bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1172/JCI134132

Orally bioavailable CDK9/2 inhibitor shows mechanism-based therapeutic potential in MYCN-driven neuroblastoma
Cited by: 38
Author(s): Evon Poon, Tong Liang, Yann Jamin, Susanne Walz, Colin Kwok, Anne Hakkert, Karen Barker, Zuzanna Urban, Khin Thway, Rhamy Zeid, Albert Hallsworth, Gary Box, Marli E. Ebus, Marco P. Licciardello, Yordan Sbirkov, Glori Lazaro, Elizabeth Calton, Barbara Martins Da Costa, Melanie Valenti, Alexis de Haven Brandon, Hannah Webber, Nicolas Tardif, Gilberto S. Almeida, Rossitza Christova, Gunther Boysen, Mark W. Richards, Giuseppe Barone, Anthony M. Ford, Richard Bayliss, Paul A. Clarke, Johann S. de Bono, Nathanael S. Gray, Julian Blagg, Simon P. Robinson, Suzanne A. Eccles, Daniella Zheleva, James E. Bradner, Jan J. Molenaar, Igor Vivanco, Martin Eilers, Paul Workman, Charles Y. Lin, Louis Chesler
Software Mentions: 2
Published: almost 6 years ago

10.1002/jcla.23428

Hsa_circ_0023642 promotes proliferation, invasion, and migration of gastric cancer by sponging microRNA‐223
Cited by: 6
Author(s): Yi Zhang, Lei Xia, Jing Wu, Xinyu Xu, Gang Li
Software Mentions: 2
Published: about 6 years ago

10.3390/jcm7110419

Unique MicroRNA and mRNA Interactions in EGFR-Mutated Lung Adenocarcinoma
Cited by: 13
Author(s): Sophia Subat, Kentaro Inamura, Hironori Ninomiya, Hiroko Nagano, Sakae Okumura
Software Mentions: 2
Published: almost 8 years ago

10.3390/jcm8111772

A CTC-Cluster-Specific Signature Derived from OMICS Analysis of Patient-Derived Xenograft Tumors Predicts Outcomes in Basal-Like Breast Cancer
Cited by: 35
Author(s): Hariprasad Thangavel, Carmine De Angelis, Suhas Vasaikar, Raksha Bhat, Mohit Kumar Jolly, Chandandeep Nagi, Chad J. Creighton, Ken Chen, Lacey E. Dobrolecki, Jason T. George, Tanya Kumar, Noor Mazin Abdulkareem, Sufeng Mao, Agostina Nardone, Mothaffar F. Rimawi, C. Kent Osborne, Michael T. Lewis, Herbert Levine, Bing Zhang, Rachel Schiff, Mario Giuliano, Meghana V. Trivedi
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12896-014-0091-y

Comparison of intracellular and secretion-based strategies for production of human α-galactosidase A in the filamentous fungus Trichoderma reesei
Cited by: 11
Author(s): Wesley Smith, Jussi Jäntti, Merja Oja, Markku Saloheimo
Software Mentions: 2
Published: almost 12 years ago

10.1186/1741-7007-10-16

Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress
Cited by: 70
Author(s): Keith E.J. Tyo, Zihe Liu, Dina Petranović, Jens Nielsen
Software Mentions: 2
Published: over 14 years ago

10.3390/jcm9051338

Genome-Wide Analysis of the DNA Methylation Profile Identifies the Fragile Histidine Triad (FHIT) Gene as a New Promising Biomarker of Crohn’s Disease
Cited by: 8
Author(s): Tae-Oh Kim, Dong Il Park, Yu Han, Keunsoo Kang, Sae-Gwang Park, Hae Ryoun Park, Joo Mi Yi
Software Mentions: 2
Published: over 6 years ago

10.1186/s12915-015-0186-5

Systems-level organization of yeast methylotrophic lifestyle
Cited by: 110
Author(s): Hannes Rußmayer, Markus Buchetics, Clemens Gruber, Minoska Valli, Karlheinz Grillitsch, Gerda Modarres, Raffaele Guerrasio, Kristaps Klavins, Stefan Neubauer, H. Drexler, Matthias G. Steiger, Christina Troyer, Ali Al Chalabi, Guido Krebiehl, Denise Sonntag, Günther Zellnig, Günther Daum, Alexandra B. Graf, Friedrich Altmann, Gunda Koellensperger, Stephan Hann, Michael Sauer, Diethard Mattanovich, Brigitte Gasser
Software Mentions: 2
Published: almost 11 years ago

10.18632/aging.103547

FGF2-induced PI3K/Akt signaling evokes greater proliferation and adipogenic differentiation of human adipose stem cells from breast than from abdomen or thigh
Cited by: 3
Author(s): Guan-Ming Lu, Yong-Xian Rong, Zheng Liang, Dong-Lin Hunag, Fengyao Wu, Yuju Ma, Zhizhai Luo, Xinheng Liu, Steven Mo, Hong-Mian Li
Software Mentions: 2
Published: about 6 years ago

10.1186/s12915-021-00959-9

A brain cyst load-associated antigen is a Toxoplasma gondii biomarker for serodetection of persistent parasites and chronic infection
Cited by: 5
Author(s): Céline Dard, Christopher Swale, Marie-Pierre Brenier-Pinchart, Dayana C Farhat, Valeria Bellini, M Robert, Dominique Cannella, H Pelloux, Isabelle Tardieux, Mohamed‐Ali Hakimi
Software Mentions: 2
Published: over 5 years ago

10.3390/jcm10122680

Methylation Status of Corticotropin-Releasing Factor (CRF) Receptor Genes in Colorectal Cancer
Cited by: 8
Author(s): Μαρία Παναγοπούλου, Antonia Cheretaki, Makrina Karaglani, Ioanna Balgkouranidou, Eirini Biziota, Kyriakos Amarantidis, Nikolaos Xenidis, Stylianos Kakolyris, Stavroula Baritaki, Εkaterini Chatzaki
Software Mentions: 2
Published: over 5 years ago

10.1155/2020/4178639

Identification of Susceptibility Modules and Genes for Cardiovascular Disease in Diabetic Patients Using WGCNA Analysis
Cited by: 41
Author(s): Weiwei Liang, Fangfang Sun, Yingxin Zhao, Peng-Fei Shan, Han-Yu Lou
Software Mentions: 2
Published: over 6 years ago

10.1186/1741-7007-7-1

Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration
Cited by: 147
Author(s): James R. Monaghan, Leonard G. Epp, Srikrishna Putta, Robert B. Page, John Walker, Chris K Beachy, Wei Zhu, Gerald M. Pao, Inder M. Verma, Tony Hunter, Susan V. Bryant, David M. Gardiner, Tim Harkins, S. Randal Voss
Software Mentions: 2
Published: over 17 years ago

10.1186/1741-7007-9-29

Lack of global meiotic sex chromosome inactivation, and paucity of tissue-specific gene expression on the Drosophila X chromosome
Cited by: 67
Author(s): Lyudmila Mikhaylova, Dmitry I. Nurminsky
Software Mentions: 2
Published: over 15 years ago

10.1186/s12915-020-00791-7

Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii
Cited by: 31
Author(s): Joachim Kloehn, Rebecca Oppenheim, Ghizal Siddiqui, Pieter Jan De Bock, Sunil Kumar Dogga, Yohann Couté, Mohamed‐Ali Hakimi, Darren J. Creek, Dominique Soldati‐Favre
Software Mentions: 2
Published: over 6 years ago

10.1093/jxb/erv285

TheIDA/IDA-LIKEandPIP/PIP-LIKEgene families inArabidopsis: phylogenetic relationship, expression patterns, and transcriptional effect of the PIPL3 peptide
Cited by: 64
Author(s): Ane Kjersti Vie, Javad Najafi, Bin Liu, Per Winge, Melinka A. Butenko, Karina S. Hornslien, Robert P. Kumpf, Reidunn B. Aalen, Atle M. Bones, Tore Brembu
Software Mentions: 2
Published: over 11 years ago

10.1093/jxb/erv516

Kresoxim-methyl primesMedicago truncatulaplants against abiotic stress factors via altered reactive oxygen and nitrogen species signalling leading to downstream transcriptional and metabolic readjustment
Cited by: 28
Author(s): Panagiota Filippou, Chrystalla Antoniou, Toshihiro Obata, Katrien Van Der Kelen, Vaggelis Harokopos, Loukas Kanetis, Vassilis Aidinis, Frank Van Breusegem, Alisdair R. Fernie, Vasileios Fotopoulos
Software Mentions: 2
Published: over 10 years ago

10.1093/jxb/erw350

The build-up of osmotic stress responses within the growing root apex using kinematics and RNA-sequencing
Cited by: 12
Author(s): Mathilde Royer, David Cohen, Nathalie Aubry, Vera Vendramin, Simone Scalabrin, Federica Cattonaro, Marie‐Béatrice Bogeat‐Triboulot, Irène Hummel
Software Mentions: 2
Published: almost 10 years ago

10.1093/jxb/erx168

The IDA-LIKE peptides IDL6 and IDL7 are negative modulators of stress responses in Arabidopsis thaliana
Cited by: 28
Author(s): Ane Kjersti Vie, Javad Najafi, Per Winge, Ester Cattan, Michael Wrzaczek, Jaakko Kangasjärvi, Gad Miller, Tore Brembu, Atle M. Bones
Software Mentions: 2
Published: over 9 years ago

10.1093/jxb/erx254

Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana
Cited by: 43
Author(s): Pavel Cherenkov, Daria D. Novikova, N. A. Omelyanchuk, Victor G. Levitsky, Ivo Große, Dolf Weijers, В. В. Миронова
Software Mentions: 2
Published: about 9 years ago

10.1186/s12915-016-0334-6

Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway
Cited by: 32
Author(s): Deborah L. McEwan, Rhonda Feinbaum, Nicholas Stroustrup, Wilhelm Haas, Annie L. Conery, Anthony Anselmo, Ruslan I. Sadreyev, Frederick M. Ausubel
Software Mentions: 2
Published: almost 10 years ago

10.3390/ijms20143444

Long Non-coding RNAs as Important Biomarkers in Laryngeal Cancer and Other Head and Neck Tumours
Cited by: 61
Author(s): Alessia Maria Cossu, Laura Mosca, Silvia Zappavigna, Gabriella Misso, Marco Bocchetti, Federica De Micco, Lucio Quagliuolo, Marina Porcelli, Michele Caraglia, Mariarosaria Boccellino
Software Mentions: 2
Published: about 7 years ago

10.1093/jxb/erw474

Nod factors potentiate auxin signaling for transcriptional regulation and lateral root formation inMedicago truncatula
Cited by: 15
Author(s): Violaine Herrbach, Ximena Chirinos, David Rodrı́guez-Lázaro, Kokoévi Agbévénou, Rémy Vincent, Stéphanie Pateyron, Stéphanie Huguet, Sandrine Balzergue, Asher Pasha, Nicholas J. Provart, Clare Gough, Sandra Bensmihen
Software Mentions: 2
Published: over 9 years ago

10.1093/jxb/eraa099

Transcriptional analysis of arogenate dehydratase genes identifies a link between phenylalanine biosynthesis and lignin biosynthesis
Cited by: 9
Author(s): Jorge El-Azaz, Fernando De la Torre, María Belén Pascual, Sandrine Debille, Francis Canlet, Luc Harvengt, Jean-François Trontin, Concepción Ávila
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms20153651

MicroRNA Profiling During Neural Differentiation of Induced Pluripotent Stem Cells
Cited by: 21
Author(s): Katarzyna Kulcenty, Joanna Wróblewska, Marcin Ruciński, Emilia Kozłowska, Karol Jopek, Wiktoria Maria Suchorska
Software Mentions: 2
Published: about 7 years ago

10.18632/oncotarget.16437

Promoter DNA methylation analysis reveals a combined diagnosis of CpG-based biomarker for prostate cancer
Cited by: 10
Author(s): Yuanyuan Tang, Sanyuan Jiang, Yinmin Gu, Weidong Li, Zengnan Mo, Yuanjie Huang, Tianyu Li, Yanling Hu
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.ppat.1000604

Lethal Influenza Virus Infection in Macaques Is Associated with Early Dysregulation of Inflammatory Related Genes
Cited by: 197
Author(s): Cristian Cillóniz, Kyoko Shinya, Xinxia Peng, Marcus J. Korth, Sean Proll, Lauri Aicher, Victoria S. Carter, Jean Chang, Darwyn Kobasa, Friedericke Feldmann, James E. Strong, Heinz Feldmann, Yoshihiro Kawaoka, Michael G. Katze
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.ppat.1002315

Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Regulates Cell Stress Response and Apoptosis
Cited by: 175
Author(s): Marta L. DeDiego, José L. Nieto-Torres, Jose M. Jiménez-Guardeño, José Ángel Regla-Nava, Enrique Álvarez, Juan Carlos Oliveros, Jincun Zhao, Craig Fett, Stanley Perlman, Luis Enjuanes
Software Mentions: 2
Published: almost 15 years ago

10.1186/1471-2105-12-228

Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics
Cited by: 24
Author(s): Tracy L. Bergemann, Jason Wilson
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.ppat.1004079

Exposure-Dependent Control of Malaria-Induced Inflammation in Children
Cited by: 135
Author(s): Sílvia Portugal, Jacqueline Moebius, Jeff Skinner, Safiatou Doumbo, Didier Doumtabé, Younoussou Koné, Seydou Dia, Kishore Kanakabandi, Daniel E. Sturdevant, Kimmo Virtaneva, Stephen F. Porcella, Shanping Li, Ogobara K. Doumbo, Kassoum Kayentao, Aissata Ongoïba, Boubacar Traoré, Peter D. Crompton
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.ppat.1004662

Prion Infections and Anti-PrP Antibodies Trigger Converging Neurotoxic Pathways
Cited by: 74
Author(s): U. Herrmann, Tiziana Sonati, Jeppe Falsig, Regina Reimann, Paolo Dametto, Tracy O’Connor, Bei Li, Agnes Lau, Simone Hornemann, Silvia Sorce, Uli Wagner, Despina Sanoudou, Adriano Aguzzi
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-015-0712-z

Seq-ing improved gene expression estimates from microarrays using machine learning
Cited by: 5
Author(s): Paul K. Korir, Paul Geeleher, Cathal Seoighe
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2105-12-413

Impact of the spotted microarray preprocessing method on fold-change compression and variance stability
Cited by: 26
Author(s): Jérôme Ambroise, Bertrand Bearzatto, Annie Robert, Bernadette Govaerts, Benoı̂t Macq, Jean‐Luc Gala
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.ppat.1005263

Interferon-γ Inhibits Ebola Virus Infection
Cited by: 69
Author(s): Bethany A. Rhein, Linda S. Powers, Kai J. Rogers, Manu Anantpadma, Brajesh K. Singh, Yoshio Sakurai, Thomas B. Bair, Catherine L. Miller-Hunt, Patrick L. Sinn, Robert A. Davey, Martha M. Monick, Wendy Maury
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.ppat.1005936

Combined Activity of DCL2 and DCL3 Is Crucial in the Defense against Potato Spindle Tuber Viroid
Cited by: 49
Author(s): Κωνσταντίνα Κατσαρού, Eleni Mavrothalassiti, Wannes Dermauw, Thomas Van Leeuwen, Kriton Kalantidis
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.ppat.1006576

Malaria-induced interferon-γ drives the expansion of Tbethi atypical memory B cells
Cited by: 122
Author(s): Nyamekye Obeng-Adjei, Sílvia Portugal, Prasida Holla, Shanping Li, Hyung Sun Sohn, Abhijit A. Ambegaonkar, Jeff Skinner, Georgina Bowyer, Ogobara K. Doumbo, Boubacar Traoré, Susan K. Pierce, Peter D. Crompton
Software Mentions: 2
Published: almost 9 years ago

10.1007/s00592-019-01464-w

Metabolite profiling paradoxically reveals favorable levels of lipids, markers of oxidative stress and unsaturated fatty acids in a diabetes susceptible group of Middle Eastern immigrants
Cited by: 6
Author(s): Mahmoud Al-Majdoub, Peter Sartipy, Louise Bennet
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-6-65

Cited by: 21
Author(s): Mayte Suárez‐Fariñas, Asifa Haider, Knut M. Wittkowski
Software Mentions: 2
Published: over 21 years ago

10.1186/s12859-017-1925-0

Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling
Cited by: 38
Author(s): Daniel Castillo, Juan Manuel Gálvez, José Benavente Herrera, Belén San Román, Fernando Rojas, Ignacio Rojas
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.ppat.1006788

Lower temperatures reduce type I interferon activity and promote alphaviral arthritis
Cited by: 34
Author(s): Natalie A. Prow, Bing Tang, Joy Gardner, Thuy T. Le, Adam Taylor, Yee Suan Poo, Eri Nakayama, Thiago Dominguez Crespo Hirata, Helder I. Nakaya, Andrii Slonchak, Pamela Mukhopadhyay, Suresh Mahalingam, Wayne A. Schroder, William B. Klimstra, Andreas Suhrbier
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.ppat.1006871

Liver macrophage-associated inflammation correlates with SIV burden and is substantially reduced following cART
Cited by: 18
Author(s): Bridget S. Fisher, Richard Green, Rachel Brown, Matthew P. Wood, Tiffany Hensley-McBain, Cole Fisher, Jean Chang, Andrew D. Miller, William J. Bosche, Jeffrey D. Lifson, Maud Mavigner, Charlene Miller, Michael Gale, Guido Silvestri, Ann Chahroudi, Nichole R. Klatt, Donald L. Sodora
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.ppat.1007276

Cellular sheddases are induced by Merkel cell polyomavirus small tumour antigen to mediate cell dissociation and invasiveness
Cited by: 24
Author(s): Nnenna Nwogu, James R. Boyne, Samuel J. Dobson, Krzysztof Poterlowicz, G. Eric Blair, Andrew Macdonald, Jamel Mankouri, Adrian Whitehouse
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2105-11-556

Assessment and optimisation of normalisation methods for dual-colour antibody microarrays
Cited by: 23
Author(s): Martin Sill, Christoph Schröder, Jörg D. Hoheisel, Axel Benner, Manuela Zucknick
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.ppat.1007298

Microvesicles from malaria-infected red blood cells activate natural killer cells via MDA5 pathway
Cited by: 48
Author(s): Weijian Ye, Marvin Chew, Jue Hou, Fritz Lai, Stije J. Leopold, Hooi Linn Loo, Aniruddha Ghose, A. K. Dutta, Yi‐Ping Phoebe Chen, Eng Eong Ooi, Nicholas J. White, Arjen M. Dondorp, Peter R. Preiser, Jianzhu Chen
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.1007528

Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans
Cited by: 62
Author(s): Kirthi C. Reddy, Tal Dror, Ryan Underwood, Guled A. Osman, Corrina R. Elder, Christopher A. Desjardins, Christina A. Cuomo, Michalis Barkoulas, Emily R. Troemel
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007684

The TLR4 adaptor TRAM controls the phagocytosis of Gram-negative bacteria by interacting with the Rab11-family interacting protein 2
Cited by: 26
Author(s): Astrid Skjesol, Mariya Yurchenko, Korbinian Bösl, Caroline S. Gravastrand, Kaja Elisabeth Nilsen, Lene Melsæther Grøvdal, Federica Agliano, Francesco Patanè, Germana Lentini, Hera Kim, Giuseppe Teti, A. Sharma, Richard K. Kandasamy, Bjørnar Sporsheim, Kristian K. Starheim, Douglas T. Golenbock, Harald Stenmark, Mary W. McCaffrey, Terje Espevik, Harald Husebye
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007748

CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo
Cited by: 42
Author(s): Bithi Chatterjee, Yun Deng, Angelika Holler, Nicolás Gonzalo Núñez, Tarik Azzi, Liliana Danusia Vanoaica, Anne Müller, Hana Zdimerova, Olga Antsiferova, Andrea Zbinden, Riccarda Capaul, Johannes H. Dreyer, David Nadal, Burkhard Becher, Mark D. Robinson, Hans J. Stauss, Christian Münz
Software Mentions: 2
Published: over 7 years ago

10.1007/s00401-019-02056-2

MYCN amplification drives an aggressive form of spinal ependymoma
Cited by: 87
Author(s): David R. Ghasemi, Martin Sill, Konstantin Okonechnikov, Andrey Korshunov, Stephen Yip, Peter W. Schütz, David Scheie, Andreas Kruse, Patrick N. Harter, Marina Kastelan, Marlies Wagner, Christian Hartmann, Julia Benzel, Kendra K. Maaß, Mustafa Khasraw, Ronald Sträter, Christian Thomas, Werner Paulus, Christian P. Kratz, Hendrik Witt, Daisuke Kawauchi, Christel Herold‐Mende, Felix Sahm, Sebastian Brandner, Marcel Kool, David Jones, Andreas von Deimling, Stefan M. Pfister, David Reuß, Kristian W. Pajtler
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.ppat.1007841

DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes
Cited by: 37
Author(s): Taylor M. Nye, Kristin M. Jacob, Elena K. Holley, Juan M Nevarez, Suzanne Dawid, Lyle A. Simmons, Michael Watson
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007880

Systems analysis of subjects acutely infected with the Chikungunya virus
Cited by: 26
Author(s): Alessandra Soares‐Schanoski, Natália Baptista Cruz, Luíza Antunes de Castro-Jorge, Roberto Gameiro de Carvalho, Cliomar Alves dos Santos, Nancy da Rós, Ursula de Oliveira, Danuza Duarte Costa, Cecília Luiza Simões Santos, Marielton dos Passos Cunha, Maria Leonor S. Oliveira, Juliana Cardoso Alves, Regina Adalva de Lucena Couto Océa, Danielle Rodrigues Ribeiro, André Nicolau Aquime Gonçalves, Patrícia Gonzalez-Dias, Andreas Suhrbier, Paolo Marinho de Andrade Zanotto, Inácio L.M. Junqueira-de-Azevedo, Dario S. Zamboni, Roque Pacheco de Almeida, Paulo Lee Ho, Jorge Kalil, Milton Yutaka Nishiyama-Jr, Helder I. Nakaya
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007960

Dafachronic acid promotes larval development in Haemonchus contortus by modulating dauer signalling and lipid metabolism
Cited by: 31
Author(s): Guangxu Ma, Tao Wang, Pasi K. Korhonen, Neil D. Young, Shuai Nie, Ching‐Seng Ang, Nicholas A. Williamson, Gavin E. Reid, Robin B. Gasser
Software Mentions: 2
Published: about 7 years ago

10.1186/s12859-019-2893-3

JCD-DEA: a joint covariate detection tool for differential expression analysis on tumor expression profiles
Cited by: 3
Author(s): Yi Li, Yanan Liu, Yiming Wu, Xudong Zhao
Software Mentions: 2
Published: about 7 years ago

10.18632/aging.102610

The correlation and role analysis of COL4A1 and COL4A2 in hepatocarcinogenesis
Cited by: 21
Author(s): Yanli Li, Jiaye Zhang, Yan Chen, Mahmodul Hasan Sohel, Xinrong Ke, Jingqi Chen, Yin‐Xiong Li
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-019-2756-y

Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies
Cited by: 5
Author(s): Ana M. Untaroiu, Maureen A. Carey, Jennifer L. Guler, Jason A. Papin
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1008468

Human papillomavirus E7 binds Oct4 and regulates its activity in HPV-associated cervical cancers
Cited by: 13
Author(s): Theofano Panayiotou, Stella Michael, Apostolos Zaravinos, Ece Demirag, Charis Achilleos, Katerina Strati
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-10-409

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation)
Cited by: 89
Author(s): Martin J. Aryee, José A. Gutiérrez‐Pabello, Igor Kramnik, Tapabrata Maiti, John Quackenbush
Software Mentions: 2
Published: almost 17 years ago

10.1186/s12859-021-04100-z

Strain-specific behavior of Mycobacterium tuberculosis in A549 lung cancer cell line
Cited by: 4
Author(s): Shima Hadifar, Shayan Mostafaei, Ava Behrouzi, Abolfazl Fateh, Parisa Riahi, Seyed Davar Siadat, Farzam Vaziri
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-017-1889-0

Repositioning drugs by targeting network modules: a Parkinson’s disease case study
Cited by: 24
Author(s): Zongliang Yue, Itika Arora, Eric Y. Zhang, Vincent A. Laufer, S. Louis Bridges, Jake Y. Chen
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2105-15-39

Statistical analysis of differential gene expression relative to a fold change threshold on NanoString data of mouse odorant receptor genes
Cited by: 26
Author(s): Evelien Vaes, Mona Khan, Peter Mombaerts
Software Mentions: 2
Published: over 12 years ago

10.1186/s12859-019-2849-7

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets
Cited by: 76
Author(s): Tobias Neumann, Veronika A. Herzog, Matthias Muhar, Arndt von Haeseler, Johannes Zuber, Stefan L. Ameres, Philipp Rescheneder
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-10-372

Illumina WG-6 BeadChip strips should be normalized separately
Cited by: 21
Author(s): Wei Shi, Aditi Banerjee, Matthew E. Ritchie, Steve Gerondakis, Gordon K. Smyth
Software Mentions: 2
Published: almost 17 years ago

10.1155/2020/6527564

The Role of Peroxisome Proliferator-Activated Receptors (PPARs) in Pan-Cancer
Cited by: 12
Author(s): Runzhi Huang, Jiaqi Zhang, Mingxiao Li, Penghui Yan, Huabin Yin, Suna Zhai, Xiaolong Zhu, Peng Hu, Jiaxin Zhang, Ling Huang, Man Li, Zehui Sun, Tong Meng, Daoke Yang, Zongqiang Huang
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-7-538

Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments
Cited by: 226
Author(s): Maureen A. Sartor, Craig R. Tomlinson, Scott C. Wesselkamper, Siva Sivaganesan, George D. Leikauf, Mario Medvedovic
Software Mentions: 2
Published: almost 20 years ago

10.1073/pnas.2000943117

Macrophage metabolic reprogramming presents a therapeutic target in lupus nephritis
Cited by: 70
Author(s): Chenzhi Jing, Tomas Castro‐Dopico, Nathan Richoz, Zewen Kelvin Tuong, John R. Ferdinand, Laurence S.C. Lok, Kevin Loudon, Gemma D. Banham, Rebeccah J. Mathews, M Zaeem Cader, Susan F. Fitzpatrick, Kathleen R. Bashant, Mariana J. Kaplan, Arthur Kaser, Randall S. Johnson, Michael P. Murphy, Richard M. Siegel, Menna R. Clatworthy
Software Mentions: 2
Published: over 6 years ago

10.1073/pnas.2008762117

Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer’s disease
Cited by: 200
Author(s): Shun‐Fat Lau, Han Cao, Amy Kit Yu Fu, Nancy Y. Ip
Software Mentions: 2
Published: almost 6 years ago

10.1002/pros.23222

Accumulation of Palmitoylcarnitine and Its Effect on Pro‐Inflammatory Pathways and Calcium Influx in Prostate Cancer
Cited by: 21
Author(s): Ala'a Al‐Bakheit, Μαρία Τράκα, Shikha Saha, Richard Mithen, Antonietta Melchini
Software Mentions: 2
Published: about 10 years ago

10.3390/proteomes8030025

Serum Glycoproteomic Alterations in Patients with Diabetic Retinopathy
Cited by: 3
Author(s): Ashok Sharma, James Shell Cox, Joshua Glass, Tae Jin Lee, Sai Karthik Kodeboyina, Wenbo Zhi, Lane Ulrich, Zachary L. Lukowski, Shruti Sharma
Software Mentions: 2
Published: about 6 years ago

10.1098/rsos.160033

Domestication and tameness: brain gene expression in red junglefowl selected for less fear of humans suggests effects on reproduction and immunology
Cited by: 24
Author(s): Johan Bélteky, Beatrix Agnvall, Martin Johnsson, I. A. Wright, Per Jensen
Software Mentions: 2
Published: about 10 years ago

10.1186/1748-717X-9-111

Integrating microRNA and mRNA expression profiles in response to radiation-induced injury in rat lung
Cited by: 27
Author(s): Ling Xie, Jundong Zhou, Shuyu Zhang, Qing Chen, Renchun Lai, Wei‐Qun Ding, Chuanjun Song, Xingjun Meng, Jinchang Wu
Software Mentions: 2
Published: over 12 years ago

10.1186/s13014-018-1129-4

Molecular signature of response to preoperative radiotherapy in locally advanced breast cancer
Cited by: 14
Author(s): Miljana Tanić, Ana Krivokuća, Milena Čavić, Jasmina Mladenović, Vesna Plešinac Karapandžić, Stephan Beck, Siniša Radulović, Snežana Šušnjar, Radmila Janković
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13014-020-01620-5

Transcriptome network of the papillary thyroid carcinoma radiation marker CLIP2
Cited by: 1
Author(s): Martin Selmansberger, Agata Michna, Herbert Braselmann, Ines Höfig, Kenji Schorpp, Peter Weber, Nataša Anastasov, Horst Zitzelsberger, Julia Heß, Kristian Unger
Software Mentions: 2
Published: about 6 years ago

10.1016/j.redox.2019.101165

Mitochondria in precision medicine; linking bioenergetics and metabolomics in platelets
Cited by: 31
Author(s): Balu K. Chacko, M. R. Smith, Michelle S. Johnson, Gloria A. Benavides, Matilda Lillian Culp, Jyotsna Pilli, Sruti Shiva, Karan Uppal, Young‐Mi Go, Dean P. Jones, Victor Darley‐Usmar
Software Mentions: 2
Published: over 7 years ago

10.1186/s12958-017-0273-2

Differentiating mouse embryonic stem cells express markers of human endometrium
Cited by: 13
Author(s): Parveen Parasar, Caitlin R. Sacha, Nicholas Ng, E. R. McGuirk, Sireesha Chinthala, Pınar Özcan, J. Suzanne Lindsey, Sophia Salas, Marc R. Laufer, Stacey A. Missmer, Raymond M. Anchan
Software Mentions: 2
Published: about 9 years ago

10.1186/s12958-021-00706-3

Identification of key pathways and genes in polycystic ovary syndrome via integrated bioinformatics analysis and prediction of small therapeutic molecules
Cited by: 14
Author(s): Praveen Devarbhavi, Lata Telang, Basavaraj Vastrad, Anandkumar Tengli, Chanabasayya Vastrad, Iranna Kotturshetti
Software Mentions: 2
Published: over 5 years ago

10.1186/s12958-021-00778-1

Construction of lncRNA-related competing endogenous RNA network and identification of hub genes in recurrent implantation failure
Cited by: 8
Author(s): Jialyu Huang, Ning Song, Leizhen Xia, Lifeng Tian, Jun Tan, Qianqian Chen, Jing Zhu, Qiongfang Wu
Software Mentions: 2
Published: about 5 years ago

10.18632/oncotarget.19848

IL2RG, identified as overexpressed by RNA-seq profiling of pancreatic intraepithelial neoplasia, mediates pancreatic cancer growth
Cited by: 13
Author(s): Michael Ayars, Eileen O’Sullivan, Anne M. Macgregor-Das, Koji Shindo, Haeryoung Kim, Michael Borges, Jun Yu, Ralph H. Hruban, Michael Goggins
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2105-11-603

Content-based microarray search using differential expression profiles
Cited by: 39
Author(s): J Engreitz, Alexander A. Morgan, Joel T. Dudley, Rong Chen, Rahul Thathoo, Russ B. Altman, Atul J. Butte
Software Mentions: 2
Published: almost 16 years ago

10.21203/rs.3.rs-784784/v1

Upper airway gene expression reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared with older adults
Cited by: 2
Author(s): Eran Mick, Alexandra Tsitsiklis, Natasha Spottiswoode, Saharai Caldera, Paula Hayakawa Serpa, Angela M. Detweiler, Norma Neff, Angela Oliveira Pisco, Lucy M Li, Hanna Retallack, Kalani Ratnasiri, Kayla Williamson, Victoria Soesanto, Eric A F Simões, Amy Kistler, Brandie D. Wagner, Joseph L. DeRisi, Lilliam Ambroggio, Peter M. Mourani, Charles Langelier
Software Mentions: 2
Published: about 5 years ago

10.1186/s12931-016-0346-3

Gene-expression profiles in lung adenocarcinomas related to chronic wood smoke or tobacco exposure
Cited by: 15
Author(s): Alette Ortega-Gómez, Claudia Rangel‐Escareño, Camilo Molina-Romero, Eleazar Omar Macedo-Pérez, Alejandro Avilés‐Salas, Alejandra Lara-García, Gerardo J. Alanis-Funes, Rubén Rodríguez‐Bautista, Alfredo Hidalgo-Miranda, Óscar Arrieta
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2105-8-386

Large scale statistical inference of signaling pathways from RNAi and microarray data
Cited by: 45
Author(s): Holger Froehlich, Mark Fellmann, Holger Sueltmann, Annemarie Poustka, Tim Beißbarth
Software Mentions: 2
Published: almost 19 years ago

10.1186/s12859-019-2825-2

Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development
Cited by: 12
Author(s): Beatriz Peñalver Bernabé, Ines Thiele, Eugene Galdones, Anaar Siletz, Sriram Chandrasekaran, Teresa K. Woodruff, Linda J. Broadbelt, Lonnie D. Shea
Software Mentions: 2
Published: over 7 years ago

10.1186/s12931-020-1317-2

Cigarette smoke and electronic cigarettes differentially activate bronchial epithelial cells
Cited by: 33
Author(s): Christian Herr, Κωνσταντίνος Τσίτουρας, Julia Niederstraßer, Christina Backes, Christoph Beißwenger, Lü Dong, Loïc Guillot, Andreas Keller, Robert Bals
Software Mentions: 2
Published: over 6 years ago

10.1186/s12931-020-01336-w

Heme metabolism genes Downregulated in COPD Cachexia
Cited by: 3
Author(s): A.C. Wilson, Preeti Lakshman Kumar, Sool Lee, Margaret M. Parker, Itika Arora, Jarrett Morrow, Emiel F.M. Wouters, Richard Casaburi, Stephen I. Rennard, David A. Lomas, Àlvar Agustí, Ruth Tal‐Singer, Mark T. Dransfield, James M. Wells, Surya P. Bhatt, George R. Washko, Victor J. Thannickal, Hemant K. Tiwari, Craig P. Hersh, Peter J. Castaldi, Edwin K. Silverman, Merry-Lynn McDonald
Software Mentions: 2
Published: over 6 years ago

10.1186/s40478-016-0334-3

Analysis of primary visual cortex in dementia with Lewy bodies indicates GABAergic involvement associated with recurrent complex visual hallucinations
Cited by: 55
Author(s): Ahmad Khundakar, Peter S. Hanson, Daniel Erskine, Nichola Z. Lax, Joseph Roscamp, Evangelia Karyka, Eliona Tsefou, Preeti Singh, Simon Cockell, Andrew Gribben, Lynne Ramsay, Peter G. Blain, Urs Peter Mosimann, Deborah Lett, Matthias Elstner, Doug M. Turnbull, Charles Xiang, Michael J. Brownstein, John T. O’Brien, John‐Paul Taylor, Johannes Attems, Alan Thomas, Ian G. McKeith, Christopher M. Morris
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2105-10-110

Data-driven normalization strategies for high-throughput quantitative RT-PCR
Cited by: 87
Author(s): Jessica C. Mar, Yoshinobu Kimura, Kate Schroder, Katharine M. Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David Hume, John Quackenbush
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2105-14-340

Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data
Cited by: 89
Author(s): Natalie L. Catlett, Anthony J Bargnesi, Stephen Ungerer, Toby Seagaran, William Ladd, Keith O. Elliston, Dexter Pratt
Software Mentions: 2
Published: almost 13 years ago

10.1186/1742-4690-9-5

Relationships of PBMC microRNA expression, plasma viral load, and CD4+ T-cell count in HIV-1-infected elite suppressors and viremic patients
Cited by: 135
Author(s): Kenneth W. Witwer, Amy P. Watson, Joel N. Blankson, Janice E. Clements
Software Mentions: 2
Published: over 14 years ago

10.1093/rheumatology/key101

Widespread epigenomic, transcriptomic and proteomic differences between hip osteophytic and articular chondrocytes in osteoarthritis
Cited by: 19
Author(s): Julia Steinberg, Brooks Ra, Lorraine Southam, Sahir Bhatnagar, Roumeliotis Ti, Konstantinos Hatzikotoulas, Eleni Zengini, Wilkinson Jm, Jyoti S. Choudhary, Andrew W. McCaskie, Eleftheria Zeggini
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-018-2308-x

BART: bioinformatics array research tool
Cited by: 27
Author(s): Maria Luisa Amaral, Galina Erikson, Maxim N. Shokhirev
Software Mentions: 2
Published: about 8 years ago

10.1186/s12859-018-2190-6

A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks
Cited by: 10
Author(s): Ankit Jambusaria, Jeff Klomp, Zhigang Hong, Shahin Rafii, Yang Dai, Asrar B. Malik, Jalees Rehman
Software Mentions: 2
Published: over 8 years ago

10.1016/j.xpro.2020.100219

Mapping protein networks in yeast mitochondria using proximity-dependent biotin identification coupled to proteomics
Cited by: 1
Author(s): Roger Salvatori, Wasim Aftab, Ignasi Forné, Axel Imhof, Martin Ott, Abeer Prakash Singh
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.schres.2019.05.011

Differential gene expression analysis in blood of first episode psychosis patients
Cited by: 23
Author(s): Daniel J. Leirer, Conrad Iyegbe, Marta Di Forti, Hamel Patel, Elena Carra, Sara Fraietta, Marco Colizzi, Valeria Mondelli, Diego Quattrone, John Lally, Olesya Ajnakina, Sang Hyuck Lee, Charles Curtis, Gerome Breen, Carmine Pariante, Katherine J. Aitchison, Paola Dazzan, Robin M. Murray, Richard Dobson, Stephen Newhouse
Software Mentions: 2
Published: about 7 years ago

10.1126/sciadv.aau8389

RUNX represses Pmp22 to drive neurofibromagenesis
Cited by: 10
Author(s): Ashley Hall, Kwangmin Choi, Wei Liu, Jonathan Rose, Chuntao Zhao, Yanan Yu, Youjin Na, Yuqi Cai, Robert A. Coover, Yi Wen Lin, Eva Dombi, Miok Kim, Ditsa Levanon, Yoram Groner, Elisa Boscolo, Dao Pan, P. Paul Liu, Qi Lu, Nancy Ratner, Gang Huang, Jianqiang Wu
Software Mentions: 2
Published: over 7 years ago

10.1126/sciadv.aba8196

A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells
Cited by: 8
Author(s): José Maria Moreira Dias, Zhanna Alekseenko, Ashwini Jeggari, Marcelo Boareto, Jannik Vollmer, M. N. Kozhevnikova, Hui Wang, Michael P. Matise, Andrey Alexeyenko, Dagmar Iber, Johan Ericson
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12859-021-04052-4

Bayesian approach for predicting responses to therapy from high-dimensional time-course gene expression profiles
Cited by: 1
Author(s): Arika Fukushima, Masahiro Sugimoto, Satoru Hiwa, Tomoyuki Hiroyasu
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-10-77

Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees
Cited by: 9
Author(s): Donna M. Toleno, Gabriel Renaud, Tyra G. Wolfsberg, Munirul Islam, Derek E. Wildman, Kimberly D. Siegmund, Joseph G. Hacia
Software Mentions: 2
Published: over 17 years ago

10.1186/s12859-015-0527-y

Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective
Cited by: 88
Author(s): E. Andrés Houseman, Karl T. Kelsey, John K. Wiencke, Carmen J. Marsit
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-8-142

Pre-processing Agilent microarray data
Cited by: 181
Author(s): Marianna Zahurak, Giovanni Parmigiani, Wayne Yu, Robert B. Scharpf, David M. Berman, Edward M. Schaeffer, Shabana Shabbeer, Leslie Cope
Software Mentions: 2
Published: over 19 years ago

10.1186/1471-2105-15-97

Multi-TGDR, a multi-class regularization method, identifies the metabolic profiles of hepatocellular carcinoma and cirrhosis infected with hepatitis B or hepatitis C virus
Cited by: 12
Author(s): Suyan Tian, Howard H. Chang, Chi Wang, Jing Jiang, Xiaomei Wang, Junqi Niu
Software Mentions: 2
Published: over 12 years ago

10.18632/oncotarget.14208

DNA methylation landscape of hepatoblastomas reveals arrest at early stages of liver differentiation and cancer-related alterations
Cited by: 20
Author(s): Mariana Maschietto, T. Rodrigues, André Yoshiaki Kashiwabara, Érica Sara Souza de Araújo, Talita Ferreira Marques Aguiar, Cecília Maria Lima da Costa, Isabela Werneck da Cunha, Luciana dos Reis Vasques, Mônica Cypriano, Helena Brentani, Sílvia Regina Caminada de Toledo, P. L. Pearson, Dirce Maria Carraro, Carla Rosenberg, Ana Cristina Victorino Krepischi
Software Mentions: 2
Published: over 9 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776