Angus I. Lamond
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-016-1140-8

Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome
Cited by: 54
Author(s): Agata Wesolowska-Andersen, Jamie L. Everman, Rebecca M. Davidson, Cydney Rios, Rachelle Herrin, Celeste Eng, William J. Janssen, Andrew H. Liu, Sam S. Oh, Rajesh Kumar, Tasha E. Fingerlin, José Rodríguez‐Santana, Esteban G. Burchard, Max A. Seibold
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0255915

Reciprocal interplay between asporin and decorin: Implications in gastric cancer prognosis
Cited by: 6
Author(s): Dipjit Basak, Zarqua Jamal, Arnab Ghosh, Pronoy Kanti Mondal, Priyanka Dey Talukdar, Semanti Ghosh, Biswadeep Ghosh Roy, Ranajoy Ghosh, Ajay Halder, Abhijit Chowdhury, Gopal Krishna Dhali, Brajadulal Chattopadhyay, Makhan Saha, Abhimanyu Basu, Sukanta Roy, Chitranjan Mukherjee, Nidhan K. Biswas, Urmi Chatterji, Shalini Datta
Software Mentions: 4
Published: about 5 years ago

10.1186/s13059-016-1137-3

Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus
Cited by: 106
Author(s): Xuan Li, Emily Speranza, César Muñoz‐Fontela, Sam Haldenby, Natasha Y. Rickett, Isabel García-Dorival, Yongxiang Fang, Yper Hall, Elsa Gayle Zekeng, Anja Lüdtke, Dong Xia, Romy Kerber, Ralf Krumkamp, Sophie Duraffour, Daouda Sissoko, John Kenny, Nichola Rockliffe, E. Diane Williamson, Thomas R. Laws, N’Faly Magassouba, David A. Matthews, Stephan Günther, Andrew R. Cossins, Armand Sprecher, John H. Connor, Miles W. Carroll, Julian A. Hiscox
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0204038

Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period
Cited by: 3
Author(s): Ramona Krauss, Belinda Phipson, Alicia Oshlack, Nikita Prasad-Gupta, Michael Cheung, Joseph J. Smolich, Salvatore Pepe
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13059-016-1088-8

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface
Cited by: 214
Author(s): Duane D. McKenna, Erin D. Scully, Yannick Pauchet, Kelli Hoover, Roy Kirsch, Scott M. Geib, Robert F. Mitchell, Robert M. Waterhouse, Seung‐Joon Ahn, Deanna Arsala, Joshua B. Benoit, Heath Blackmon, Tiffany Bledsoe, Julia H. Bowsher, André Busch, Bernarda Calla, Hsu Chao, Anna K. Childers, Christopher P. Childers, Dave J. Clarke, Lorna Cohen, Jeffery P. Demuth, Huyen Dinh, Harshavardhan Doddapaneni, Amanda Dolan, Jian J. Duan, Shannon Dugan, Markus Friedrich, Karl M. Glastad, Michael A. D. Goodisman, Stéphanie Haddad, Yi Han, Daniel Hughes, Panagiotis Ioannidis, J. Spencer Johnston, Jeffery W. Jones, Leslie A. Kuhn, D. R. Lance, Chien Yueh Lee, Sandra L. Lee, Han Lin, Jeremy A. Lynch, Armin P. Moczek, Shwetha C. Murali, Donna M. Muzny, David R. Nelson, Subba Reddy Palli, Kristen A. Panfilio, Dan Pers, Monica F. Poelchau, Honghu Quan, Jiaxin Qu, Anandasankar Ray, Joseph P. Rinehart, Hugh M. Robertson, Richard L. Roehrdanz, Andrew J. Rosendale, Seunggwan Shin, Christian Silva, Alex S. Torson, Iris M. Vargas Jentzsch, John H. Werren, Kim C. Worley, George D. Yocum, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards
Software Mentions: 4
Published: almost 10 years ago

10.1111/mec.15216

Sex‐specific changes in the aphid DNA methylation landscape
Cited by: 32
Author(s): Thomas C. Mathers, Sam T. Mugford, Lawrence Percival‐Alwyn, Yazhou Chen, Gemy Kaithakottil, David Swarbreck, Saskia A. Hogenhout, Cock van Oosterhout
Software Mentions: 4
Published: almost 7 years ago

10.1128/mSystems.00038-18

Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation
Cited by: 66
Author(s): Andrea Söllinger, Alexander Tøsdal Tveit, Morten Poulsen, Samantha Joan Noel, Mia M. Bengtsson, Jörg Bernhardt, Anne Louise Frydendahl Hellwing, Peter Lund, Katharina Riedel, Christa Schleper, Ole Højberg, Tim Urich
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-020-07218-1

Targeted mutagenesis of ∆5 and ∆6 fatty acyl desaturases induce dysregulation of lipid metabolism in Atlantic salmon (Salmo salar)
Cited by: 6
Author(s): Yang Jin, Alex K. Datsomor, Rolf Erik Olsen, Jon Olav Vik, Jacob Torgersen, Rolf B. Edvardsen, Anna Wargelius, Per Winge, Fabian Grammes
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0120385

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize
Cited by: 58
Author(s): Malachy T. Campbell, Christopher A. Proctor, Yongchao Dou, Aaron J. Schmitz, Piyaporn Phansak, Greg R. Kruger, Chi Zhang, Harkamal Walia
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0192947

Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men
Cited by: 26
Author(s): Kathryn Burton, Grégory Pimentel, Nadine Zangger, Nathalie Vionnet, Jocelyne Drai, P. G. McTernan, François P. Pralong, Mauro Delorenzi, Guy Vergères
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0101467

Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation
Cited by: 22
Author(s): Panu Somervuo, Jouni Kvist, Suvi Ikonen, Petri Auvinen, Lars Paulín, Patrik Koskinen, Liisa Holm, Minna Taipale, Anne Duplouy, Annukka Ruokolainen, Suvi Saarnio, Jukka Sirén, Jukka Kohonen, Jukka Corander, Mikko J. Frilander, Virpi Ahola, Ilkka Hanski
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0168573

Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil
Cited by: 33
Author(s): Seung‐Yoon Oh, Jonathan J. Fong, Myung Soo Park, Young Woon Lim
Software Mentions: 4
Published: over 9 years ago

10.1128/mSphereDirect.00120-18

Zika Virus Infection Preferentially Counterbalances Human Peripheral Monocyte and/or NK Cell Activity
Cited by: 26
Author(s): Fok‐Moon Lum, David Lee, Tze-Kwang Chua, Jeslin J. L. Tan, Cheryl Yi‐Pin Lee, Xuan Li, Yongxiang Fang, Bernett Lee, Wearn‐Xin Yee, Natasha Y. Rickett, Po Ying Chia, Vanessa Lim, Yee‐Sin Leo, David A. Matthews, Julian A. Hiscox, Lisa F. P. Ng
Software Mentions: 4
Published: over 8 years ago

10.1128/mSphere.00231-18

Kinome Expansion in the Fusarium oxysporum Species Complex Driven by Accessory Chromosomes
Cited by: 28
Author(s): Gregory A. DeIulio, Li Guo, Yong Zhang, Jonathan M. Goldberg, H. Corby Kistler, Lijun Ma
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0236679

Characterisation of protein isoforms encoded by the Drosophila Glycogen Synthase Kinase 3 gene shaggy
Cited by: 4
Author(s): Dagmara Korona, Daniel J.H. Nightingale, Bertrand Fabre, Michael G. Nelson, Bettina Fischer, Glynnis Johnson, Jonathan G. Lees, Simon J. Hubbard, Kathryn S. Lilley, Steven Russell
Software Mentions: 4
Published: about 6 years ago

10.1128/mBio.00617-20

EspFu-Mediated Actin Assembly Enhances Enteropathogenic Escherichia coli Adherence and Activates Host Cell Inflammatory Signaling Pathways
Cited by: 12
Author(s): Fernando Henrique Martins, Ashwani Kumar, Cecília M. Abe, Enéas Carvalho, Milton Yutaka Nishiyama-Jr, Chao Xing, Vanessa Sperandio, Waldir P. Elias
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-020-6541-0

iREAD: a tool for intron retention detection from RNA-seq data
Cited by: 33
Author(s): Hong Dong Li, Cory C. Funk, Nathan D. Price
Software Mentions: 4
Published: over 6 years ago

10.1128/mBio.00588-21

An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin
Cited by: 6
Author(s): Gabriela Balderrama-Gutierrez, Ana Milovic, Vanessa J. Cook, M. Nurul Islam, Youwen Zhang, Hippokratis Kiaris, John T. Belisle, A Mortazavi, Alan G. Barbour
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pntd.0001409

A Deep Sequencing Approach to Comparatively Analyze the Transcriptome of Lifecycle Stages of the Filarial Worm, Brugia malayi
Cited by: 86
Author(s): Young Jun Choi, Elodie Ghedin, Matthew Berriman, Jacqueline A. McQuillan, Nancy Holroyd, George F. Mayhew, Bruce M. Christensen, Michelle L. Michalski
Software Mentions: 4
Published: over 14 years ago

10.1371/journal.pntd.0007680

Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes
Cited by: 24
Author(s): Luís Miguel González, Karel Estrada, Ricardo Grande, Verónica Jiménez-Jacinto, Leticia Vega‐Alvarado, Elena Sevilla, Jorge de la Barrera, Isabel Cuesta, Ángel Zaballos, José M. Bautista, Cheryl A. Lobo, Alejandro Sánchez-Flores, Estrella Montero
Software Mentions: 4
Published: about 7 years ago

10.1128/mBio.02504-18

The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium
Cited by: 73
Author(s): Alexander J. Westermann, Elisa Venturini, Mikael E. Sellin, Konrad U. Förstner, Wolf‐Dietrich Hardt, Jörg Vogel
Software Mentions: 4
Published: over 7 years ago

10.1186/s13059-015-0843-6

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
Cited by: 291
Author(s): Wei Li, Johannes Köster, Xu Han, Chen Hao Chen, Tengfei Xiao, Jun S. Liu, Myles Brown, X. Shirley Liu
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-015-0590-8

Field pathogenomics reveals the emergence of a diverse wheat yellow rust population
Cited by: 175
Author(s): Amelia Hubbard, Clare M. Lewis, Kentaro Yoshida, Ricardo H. Ramírez-González, C. de Vallavieille‐Pope, Jane Thomas, Sophien Kamoun, R. A. Bayles, Cristóbal Uauy, Diane G. O. Saunders
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pcbi.1006760

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data
Cited by: 6
Author(s): Vikash Pandey, Vassily Hatzimanikatis
Software Mentions: 4
Published: over 7 years ago

10.26508/lsa.201900535

The molecular clock protein Bmal1 regulates cell differentiation in mouse embryonic stem cells
Cited by: 12
Author(s): Amador Gallardo, Ana Rodríguez Molina, Helena G Asenjo, Jordi Martorell-Marugán, Rosa Montes, Verónica Ramos-Mejía, Antonio Sánchez–Pozo, Pedro Carmona-Sáez, Lourdes López-Onieva, David Landeira
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-6021-6

Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis)
Cited by: 17
Author(s): Liqing Zhou, Zhihong Liu, Yan Dong, Xiujun Sun, Biao Wu, Tao Yu, Yao Zheng, Aiguo Yang, Qing Zhao, Dan Zhao
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41398-017-0050-1

Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study
Cited by: 56
Author(s): Pei‐Fen Kuan, Monika A. Waszczuk, Roman Kotov, Sean Clouston, Xiaohua Yang, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 4
Published: over 8 years ago

10.1038/s41398-019-0472-z

DLPFC transcriptome defines two molecular subtypes of schizophrenia
Cited by: 26
Author(s): Elijah F. W. Bowen, Jack L. Burgess, Richard Granger, Joel E. Kleinman, C. Harker Rhodes
Software Mentions: 4
Published: over 7 years ago

10.1093/bioinformatics/btx094

Glimma: interactive graphics for gene expression analysis
Cited by: 120
Author(s): Shian Su, Charity W. Law, Casey Ah-Cann, Marie Liesse Asselin-Labat, Marnie E. Blewitt, Matthew E. Ritchie
Software Mentions: 4
Published: over 9 years ago

10.1038/tp.2016.67

Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report
Cited by: 26
Author(s): Michael S. Breen, Anne Uhlmann, Christiane M. Nday, Stephen J. Glatt, Mario Mitt, A. Metsalpu, Dan J. Stein, Nicola Illing
Software Mentions: 4
Published: over 10 years ago

10.1093/bioinformatics/btu274

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
Cited by: 64
Author(s): Tarmo Äijö, Vincent Butty, Zhi Chen, Verna Salo, Subhash Tripathi, Christopher B. Burge, Riitta Lahesmaa, Harri Lähdesmäki
Software Mentions: 4
Published: about 12 years ago

10.1186/s12864-016-3390-y

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells
Cited by: 11
Author(s): Alicja Pacholewska, Eliane Marti, Tosso Leeb, Vidhya Jagannathan, Vinzenz Gerber
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pbio.2004986

Canonical PRC2 function is essential for mammary gland development and affects chromatin compaction in mammary organoids
Cited by: 10
Author(s): Ewa M. Michalak, Michael J. G. Milevskiy, Rachel Joyce, Johanna F. Dekkers, Paul Jamieson, Bhupinder Pal, Caleb A. Dawson, Yifang Hu, Stuart H. Orkin, Warren S. Alexander, Geoffrey J. Lindeman, Gordon K. Smyth, Jane E. Visvader
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pbio.3000166

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival
Cited by: 32
Author(s): Oliver Smith, Glenn Dunshea, Mikkel‐Holger S. Sinding, Sergey Fedorov, Mietje Germonpré, Hervé Bocherens, M. Thomas P. Gilbert
Software Mentions: 4
Published: about 7 years ago

10.1186/s13059-014-0410-6

Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
Cited by: 278
Author(s): N. Davidson, Alicia Oshlack
Software Mentions: 4
Published: about 12 years ago

10.1038/s41375-021-01221-5

Temporal multiomic modeling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia
Cited by: 5
Author(s): Cédric Schleiss, Raphaël Carapito, Luc‐Matthieu Fornecker, Leslie Muller, Nicodème Paul, Ouria Tahar, Angélique Pichot, Manuela Tavian, Alina Nicolae, Laurent Miguet, Laurent Mauvieux, Raoul Herbrecht, Sarah Cianférani, Jean–Noël Freund, Myriam Maumy-Bertrand, Seiamak Bahram, Frédèric Bertrand, Laurent Vallat
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-014-0554-4

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
Cited by: 1,433
Author(s): Wei Li, Xu Han, Tengfei Xiao, Le Cong, Michael I. Love, Feng Zhang, Rafael A. Irizarry, Jun S. Liu, Myles Brown, X Shirley Liu
Software Mentions: 4
Published: over 11 years ago

10.7554/eLife.65979

Unbiased identification of novel transcription factors in striatal compartmentation and striosome maturation
Cited by: 8
Author(s): Maria-Daniela Cirnaru, Sicheng Song, Kizito-Tshitoko Tshilenge, Chuhyon Corwin, Justyna Mleczko, Carlos Galicia Aguirre, Houda Benlhabib, Jaroslav Bendl, Pasha Apontes, John F. Fullard, Jordi Creus-Muncunill, Azadeh Reyahi, Ali Moussavi Nik, Peter Carlsson, Panos Roussos, Sean D. Mooney, Lisa M. Ellerby, Michelle E. Ehrlich
Software Mentions: 4
Published: almost 5 years ago

10.1093/bioinformatics/bts394

An accurate paired sample test for count data
Cited by: 58
Author(s): Thang V. Pham, Connie R. Jiménez
Software Mentions: 4
Published: almost 14 years ago

10.1186/gb-2014-15-2-r32

KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation
Cited by: 112
Author(s): Benjamin L. Kidder, Gangqing Hu, Keji Zhao
Software Mentions: 4
Published: over 12 years ago

10.1038/leu.2016.251

Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts
Cited by: 99
Author(s): Annalisa Mupo, Monika Seiler, Vijitha Sathiaseelan, Alena Pance, Yi Yang, Anant A. Agrawal, Francesco Iorio, Rubén Bautista, Suruchi Pacharne, Konstantinos Tzelepis, Nicla Manes, Penny Wright, Elli Papaemmanuil, David G. Kent, Peter Campbell, Silvia Buonamici, Niccolò Bolli, George S. Vassiliou
Software Mentions: 4
Published: almost 10 years ago

10.7150/thno.55645

Deciphering the autophagy regulatory network via single-cell transcriptome analysis reveals a requirement for autophagy homeostasis in spermatogenesis
Cited by: 18
Author(s): Mei Wang, Yanwen Xu, Yuncong Zhang, Yuhan Chen, Gang Chang, Geng An, Xinyan Yang, Caihong Zheng, Jiexiang Zhao, Zhaoting Liu, Dazhuang Wang, Masahiro Kai, Rao S, Meng Dai, Dong Wang, Xiaoyang Zhao
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pbio.2003862

Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice
Cited by: 290
Author(s): Joseph Edwards, Christian Santos‐Medellín, Zachary Liechty, Bao‐Anh Thi Nguyen, Eugene Lurie, Shane Eason, Gregory C. Phillips, Venkatesan Sundaresan
Software Mentions: 4
Published: over 8 years ago

10.1186/s13148-021-01050-4

Epigenetic evidence of an Ac/Dc axis by VPA and SAHA
Cited by: 10
Author(s): Sebastian Lunke, Scott Maxwell, Ishant Khurana, K N Harikrishnan, Jun Okabe, Keith Al-Hasani, Assam El‐Osta
Software Mentions: 4
Published: over 5 years ago

10.3390/plants8120531

Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship between Photosynthesis and Leaf Development
Cited by: 9
Author(s): Giulio Testone, Elena Baldoni, Maria Adelaide Iannelli, Chiara Nicolodi, Elisabetta Di Giacomo, Fabrizio Pietrini, Giovanni Mele, Donato Giannino, Giovanna Frugis
Software Mentions: 4
Published: over 6 years ago

10.1186/gb-2012-13-10-r88

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
Cited by: 72
Author(s): Alok K. Tewari, Galip Gürkan Yardımcı, Yoichiro Shibata, Nathan C. Sheffield, Lingyun Song, Barry S. Taylor, Stoyan Georgiev, Gerhard A. Coetzee, Uwe Ohler, Terrence S. Furey, Gregory E. Crawford, Phillip G. Febbo
Software Mentions: 4
Published: over 14 years ago

10.1186/s13148-020-00989-0

Identification and validation of methylated differentially expressed miRNAs and immune infiltrate profile in EBV-associated gastric cancer
Cited by: 4
Author(s): Man-Sheng Zhu, Qi Liang, Tao Chen, Qian Kong, Gengtai Ye, Shitong Yu, Xunjun Li, Qinglie He, Hao Líu, Yanfeng Hu, Jiang Yu, Guoxin Li
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.11820

Clinical and prognostic relevance of CXCL12 expression in acute myeloid leukemia
Cited by: 2
Author(s): Shi-sen Wang, Zi‐jun Xu, Yue Jin, Ji‐chun Ma, Pei‐hui Xia, Xiang‐mei Wen, Zhen-wei Mao, Lin Jiang, Jun Qian
Software Mentions: 4
Published: about 5 years ago

10.1186/s13148-020-00836-2

Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer
Cited by: 15
Author(s): Mitchell G. Lawrence, Ruth Pidsley, Birunthi Niranjan, Melissa Papargiris, Brooke A. Pereira, Michelle Richards, Linda Teng, Sam Norden, Andrew Ryan, Mark Frydenberg, Clare Stirzaker, Renea A. Taylor, Gail P. Risbridger, Susan J. Clark
Software Mentions: 4
Published: over 6 years ago

10.1534/genetics.118.301515

PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in Arabidopsis thaliana
Cited by: 17
Author(s): Tohru Kanno, Peter Venhuizen, Wen Teng, Wen-Dar Lin, Phebe Chiou, Maria Kalyna, A. J. M. Matzke, Marjori Matzke
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2021.605095

Improvement of Free Fatty Acid Secretory Productivity in Aspergillus oryzae by Comprehensive Analysis on Time-Series Gene Expression
Cited by: 4
Author(s): Pui Shan Wong, Koichi Tamano, Sachiyo Aburatani
Software Mentions: 4
Published: over 5 years ago

10.7150/thno.36378

Exosome-dependent immune surveillance at the metastatic niche requires BAG6 and CBP/p300-dependent acetylation of p53
Cited by: 41
Author(s): Maximiliane Schuldner, Bastian Dörsam, Olga Shatnyeva, Katrin S. Reiners, Andriy V. Kubarenko, Hinrich P. Hansen, Florian Finkernagel, Katrin Roth, Sebastian Theurich, Andrea Nist, Thorsten Stiewe, Annette Paschen, Gero Knittel, Hans Christian Reinhardt, Rolf Müller, Michael Hallek, Elke Pogge von Strandmann
Software Mentions: 4
Published: over 7 years ago

10.1186/s40170-020-00229-2

Metabolic plasticity of IDH1-mutant glioma cell lines is responsible for low sensitivity to glutaminase inhibition
Cited by: 13
Author(s): Victor Ruiz‐Rodado, Adrian Lita, Tyrone Dowdy, Orieta Celiku, Alejandra Cavazos Saldana, Herui Wang, Chunzhang Yang, Raj Chari, Aiguo Li, Wei Zhang, Hua Song, Meili Zhang, Susie Ahn, Dionne L. Davis, Xiang Chen, Zhengping Zhuang, Christel Herold‐Mende, Kylie J. Walters, Mark R. Gilbert, Mioara Larion
Software Mentions: 4
Published: almost 6 years ago

10.3390/plants9091149

Response of Downy Oak (Quercus pubescens Willd.) to Climate Change: Transcriptome Assembly, Differential Gene Analysis and Targeted Metabolomics
Cited by: 7
Author(s): Jean-Philippe Mévy, Béatrice Loriod, Xi Liu, Erwan Corre, Magali Torres, Michael Büttner, Anne Haguenauer, Ilja M. Reiter, Catherine Fernandez, Thierry Gauquelin
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40169-017-0150-9

Single‐cell RNA‐sequencing of the brain
Cited by: 46
Author(s): Raquel Durán, Haichao Wei, Jia Qian Wu
Software Mentions: 4
Published: about 9 years ago

10.7150/thno.47830

LncRNA DSCAM-AS1 interacts with YBX1 to promote cancer progression by forming a positive feedback loop that activates FOXA1 transcription network
Cited by: 68
Author(s): Yin Zhang, Yong-Xin Huang, Dan-Lan Wang, Bing Yang, Haiyan Yan, Lehang Lin, Yun Li, Jie Chen, Lisha Xie, Yongsheng Huang, Jian-You Liao, Kaishun Hu, Jun He, Phei Er Saw, Xiaoding Xu, Yin Ding
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-021-97306-3

Differentially expressed genes in the femur cartilage transcriptome clarify the understanding of femoral head separation in chickens
Cited by: 3
Author(s): Ludmila Mudri Hul, A. M. G. Ibelli, Igor Ricardo Savoldi, Débora Ester Petry Marcelino, Lana Teixeira Fernandes, J. O. Peixoto, Maurício Egídio Cantão, R. H. Higa, P. F. Giachetto, Luiz Lehmann Coutinho, Mônica Corrêa Ledur
Software Mentions: 4
Published: almost 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568