bioconductor: ReactomePA | Projects

10.12688/f1000research.8923.2

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
Cited by: 105
Author(s): Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D’Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Software Mentions: 17
Published: over 7 years ago

10.3390/ijms21239157

NF-Y Overexpression in Liver Hepatocellular Carcinoma (HCC)
Cited by: 16
Author(s): Eugenia Bezzecchi, Mirko Ronzio, Roberto Mantovani, Diletta Dolfini
Software Mentions: 15
Published: over 3 years ago

10.1186/s12859-018-2486-6

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Cited by: 650
Author(s): Xijin Ge, Eun Wo Son, Runan Yao
Software Mentions: 14
Published: over 5 years ago

10.3390/jcm10184071

Diagnostic and Prognostic Potential of MiR-379/656 MicroRNA Cluster in Molecular Subtypes of Breast Cancer
Cited by: 2
Author(s): Megha Lal, Asgar Hussain Ansari, Anurag Agrawal, Arijit Mukhopadhyay
Software Mentions: 12
Published: almost 3 years ago

10.3390/cancers13081788

Analysis of Intra-Tumoral Macrophages and T Cells in Non-Small Cell Lung Cancer (NSCLC) Indicates a Role for Immune Checkpoint and CD200-CD200R Interactions
Cited by: 7
Author(s): Anders Tøndell, Yashwanth Subbannayya, Sissel Gyrid Freim Wahl, Arnar Flatberg, Sveinung Sørhaug, Magne Børset, Markus Haug
Software Mentions: 12
Published: over 3 years ago

10.1186/s12885-019-5965-x

Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response
Cited by: 32
Author(s): Marta Lucchetta, Isabelle da Piedade, Mohamed Mounir, Marina Vabistsevits, Thilde Terkelsen, Elena Papaleo
Software Mentions: 11
Published: almost 5 years ago

10.3389/fmolb.2021.635074

Decoding Neuromuscular Disorders Using Phenotypic Clusters Obtained From Co-Occurrence Networks
Cited by: 3
Author(s): Elena Díaz-Santiago, M. Gonzalo Claros, Raquel Yahyaoui, Yolanda de Diego-Otero, Rocío Velasco Calvo, Janet Hoenicka, Francesc Palau, Juan A. G. Ranea, James R. Perkins
Software Mentions: 11
Published: over 3 years ago

10.3389/fgene.2021.640242

A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects
Cited by: 7
Author(s): Dustin Miller, Stephen R. Piccolo
Software Mentions: 11
Published: over 3 years ago

10.1186/s12864-017-3819-y

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples
Cited by: 67
Author(s): Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Máximo, Philippe Birembaut, Nhan L. Tran, Gunnar Dittmar, Laurent Vallar
Software Mentions: 11
Published: about 7 years ago

10.15252/msb.20209522

Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma
Cited by: 19
Author(s): Samantha O'Connor, Heather Feldman, Sonali Arora, Pia Hoellerbauer, Chad M. Toledo, Philip Corrin, Lucas Carter, Megan Kufeld, Hamid Bolouri, Ryan Basom, Jeffrey J. Delrow, José L. McFaline-Figueroa, Cole Trapnell, Steven M. Pollard, Anoop P. Patel, Patrick J. Paddison, Christopher Plaisier
Software Mentions: 10
Published: about 3 years ago

10.1186/s12920-020-00754-5

Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis
Cited by: 15
Author(s): Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye, Guowei Li
Software Mentions: 10
Published: about 4 years ago

10.1371/journal.pone.0224750

Gene expression microarray public dataset reanalysis in chronic obstructive pulmonary disease
Cited by: 3
Author(s): Lavida R. K. Rogers, Madison Verlinde, George I. Mias
Software Mentions: 10
Published: over 4 years ago

10.3390/ijms22157974

Transcriptomic and Metabolic Network Analysis of Metabolic Reprogramming and IGF-1 Modulation in SCA3 Transgenic Mice
Cited by: 4
Author(s): Yu Te Lin, Yong Shiou Lin, Wen Cheng, Jui-Chih Chang, Yi Chun Chao, Chin San Liu, An-Chi Wei
Software Mentions: 10
Published: about 3 years ago

10.1038/s41598-017-06110-5

High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
Cited by: 10
Author(s): Brian Gloss, Bethany Signal, Seth W. Cheetham, Franziska Gruhl, Dominik C. Kaczorowski, Andrew C. Perkins, Marcel E. Dinger
Software Mentions: 10
Published: about 7 years ago

10.1186/s12974-018-1113-9

Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness
Cited by: 45
Author(s): David G. Ashbrook, Benjamin Hing, Lindsay T. Michalovicz, Kimberly A. Kelly, Julie V. Miller, Wilfred C. de Vega, Diane B. Miller, Gordon Broderick, James P. O’Callaghan, Patrick O. McGowan
Software Mentions: 9
Published: over 6 years ago

10.1128/mBio.00399-21

Salmonella enterica Serovar Typhimurium SPI-1 and SPI-2 Shape the Global Transcriptional Landscape in a Human Intestinal Organoid Model System
Cited by: 12
Author(s): Anna-Lisa E. Lawrence, Basel H. Abuaita, Ryan P. Berger, David R. Hill, Sha Huang, Veda K. Yadagiri, Brooke Bons, Courtney Fields, Christiane E. Wobus, Jason R. Spence, Vincent B. Young, Mary X. O’Riordan
Software Mentions: 9
Published: about 3 years ago

10.1371/journal.pbio.3001158

Disparate temperature-dependent virus–host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium
Cited by: 66
Author(s): Philip V’kovski, Mitra Gultom, Jenna N. Kelly, Silvio Steiner, Julie Russeil, Bastien Mangeat, Elisa Cora, Joern Pezoldt, Melle Holwerda, Annika Kratzel, Laura Laloli, Manon Wider, Jasmine Portmann, Thao Thi Phuong Tran, Nadine Ebert, Hanspeter Stalder, Rune Hartmann, Vincent Gardeux, Daniel Alpern, Bart Deplancke, Volker Thiel, Ronald Dijkman
Software Mentions: 9
Published: over 3 years ago

10.3390/cancers12051122

The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer
Cited by: 11
Author(s): M. Friedrich, Karolin Wiedemann, Kristin Reiche, Sven-Holger Puppel, Gabriele Pfeifer, Ivonne Zipfel, Stefanie Petrou Binder, Ulrike Köhl, G Müller, Kurt Engeland, Achim Aigner, S. Füssel, M. Fröhner, Claudia Peitzsch, Anna Dubrovska, Michael Rade, Sabina Christ, S Schreiber, Jörg Hackermüller, Jörg Lehmann, Marieta Toma, Michael H. Muders, Ulrich Sommer, Gustavo Baretton, Manfred P. Wirth, Friedemann Horn
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pgen.1009094

Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression
Cited by: 2
Author(s): Aziz Aiderus, Justin Y. Newberg, Liliana Guzmán-Rojas, Ana M. Contreras-Sandoval, Amanda L. Meshey, Devin J. Jones, Felipe Amaya-Manzanares, Roberto Rangel, Jerrold M. Ward, Song Choon Lee, Kenneth Ban, Keith Rogers, Susan Rogers, Luxmanan Selvanesan, Leslie A. McNoe, Neal G. Copeland, Nancy A. Jenkins, Kenneth Y. Tsai, Michael A. Black, Karen Mann, Michael B. Mann
Software Mentions: 8
Published: almost 3 years ago

10.1371/journal.pone.0200925

PNPase knockout results in mtDNA loss and an altered metabolic gene expression program
Cited by: 12
Author(s): Eriko Shimada, Fasih M. Ahsan, Mahta Nili, Dian Huang, Sean Atamdede, Tara TeSlaa, Dana Case, Xiang Yu, Brian D. Gregory, Benjamin J. Perrin, Carla M. Koehler, Michael A. Teitell
Software Mentions: 8
Published: about 6 years ago

10.1080/15592294.2019.1603963

Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects
Cited by: 32
Author(s): Jyotirmoy Das, Deepti Verma, Mika Gustafsson, Maria Lerm
Software Mentions: 8
Published: over 5 years ago

10.1186/s12967-021-02914-2

The landscape of gene co-expression modules correlating with prognostic genetic abnormalities in AML
Cited by: 14
Author(s): Chao Guo, Ya-yue Gao, Qianqian Ju, Chunxia Zhang, Ming Gong, Zhenling Li
Software Mentions: 8
Published: about 3 years ago

10.1038/s42003-020-1097-8

CD70 expression determines the therapeutic efficacy of expanded human regulatory T cells
Cited by: 30
Author(s): Rebeca Arroyo Hornero, Christos Georgiadis, Peng Hua, Dominik Trzupek, He L-Z., Waseem Qasim, John A. Todd, Ricardo C. Ferreira, Kathryn J. Wood, Fadi Issa, Joanna Hester
Software Mentions: 8
Published: about 4 years ago

10.1038/s41421-021-00279-w

Targeting novel LSD1-dependent ACE2 demethylation domains inhibits SARS-CoV-2 replication
Cited by: 7
Author(s): Wen Juan Tu, Robert McCuaig, Michelle Melino, Daniel J. Rawle, Thuy T. Le, Kexin Yan, Andreas Suhrbier, Rebecca L. Johnston, Lambros T. Koufariotis, Nicola Waddell, E.M. Cross, S. Tsimbalyuk, Amanda L. Bain, Elizabeth Ahern, Natasha Collinson, Simon Phipps, Jade K. Forwood, Nabila Seddiki, Sudha Rao
Software Mentions: 8
Published: about 3 years ago

10.18632/aging.202486

Constructing a ceRNA-immunoregulatory network associated with the development and prognosis of human atherosclerosis through weighted gene co-expression network analysis
Cited by: 11
Author(s): Yaozhong Liu, Na Liu, Qiming Liu
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-021-87890-9

Epigenetic alteration contributes to the transcriptional reprogramming in T-cell prolymphocytic leukemia
Cited by: 2
Author(s): Shulan Tian, Henan Zhang, Pan Zhang, Michael Kalmbach, Jeong Heon Lee, Tamás Ördög, Paul J. Hampel, Timothy G. Call, Thomas E. Witzig, Neil E. Kay, Eric W. Klee, Susan L. Slager, Huihuang Yan, Wei Ding
Software Mentions: 8
Published: over 3 years ago

10.3390/ijms21072337

Differential Targeting of Gr-MDSCs, T Cells and Prostate Cancer Cells by Dactolisib and Dasatinib
Cited by: 10
Author(s): Guoqiang Lü, Zhijian Jin, Xin Lü
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.59442

Collagen-rich omentum is a premetastatic niche for integrin α2-mediated peritoneal metastasis
Cited by: 33
Author(s): Yen‐Lin Huang, Ching-Yeu Liang, Danilo Ritz, Ruimário Inácio Coelho, Dedy Septiadi, Manuela Estermann, Cécile Cumin, Natalie Rimmer, Andreas Schötzau, Mónica Núñez López, André Fedier, Martina Konantz, Tatjana Vlajnic, Diego Calabrese, Claudia Lengerke, Leonor David, Barbara Rothen‐Rutishauser, Francis Jacob, Viola Heinzelmann‐Schwarz
Software Mentions: 8
Published: almost 4 years ago

10.1007/s13365-020-00931-3

Transcriptional signatures of Zika virus infection in astrocytes
Cited by: 3
Author(s): Blake Schouest, Tiffany A. Peterson, Dawn Szeltner, Elizabeth A. Scheef, Melody Baddoo, Nathan Ungerleider, Erik K. Flemington, Andrew G. MacLean, Nicholas J. Maness
Software Mentions: 8
Published: over 3 years ago

10.1186/s10194-021-01285-9

Identification of disease- and headache-specific mediators and pathways in migraine using blood transcriptomic and metabolomic analysis
Cited by: 13
Author(s): Tímea Aczél, Tamás Körtési, József Kun, Péter Urbán, Witold Bauer, Róbert Herczeg, Robert Farkaš, K Kovács, Barna Vásárhelyi, Gellért Balázs Karvaly, Attila Gyenesei, Bernadett Tuka, János Tajti, László Vécsei, Kata Bölcskei, Zsuzsanna Helyes
Software Mentions: 7
Published: almost 3 years ago

10.3389/fimmu.2020.02149

CXCL4 Links Inflammation and Fibrosis by Reprogramming Monocyte-Derived Dendritic Cells in vitro
Cited by: 23
Author(s): Sandra Silva-Cardoso, Weiyang Tao, Chiara Angiolilli, Ana P Lopes, Cornelis P. J. Bekker, Abhinandan Devaprasad, Barbara Giovannone, Jaap van Laar, Marta Cossu, Wioleta Marut, Erik Hack, Rob J. de Boer, Marianne Boes, Timothy R D J Radstake, Aridaman Pandit
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12967-019-1909-0

ALS blood expression profiling identifies new biomarkers, patient subgroups, and evidence for neutrophilia and hypoxia
Cited by: 38
Author(s): William R. Swindell, Colin Kruse, Edward O. List, Darlene E. Berryman, John J. Kopchick
Software Mentions: 7
Published: about 5 years ago

10.3389/fimmu.2019.02616

Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination
Cited by: 12
Author(s): Lavida R. K. Rogers, Gustavo de los Campos, George I. Mias
Software Mentions: 7
Published: over 4 years ago

10.3389/fimmu.2018.01444

Elucidating T Cell Activation-Dependent Mechanisms for Bifurcation of Regulatory and Effector T Cell Differentiation by Multidimensional and Single-Cell Analysis
Cited by: 10
Author(s): Alla Bradley, Takeji Hashimoto, M. Ono
Software Mentions: 7
Published: about 6 years ago

10.1186/s12864-019-6415-5

A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex
Cited by: 19
Author(s): Jouni Kvist, Camila Gonçalves Athanásio, Michael E. Pfrender, James Brown, John K. Colbourne, Leda Mirbahai
Software Mentions: 7
Published: over 4 years ago

10.3390/microorganisms8020270

In Vitro Zika Virus Infection of Human Neural Progenitor Cells: Meta-Analysis of RNA-Seq Assays
Cited by: 15
Author(s): Rossella Gratton, Paola Maura Tricarico, Almerinda Agrelli, Heverton Valentim Colaço da Silva, Lucas Coêlho Bernardo, Sérgio Crovella, Antônio Victor Campos Coelho, Ronald Moura, Lucas André Cavalcanti Brandão
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0225216

Abundance of ethnically biased microsatellites in human gene regions
Cited by: 3
Author(s): Nicholas A. Kinney, Lin Kang, Laurel Eckstrand, Arichanah Pulenthiran, Peter Samuel, Ramu Anandakrishnan, Robin Varghese, Pawel Michalak, Harold R. Garner
Software Mentions: 7
Published: over 4 years ago

10.15252/emmm.201910812

Synthetic lethality between <scp>VPS</scp> 4A and <scp>VPS</scp> 4B triggers an inflammatory response in colorectal cancer
Cited by: 26
Author(s): Ewelina Szymańska, Paulina Nowak, Krzysztof Kolmus, Magdalena Cybulska, Krzysztof Goryca, Edyta Derezińska-Wołek, Anna Szumera‐Ciećkiewicz, Marta Brewinska‐Olchowik, Aleksandra Grochowska, Katarzyna Piwocka, Monika Prochorec‐Sobieszek, Michał Mikula, Marta Miączyńska
Software Mentions: 7
Published: over 4 years ago

10.3390/microorganisms8101505

Reanalysis of Gene Expression Profiles of CD4+ T Cells Treated with HIV-1 Latency Reversal Agents
Cited by: 3
Author(s): Antônio Victor Campos Coelho, Romero Marinho de Moura, Sérgio Crovella
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-021-94343-w

Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite
Cited by: 7
Author(s): Fernando M. Jabato, José Córdoba-Caballero, Elena Rojano, Carlos Romá‐Mateo, Pascual Sanz, Belén Pérez, Diana Gallego, Pedro Seoane, Juan A. G. Ranea, James R. Perkins
Software Mentions: 7
Published: about 3 years ago

10.7150/thno.54134

Single-cell melanoma transcriptomes depicting functional versatility and clinical implications of STIM1 in the tumor microenvironment
Cited by: 2
Author(s): Henry Sung Ching Wong, Wei Chiao Chang
Software Mentions: 7
Published: over 3 years ago

10.3390/ijms21165923

Oxidant-Induced Alterations in the Adipocyte Transcriptome: Role of the Na,K-ATPase Oxidant Amplification Loop
Cited by: 7
Author(s): Komal Sodhi, James Denvir, Jiang Liu, Juan Sanabria, Yiliang Chen, Roy L. Silverstein, Zijian Xie, Nader G. Abraham, Joseph I. Shapiro
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13148-019-0658-5

Gene domain-specific DNA methylation episignatures highlight distinct molecular entities of ADNP syndrome
Cited by: 65
Author(s): Eric G. Bend, Erfan Aref‐Eshghi, David B. Everman, R. Curtis Rogers, Sara Cathey, Eloise J. Prijoles, Michael J. Lyons, Heather L. Davis, Katie Clarkson, Karen W. Gripp, Dong Liu, Elizabeth Bhoj, Elaine H. Zackai, Paul R. Mark, Hákon Hákonarson, Laurie A. Demmer, Michael A. Levy, Jennifer Kerkhof, Alan Stuart, David I. Rodenhiser, Michael J. Friez, Roger E. Stevenson, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 7
Published: over 5 years ago

10.1016/j.virol.2021.03.019

Zika virus infection during pregnancy protects against secondary infection in the absence of CD8+ cells
Cited by: 3
Author(s): Blake Schouest, Brandon J Beddingfield, Margaret H. Gilbert, Rudolf P. Bohm, Faith Schiro, Pyone P. Aye, Antonito T. Panganiban, Diogo M. Magnani, Nicholas J. Maness
Software Mentions: 7
Published: about 3 years ago

10.1186/s12885-021-08520-1

Computational analysis for identification of early diagnostic biomarkers and prognostic biomarkers of liver cancer based on GEO and TCGA databases and studies on pathways and biological functions affecting the survival time of liver cancer
Cited by: 21
Author(s): Shuangquan Gao, Jian Gang, Man Yu, Guiliang Xin, Huixin Tan
Software Mentions: 6
Published: about 3 years ago

10.7554/eLife.61405

Cohesin mutations are synthetic lethal with stimulation of WNT signaling
Cited by: 17
Author(s): Chue Vin Chin, Jisha Antony, Sarada Ketharnathan, Anastasia Labudina, Grégory Gimenez, Kate M Parsons, Jin-Shu He, Amee J. George, Maria Michela Pallotta, Antonio Musio, Antony W. Braithwaite, Parry Guilford, Ross D. Hannan, Julia A. Horsfield
Software Mentions: 6
Published: over 3 years ago

10.1186/s13045-018-0679-0

Whole-exon sequencing of human myeloma cell lines shows mutations related to myeloma patients at relapse with major hits in the DNA regulation and repair pathways
Cited by: 31
Author(s): Benoît Tessoulin, Agnès Moreau-Aubry, Géraldine Descamps, Patricia Gomez‐Bougie, Sophie Maïga, Alban Gaignard, David Chiron, Emmanuelle Ménoret, Steven Le Gouill, Philippe Moreau, Martine Amiot, Catherine Pellat‐Deceunynck
Software Mentions: 6
Published: over 5 years ago

10.7150/ijms.46456

Lipid Metabolism is the common pathologic mechanism between Type 2 Diabetes Mellitus and Parkinson's disease
Cited by: 6
Author(s): Xi Zhang, Yu Fan, Yuan Luo, Lingjing Jin, Siguang Li
Software Mentions: 6
Published: over 4 years ago

10.1128/mBio.02399-20

Hemozoin Promotes Lung Inflammation via Host Epithelial Activation
Cited by: 1
Author(s): Shivang S. Shah, David A. Fidock, Alice Prince
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-91214-2

Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction
Cited by: 12
Author(s): Xin Luo, Jun Yin, Denise Dwyer, Tracy M. Yamawaki, Hong Zhou, Hongfei Ge, Chun-Ya Han, Artem Shkumatov, K. F. Snyder, Brandon Ason, Chi-Ming Li, Oliver Homann, Marina Stolina
Software Mentions: 6
Published: about 3 years ago

10.3389/fimmu.2021.720841

Unsupervised Clustering Reveals Distinct Subtypes of Biliary Atresia Based on Immune Cell Types and Gene Expression
Cited by: 9
Author(s): Xiaoyan Pang, Jing Cao, Shuru Chen, Zhiliang Gao, Guangjian Liu, Yutian Chong, Zhuang‐Gui Chen, Jiao Gong, Xinhua Li
Software Mentions: 6
Published: almost 3 years ago

10.1371/journal.pcbi.1008685

ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways
Cited by: 9
Author(s): Agatha Treveil, Balázs Bohár, Padhmanand Sudhakar, Lejla Gul, Luca Csabai, Márton Ölbei, Martina Poletti, Matthew Madgwick, Tahila Andrighetti, Isabelle Hautefort, Dezső Módos, Tamás Korcsmáros
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-86032-5

A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes
Cited by: 18
Author(s): Timothy Warwick, Marcel H. Schulz, Stefan Günther, Ralf Gilsbach, Antonio Neme, Carsten Carlberg, Ralf P. Brandes, Sabine Seuter
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-020-72671-7

Molecular signatures of anthroponotic cutaneous leishmaniasis in the lesions of patients infected with Leishmania tropica
Cited by: 10
Author(s): Nasrin Masoudzadeh, Malin Östensson, Josefine Persson, Vahid Mashayekhi Goyonlo, Christopher Agbajogu, Yasaman Taslimi, Reza Erfanian Salim, Farnaz Zahedifard, Amir Mizbani, Housein Malekafzali Ardekani, Bronwyn M. Gunn, Sima Rafati, Ali M. Harandi
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41598-020-66224-1

Genomic deregulation of PRMT5 supports growth and stress tolerance in chronic lymphocytic leukemia
Cited by: 5
Author(s): Ann-Kathrin Schnormeier, Claudia Pommerenke, Maren Kaufmann, Hans Drexler, Max Koeppel
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-019-50119-x

Tissue-specific mouse mRNA isoform networks
Cited by: 12
Author(s): Gaurav Kandoi, Julie A. Dickerson
Software Mentions: 6
Published: almost 5 years ago

10.1523/JNEUROSCI.1675-19.2019

Midkine-a Is Required for Cell Cycle Progression of Müller Glia during Neuronal Regeneration in the Vertebrate Retina
Cited by: 28
Author(s): Mikiko Nagashima, Travis S. D’Cruz, Antoinette Eyram Danku, Doneen Hesse, Christopher J. Sifuentes, Pamela A. Raymond, Peter F. Hitchcock
Software Mentions: 6
Published: over 4 years ago

10.1186/s13059-018-1407-3

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
Cited by: 90
Author(s): Yohei Sasagawa, Hiroki Danno, Hitomi Takada, Masashi Ebisawa, Kaori Tanaka, Tetsutaro Hayashi, Akira Kurisaki, Itoshi Nikaido
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2019.00325

The Cord Blood Insulin and Mitochondrial DNA Content Related Methylome
Cited by: 5
Author(s): Brigitte Reimann, Bram G. Janssen, Rossella Alfano, Akram Ghantous, Almudena Espín-Pérez, Theo M. de Kok, Nelly D. Saenen, Bianca Cox, Oliver Robinson, Marc Chadeau‐Hyam, Joris Penders, Zdenko Herceg, Paolo Víneis, Tim S. Nawrot, Michelle Plusquin
Software Mentions: 6
Published: over 5 years ago

10.3390/genes12040491

Dissection of the Genetic Association between Anorexia Nervosa and Obsessive–Compulsive Disorder at the Network and Cellular Levels
Cited by: 4
Author(s): Weichen Song, Weidi Wang, Shunying Yu, Guan Ning Lin
Software Mentions: 6
Published: over 3 years ago

10.3389/fnins.2019.00392

Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease
Cited by: 19
Author(s): Lavida R. K. Brooks, George I. Mias
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms22094531

Knockdown of the Ribosomal Protein eL38 in HEK293 Cells Changes the Translational Efficiency of Specific Genes
Cited by: 4
Author(s): Alexander V. Gopanenko, Alena V. Kolobova, Alexey E. Tupikin, Мarsel R. Kabilov, Alexey A. Malygin, Г. Г. Карпова
Software Mentions: 6
Published: over 3 years ago

10.1186/s12915-018-0615-3

Mitochondrial unfolded protein response transcription factor ATFS-1 promotes longevity in a long-lived mitochondrial mutant through activation of stress response pathways
Cited by: 79
Author(s): Ziyun Wu, Megan M. Senchuk, Dylan J. Dues, Benjamin K. Johnson, Jason Cooper, Leira Lew, Emily Machiela, Claire E. Schaar, Heather DeJonge, T. Keith Blackwell, Jeremy M. Van Raamsdonk
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1007981

Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes
Cited by: 29
Author(s): Eva Gómez-Orte, Beatriz Sáenz-Narciso, Angelina Zheleva, Begoña Ezcurra, María de Toro, Rosa López, Irene Gastaca, Hilde Nilsen, María P. Sacristán, Ralf Schnabel, Juan Cabello
Software Mentions: 5
Published: over 5 years ago

10.18632/aging.103721

Gene expression-based clinical predictions in lung adenocarcinoma
Cited by: 3
Author(s): Yanlu Xiong, Jie Lei, Jinbo Zhao, Yangbo Feng, Tianyun Qiao, Yongsheng Zhou, Tao Jiang, Han Ye
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12859-021-04046-2

DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks
Cited by: 0
Author(s): Heeju Noh, Hua Ziyi, Panagiotis Chrysinas, Jason E. Shoemaker, Rudiyanto Gunawan
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-015-0708-8

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment
Cited by: 13
Author(s): Anwesha Bohler, Lars Eijssen, Martijn P. van Iersel, C. René Leemans, Egon Willighagen, Martina Kutmon, Magali Jaillard, Chris T. Evelo
Software Mentions: 5
Published: almost 9 years ago

10.3390/microarrays3040212

The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma
Cited by: 1
Author(s): Andrew R. Dalby, Ian Bailey
Software Mentions: 5
Published: almost 10 years ago

10.1016/j.celrep.2019.07.039

Activation and In Vivo Evolution of the MAIT Cell Transcriptome in Mice and Humans Reveals Tissue Repair Functionality
Cited by: 130
Author(s): Timothy S C Hinks, Emanuele Marchi, Maisha Jabeen, Moshe Olshansky, Ayako Kurioka, Troi Pediongco, Bronwyn S. Meehan, Lyudmila Kostenko, Stephen J. Turner, Alexandra J. Corbett, Zhenjun Chen, Paul Klenerman, James McCluskey
Software Mentions: 5
Published: almost 5 years ago

10.12688/f1000research.18705.2

Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models
Cited by: 1
Author(s): Katharina Baum, Jagath C. Rajapakse, Francisco Azuaje
Software Mentions: 5
Published: almost 5 years ago

10.12688/f1000research.10465.1

Meta-analysis of crowdsourced data compendia suggests pan-disease transcriptional signatures of autoimmunity
Cited by: 5
Author(s): William Lau, Rachel Sparks, John S. Tsang
Software Mentions: 5
Published: over 7 years ago

10.3389/fcimb.2021.641261

Common Dysregulation of Innate Immunity Pathways in Human Primary Astrocytes Infected With Chikungunya, Mayaro, Oropouche, and Zika Viruses
Cited by: 5
Author(s): Victor Emmanuel Viana Geddes, Otávio J. B. Brustolini, Liliane Tavares de Faria Cavalcante, Filipe Romero Rebello Moreira, Fernando Luz de Castro, Ana P. Guimarães, Alexandra Lehmkuhl Gerber, C. Figueiredo, Luan Pereira Diniz, Eurico de Arruda Neto, Amílcar Tanuri, Renan Pedra de Souza, Iranaia Assunção‐Miranda, Soniza Vieira Alves-Leon, Luciana Romão, Jorge Paes Barreto Marcondes de Souza, Ana Tereza Ribeiro de Vasconcelos, Renato Santana Aguiar
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2021.697043

A Ferroptosis-Related Gene Model Predicts Prognosis and Immune Microenvironment for Cutaneous Melanoma
Cited by: 12
Author(s): Congcong Xu, Hao Chen
Software Mentions: 5
Published: almost 3 years ago

10.3389/fimmu.2021.670574

Single-Cell Transcriptional Heterogeneity of Neutrophils During Acute Pulmonary Cryptococcus neoformans Infection
Cited by: 14
Author(s): M. Elizabeth Deerhake, Estefany Y. Reyes, Shengjie Xu-Vanpala, Mari L. Shinohara
Software Mentions: 5
Published: about 3 years ago

10.1002/hep4.1749

Meta‐analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions
Cited by: 4
Author(s): Emilian Jungwirth, Katrin Panzitt, Hanns‐Ulrich Marschall, Gerhard Thallinger, Martin Wagner
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.ppat.1008057

Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape
Cited by: 65
Author(s): Abimbola O. Kolawole, Carmen Mirabelli, David R. Hill, Sophia A. Svoboda, Andrew B. Janowski, Karla D. Passalacqua, Benancio N. Rodriguez, Michael K. Dame, Pamela Freiden, Ryan P. Berger, Diem Vu, Myra Hosmillo, Mary X. O’Riordan, Stacey Schultz‐Cherry, Susana Guix, Jason R. Spence, David Wang, Christiane E. Wobus
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-66721-3

Cardiac transcriptional and metabolic changes following thoracotomy
Cited by: 0
Author(s): Markus Heckmann, Ashraf Yusuf Rangrez, Daniel Finke, Andreas Jungmann, Julia S. Kreußer, Alexandra Rosskopf, Nesrin Schmiedel, Hugo A. Katus, Norbert Frey, Oliver Müller
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-021-96966-5

Molecular characterization and cell type composition deconvolution of fibrosis in NAFLD
Cited by: 26
Author(s): Lorena Pantano, George Agyapong, Yang Shen, Zhuo Zhu, Francesc Fernández-Albert, Werner Rust, Dagmar Knebel, Jon Hill, Carine M. Boustany-Kari, Julia F. Doerner, Jörg F. Rippmann, Raymond T. Chung, Shannan Ho Sui, Eric J. Simon, Kathleen E. Corey
Software Mentions: 5
Published: almost 3 years ago

10.7554/eLife.63324

Adipocyte NR1D1 dictates adipose tissue expansion during obesity
Cited by: 20
Author(s): Louise Hunter, Charlotte E Pelekanou, Nichola J Barron, Rebecca C Northeast, M Grudzień, Antony Adamson, Polly Downton, Thomas Cornfield, Peter Cunningham, Jean-Noël Billaud, Leanne Hodson, Andrew S. I. Loudon, Richard D. Unwin, Mudassar Iqbal, David Ray, David A. Bechtold
Software Mentions: 5
Published: almost 3 years ago

10.18632/oncotarget.23563

Effect of the diet type and temperature on theC. eleganstranscriptome
Cited by: 37
Author(s): Eva Gómez-Orte, Eric Cornes, Angelina Zheleva, Beatriz Sáenz-Narciso, María de Toro, María Íñiguez, Rosa López, Juan F. San-Juan, Begoña Ezcurra, Begoña Sacristán, Adolfo Sánchez-Blanco, Julián Cerón, Juan Cabello
Software Mentions: 5
Published: over 6 years ago

10.1534/g3.120.401545

Genome-Wide Screen for Context-Dependent Tumor Suppressors Identified Using in Vivo Models for Neoplasia in Drosophila
Cited by: 3
Author(s): Casper Groth, Pooja Vaid, Aditi S. Khatpe, Nelchi Prashali, Avantika Ahiya, Diāna Andrējeva, Madhumita Chakladar, Sanket Nagarkar, Rachel Paul, Devaki A. Kelkar, Teresa Eichenlaub, Héctor Herranz, T.S. Sridhar, Stephen M. Cohen, L. S. Shashidhara
Software Mentions: 4
Published: almost 4 years ago

10.3390/genes10090725

A Transcriptome Analysis Identifies Biological Pathways and Candidate Genes for Feed Efficiency in DLY Pigs
Cited by: 9
Author(s): Xingwang Wang, Shaoyun Li, Jie Wu, Rongrong Ding, Jianping Quan, Enqin Zheng, Jie Yang, Zhenfang Wu
Software Mentions: 4
Published: almost 5 years ago

10.3389/fimmu.2021.679458

Comparative Proteomic Analysis Reveals Varying Impact on Immune Responses in Phorbol 12-Myristate-13-Acetate-Mediated THP-1 Monocyte-to-Macrophage Differentiation
Cited by: 21
Author(s): Sneha M. Pinto, Hera Kim, Yashwanth Subbannayya, Miriam S. Giambelluca, Korbinian Bösl, Liv Ryan, Animesh Sharma, Richard K. Kandasamy
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pgen.1009054

Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases
Cited by: 13
Author(s): Elena Díaz-Santiago, Fernando M. Jabato, Elena Rojano, Pedro Seoane, Florencio Pazos, James R. Perkins, Juan A. G. Ranea
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0234986

Molecular analyses of glioblastoma stem-like cells and glioblastoma tissue
Cited by: 7
Author(s): Marco Wallenborn, Leiming Xu, Holger Kirsten, Leili Rohani, Daniela Rudolf, Peter Ahnert, Christian Schmidt, R. Schulz, Mandy Richter, Wolfgang Krupp, Wolf Mueller, Adiv A. Johnson, Jürgen Meixensberger, Heidrun Holland
Software Mentions: 4
Published: about 4 years ago

10.3390/ijms20051182

Temporal Splicing Switches in Elements of the TNF-Pathway Identified by Computational Analysis of Transcriptome Data for Human Cell Lines
Cited by: 6
Author(s): Nikolaï Genov, Alireza Basti, Marconi Abreu, Angela Relógio
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-80158-8

Gene expression in blood reflects smoking exposure among cancer-free women in the Norwegian Women and Cancer (NOWAC) postgenome cohort
Cited by: 6
Author(s): Nikita Baiju, Torkjel M. Sandanger, Pål Sætrom, Therese Haugdahl Nøst
Software Mentions: 4
Published: over 3 years ago

10.1172/jci.insight.147703

Integration of spatial and single-cell transcriptomics localizes epithelial cell–immune cross-talk in kidney injury
Cited by: 68
Author(s): Ricardo Melo Ferreira, Angela R Sabo, Seth Winfree, Kimberly S. Collins, Danielle Janosevic, Connor J. Gulbronson, Ying‐Hua Cheng, Lauren Casbon, Daria Barwinska, Michael J. Ferkowicz, Xiaoling Xuei, Chi Zhang, Kenneth W. Dunn, Katherine J. Kelly, Timothy A. Sutton, Takashi Hato, Pierre C. Dagher, Tarek M. El‐Achkar, Michael T. Eadon
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pntd.0009425

Profound downregulation of neural transcription factor Npas4 and Nr4a family in fetal mice neurons infected with Zika virus
Cited by: 3
Author(s): Sergio P. Alpuche-Lazcano, James Saliba, Vivian Vasconcelos Costa, Gabriel Henrique Campolina-Silva, Fernanda Martins Marim, Lucas S. Ribeiro, Volker Blank, Andrew J. Mouland, Mauro M. Teixeira, Anne Gatignol
Software Mentions: 4
Published: about 3 years ago

10.21203/rs.3.rs-287183/v1

Rapid Identification of Druggable Targets and the Power of the PHENotype SIMulator for Effective Drug Repurposing in COVID-19
Cited by: 1
Author(s): Naomi I. Maria, Rosaria Valentina Rapicavoli, Salvatore Alaimo, Evelyne Bischof, Alessia Stasuzzo, Jantine A.C. Broek, Alfredo Pulvirenti, Bud Mishra, Ashley J. Duits, Alfredo Ferro
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.638571

Different Disease Endotypes in Phenotypically Similar Vasculitides Affecting Small-to-Medium Sized Blood Vessels
Cited by: 7
Author(s): Erin E. Gill, Maren L. Smith, Kristen M Gibson, Kimberly Morishita, Ahwon Lee, Reza Falsafi, Jinko Graham, Dirk Foell, Susanne M. Benseler, Colin J. Ross, Raashid Luqmani, David A. Cabral, Robert E. W. Hancock, Kelly L. Brown, PedVas Initiative Investigators
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2018.03137

The Schistosomiasis SpleenOME: Unveiling the Proteomic Landscape of Splenomegaly Using Label-Free Mass Spectrometry
Cited by: 6
Author(s): Miguel Cosenza-Contreras, Renata Alves de Oliveira e Castro, Bruno Mattei, Jonatan Marques Campos, Gustavo Gonçalves Silva, Nívia Carolina Nogueira de Paiva, Rodrigo Dian de Oliveira Aguiar-Soares, Cláudia Martins Carneiro, Luís Afonso, William Castro-Borges
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.29132

Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium
Cited by: 122
Author(s): David R. Hill, Sha Huang, Melinda S. Nagy, Veda K. Yadagiri, Courtney Fields, Dishari Mukherjee, Brooke Bons, Priya H. Dedhia, Alana M. Chin, Yu Hwai Tsai, Shrikar Thodla, Thomas M. Schmidt, Seth T. Walk, Vincent B. Young, Jason R. Spence
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms22010275

The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function
Cited by: 8
Author(s): Yashwanth Subbannayya, Markus Haug, Sneha M. Pinto, Varshasnata Mohanty, Hany Zakaria Meås, Trude Helen Flo, T. S. Keshava Prasad, Richard K. Kandasamy
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.684052

Low Energy Electron Irradiation Is a Potent Alternative to Gamma Irradiation for the Inactivation of (CAR-)NK-92 Cells in ATMP Manufacturing
Cited by: 11
Author(s): Lia Walcher, Ann-Kathrin Kistenmacher, Charline Sommer, Sebastian Böhlen, Christina Ziemann, Susann Dehmel, Armin Braun, U. Sandy Tretbar, Stephan Klöß, Axel Schambach, Michael Morgan, Dennis Löffler, Christoph Kämpf, Conny Blumert, Kristin Reiche, Jana Beckmann, Ulla König, Bastian Standfest, Martin Thoma, Gustavo R. Makert, Sebastian Ulbert, Uta Kossatz-Böhlert, Ulrike Köhl, Anna Dünkel, Frank Stephan
Software Mentions: 4
Published: about 3 years ago

10.15252/embj.2019104159

Deciphering the regulatory landscape of fetal and adult γδ T‐cell development at single‐cell resolution
Cited by: 38
Author(s): Sagar, Maria Pokrovskii, Josip Stefan Herman, Shruti Naik, Elisabeth Sock, Patrice Zeis, Ute Lausch, Michael Wegner, Yakup Tanriver, Dan R. Littman, Dominic Grün
Software Mentions: 4
Published: about 4 years ago

10.3390/cells9051228

Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level
Cited by: 8
Author(s): Alexander V. Gopanenko, Alena V. Kolobova, Mariya I. Meschaninova, Alya G. Venyaminova, Alexey E. Tupikin, Мarsel R. Kabilov, Alexey A. Malygin, Г. Г. Карпова
Software Mentions: 4
Published: about 4 years ago

10.1038/s41388-020-01429-2

Androgen receptor signaling regulates the transcriptome of prostate cancer cells by modulating global alternative splicing
Cited by: 21
Author(s): Kalpit Shah, Teresa Gagliano, L. H. Garland, Timothy O’Hanlon, Daria Bortolotti, Valentina Gentili, Roberta Rizzo, Georgios Giamas, Michael Dean
Software Mentions: 4
Published: almost 4 years ago

10.3389/fnmol.2021.624881

Identification of Natural Antisense Transcripts in Mouse Brain and Their Association With Autism Spectrum Disorder Risk Genes
Cited by: 0
Author(s): Baran Koç, Geoffrey Fucile, Roland Schmucki, Nicolas Giroud, Tobias Bergauer, Benjamin J. Hall
Software Mentions: 4
Published: over 3 years ago

10.4049/jimmunol.1901358

TNF-α Regulates Human Plasmacytoid Dendritic Cells by Suppressing IFN-α Production and Enhancing T Cell Activation
Cited by: 29
Author(s): Antonios Psarras, Agne Antanaviciute, Adewonuola Alase, Ian Carr, Miriam Wittmann, Paul Emery, George C. Tsokos, Edward M Vital
Software Mentions: 4
Published: over 3 years ago

Projects: bioconductor: ReactomePA

Papers Mentioning ReactomePA 171