bioconductor: genefilter | Projects

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: about 16 years ago

Comparative Proteome Identifies Complement Component 3-Mediated Immune Response as Key Difference of Colon Adenocarcinoma and Rectal Adenocarcinoma
Cited by: 9
Author(s): Jun-Ze Liang, Xiaoling Liang, Liye Zhong, Chutian Wu, Jing Zhang, Yang Wang
Software Mentions: 30
Published: almost 4 years ago

10.1371/journal.pcbi.1007792

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
Cited by: 38
Author(s): Augusto Anguita‐Ruiz, Alberto Segura‐Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá‐Fdez
Software Mentions: 23
Published: over 4 years ago

10.3389/fimmu.2021.632333

Immunological Feature and Transcriptional Signaling of Ly6C Monocyte Subsets From Transcriptome Analysis in Control and Hyperhomocysteinemic Mice
Cited by: 7
Author(s): Panpan Yang, Lu Liu, Lili Sun, Fang Pu, Nathaniel W. Snyder, Jason Saredy, Yong Ji, Wen Shen, Xuebin Qin, Qinghua Wu, Xiaofeng Yang, Hong Wang
Software Mentions: 21
Published: almost 4 years ago

10.1016/j.patter.2021.100322

The role of metadata in reproducible computational research
Cited by: 38
Author(s): Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
Software Mentions: 21
Published: over 3 years ago

10.1038/s41598-019-55469-0

Minor compositional alterations in faecal microbiota after five weeks and five months storage at room temperature on filter papers
Cited by: 6
Author(s): Sebastian von Huth, Louise B. Thingholm, Corinna Bang, Malte Rühlemann, André Franke, Uffe Holmskov
Software Mentions: 20
Published: about 5 years ago

10.1093/bioinformatics/bty947

SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data
Cited by: 19
Author(s): Jamie Soul, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Software Mentions: 18
Published: about 6 years ago

10.1186/s13059-019-1805-1

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
Cited by: 65
Author(s): Amanda J. Price, Leonardo Collado‐Torres, Н. А. Иванов, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Software Mentions: 18
Published: about 5 years ago

10.1002/1878-0261.12960

KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix
Cited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
Software Mentions: 18
Published: over 3 years ago

10.3390/cancers11010091

The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics Analysis
Cited by: 5
Author(s): Yingbo Zhang, Xiaomin Tang, Yuxin Pang, Luqi Huang, Dan Wang, Chao Yuan, Xuan Hu, Liping Qu
Software Mentions: 13
Published: almost 6 years ago

10.1186/1471-2164-14-46

Systems infection biology: a compartmentalized immune network of pig spleen challenged with Haemophilus parasuis
Cited by: 9
Author(s): Ming Zhao, Xiangdong Liu, Xinyun Li, Hongbo Chen, Hui Jin, Rui Zhou, Mengjin Zhu, Shuhong Zhao
Software Mentions: 13
Published: almost 12 years ago

10.1002/cam4.2786

FOLFOX treatment response prediction in metastatic or recurrent colorectal cancer patients via machine learning algorithms
Cited by: 24
Author(s): Wei Lu, Dongliang Fu, Xianglong Kong, Zhiheng Huang, Maxwell Hwang, Yaowu Zhu, Liubo Chen, Kai Jiang, Xinlin Li, Yihua Wu, Jun Li, Ying Yuan, Kefeng Ding
Software Mentions: 12
Published: almost 5 years ago

10.1038/s41598-018-28356-3

Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver
Cited by: 34
Author(s): Chris Duncan, Sara A. Grimm, Daniel L. Morgan, Pierre R. Bushel, Brian D. Bennett, John D. Roberts, Frederick L. Tyson, B. Alex Merrick, Paul A. Wade
Software Mentions: 11
Published: over 6 years ago

10.1155/2008/147563

Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data: Tools for the First Steps
Cited by: 6
Author(s): Grier P. Page, Issa Coulibaly
Software Mentions: 10
Published: over 16 years ago

10.1371/journal.pone.0066902

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data
Cited by: 16
Author(s): Darragh G. McArt, Philip D. Dunne, Jaine K. Blayney, Manuel Salto-Tellez, Sandra Van Schaeybroeck, Peter Hamilton, Shudong Zhang
Software Mentions: 9
Published: over 11 years ago

10.3390/cancers13081768

Systematic Analysis of the Transcriptome Profiles and Co-Expression Networks of Tumour Endothelial Cells Identifies Several Tumour-Associated Modules and Potential Therapeutic Targets in Hepatocellular Carcinoma
Cited by: 8
Author(s): Thomas Mohr, Sonja Katz, Verena Paulitschke, Nadim Aizarani, Alexander Tolios
Software Mentions: 9
Published: over 3 years ago

10.1186/1471-2164-15-139

Unique features of the transcriptional response to model aneuploidy in human cells
Cited by: 85
Author(s): Milena Dürrbaum, Anastasia Yurievna Kuznetsova, Verena Passerini, Silvia Stingele, Gabriele Stoehr, Zuzana Storchová
Software Mentions: 9
Published: almost 11 years ago

10.1186/s12867-018-0111-x

Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis
Cited by: 4
Author(s): Paola M. Boggiatto, Daniel Fitzsimmons, Darrell O. Bayles, David P. Alt, Catherine E. Vrentas, Steven C. Olsen
Software Mentions: 9
Published: over 6 years ago

10.18632/oncotarget.26668

mTOR inhibition affects Yap1-β-catenin-induced hepatoblastoma growth and development
Cited by: 11
Author(s): Laura Molina, Hong Yang, Adeola O. Adebayo Michael, Michael Oertel, Aaron Bell, Sucha Singh, Xin Chen, Junyan Tao, Satdarshan P. Monga
Software Mentions: 8
Published: almost 6 years ago

10.1016/j.molcel.2019.01.009

Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing
Cited by: 195
Author(s): Alba Rodríguez-Meira, Gemma Buck, Sally-Ann Clark, Benjamin Povinelli, Verónica Alcolea, Eleni Louka, Simon J. McGowan, Angela Hamblin, Nikolaos Sousos, Nikolaos Barkas, Alice Giustacchini, Bethan Psaila, Sten Eirik W. Jacobsen, Supat Thongjuea, Adam J. Mead
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-017-13731-3

The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation
Cited by: 16
Author(s): Mahdi Golkaram, Jaeshin Jang, Stefan Hellander, Kenneth S. Kosik, Linda R. Petzold
Software Mentions: 8
Published: about 7 years ago

10.1186/s40478-017-0421-0

Integrated analysis of genetic, behavioral, and biochemical data implicates neural stem cell-induced changes in immunity, neurotransmission and mitochondrial function in Dementia with Lewy Body mice
Cited by: 5
Author(s): Anita Lakatos, Natalie R.S. Goldberg, Mathew Blurton‐Jones
Software Mentions: 8
Published: almost 8 years ago

10.1186/1471-2105-11-450

Filtering, FDR and power
Cited by: 43
Author(s): Maarten van Iterson, Judith M. Boer, Renée X. de Menezes
Software Mentions: 8
Published: over 14 years ago

10.1186/s12859-018-2069-6

A gene profiling deconvolution approach to estimating immune cell composition from complex tissues
Cited by: 12
Author(s): Shu Hwa Chen, Wen Yu Kuo, Sheng Su, Wei Chun Chung, Jen Ming Ho, Henry Horng Shing Lu, Chung Yen Lin
Software Mentions: 8
Published: over 6 years ago

10.1186/s12864-015-2319-1

Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes
Cited by: 3
Author(s): Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masahiro Fujita, Hajime Ohyanagi, Nori Kurata
Software Mentions: 8
Published: about 9 years ago

10.18632/oncotarget.24506

Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data
Cited by: 13
Author(s): Mahmoud Ahmed, Huynh Quoc Nguyen, Jin Seok Hwang, Sahib Zada, Trang Huyen Lai, Sang Soo Kang, Deok Ryong Kim
Software Mentions: 8
Published: almost 7 years ago

10.1016/j.csbj.2021.04.056

A computational analysis of transcriptional profiles from CD8(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression
Cited by: 3
Author(s): Sergey Ivanov, Dmitry Filimonov, O. Tarasova
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13148-020-00837-1

Differential CpG DNA methylation in peripheral naïve CD4+ T-cells in early rheumatoid arthritis patients
Cited by: 21
Author(s): Rujiraporn Pitaksalee, AN Burska, Shoaib Ajaib, Joshua Hugh Rogers, Rekha Parmar, K. Mydlova, Xuanxiao Xie, Alastair Droop, Jagtar Singh Nijjar, P Chambers, Paul Emery, Richard Hodgett, Iain B. McInnes, Frédérique Ponchel
Software Mentions: 7
Published: over 4 years ago

10.3389/fmicb.2020.607325

Effects of Rare Microbiome Taxa Filtering on Statistical Analysis
Cited by: 53
Author(s): Quy Cao, Xinxin Sun, Karun Rajesh, Naga Chalasani, Kayla Gelow, Barry P. Katz, Vijay H. Shah, Arun J. Sanyal, Ekaterina Smirnova
Software Mentions: 7
Published: almost 4 years ago

10.3389/fcell.2021.624053

“All-In-One” Genetic Tool Assessing Endometrial Receptivity for Personalized Screening of Female Sex Steroid Hormones
Cited by: 7
Author(s): Pavel Deryabin, А. П. Домнина, Inga V. Gorelova, M. V. Rulev, М. А. Petrosyan, Nikolay Nikolsky, Aleksandra Borodkina
Software Mentions: 7
Published: almost 4 years ago

10.18632/aging.203208

miRNAs generated from Meg3-Mirg locus are downregulated during aging
Cited by: 1
Author(s): Ana-Mihaela Lupan, Evelyn Gabriela Rusu, Mihai Bogdan Preda, Catalina Iolanda Marinescu, Cristina Ivan, Alexandrina Burlacu
Software Mentions: 7
Published: over 3 years ago

10.1186/s13073-015-0237-0

Identification of global regulators of T-helper cell lineage specification
Cited by: 36
Author(s): Kartiek Kanduri, Subhash Tripathi, Antti Larjo, Henrik Mannerström, Ubaid Ullah, Riikka Lund, R. David Hawkins, Bing Ren, Harri Lähdesmäki, Riitta Lahesmaa
Software Mentions: 6
Published: about 9 years ago

10.12688/f1000research.25713.2

VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach
Cited by: 1
Author(s): Priyansh Srivastava, Mehak Talwar, Aishwarya Yadav, Alakto Choudhary, Sabyasachi Mohanty, Samuel Bharti, Priyanka Narad, Abhishek Sengupta
Software Mentions: 6
Published: almost 4 years ago

10.3389/fonc.2021.597536

Systems Biomedicine of Primary and Metastatic Colorectal Cancer Reveals Potential Therapeutic Targets
Cited by: 7
Author(s): Mehran Piran, Neda Sepahi, Afagh Moattari, A. M. Rahimi, Ali Ghanbariasad
Software Mentions: 6
Published: over 3 years ago

10.3389/fcell.2021.561086

Comprehensive miRNome-Wide Profiling in a Neuronal Cell Model of Synucleinopathy Implies Involvement of Cell Cycle Genes
Cited by: 6
Author(s): Elisabeth Findeiss, Sigrid C. Schwarz, Valentin Evsyukov, Thomas W. Rösler, Matthias Höllerhage, Tasnim Chakroun, Niko-Petteri Nykänen, Yimin Shen, Wolfgang Wurst, Michael Köhl, Jörg Tost, Günter U. Höglinger
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12864-016-3199-8

Identification of novel targets of diabetic nephropathy and PEDF peptide treatment using RNA-seq
Cited by: 29
Author(s): Ana Rubín, Anna C. Salzberg, Yuka Imamura, Anzor Grivitishvilli, Joyce Tombran-Tink
Software Mentions: 6
Published: about 8 years ago

10.1186/s12967-017-1201-0

Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival
Cited by: 46
Author(s): Chinh Bkrong Nguyen, Lene Alsøe, Jessica M. Lindvall, Dag Sulheim, Even Fagermoen, Anette Winger, Mari Kaarbø, Hilde Nilsen, Vegard Bruun Wyller
Software Mentions: 6
Published: over 7 years ago

10.1080/21623945.2019.1595269

Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in Asian Indians
Cited by: 17
Author(s): Aditya Saxena, Prabhat Tiwari, Nitin Wahi, Arpana Soni, Ram Chandra Bansiwal, Anshul Kumar, Balram Sharma, Prakash P Punjabi, Nidhi Gupta, Babita Malik, Krishna Mohan Medicherla, Prashanth Suravajhala, Sandeep Kumar Mathur
Software Mentions: 6
Published: almost 6 years ago

10.1186/1471-2105-14-370

Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching
Cited by: 36
Author(s): Hubert Rehrauer, Lennart Opitz, Ge Tan, Lina Sieverling, Ralph Schlapbach
Software Mentions: 6
Published: about 11 years ago

10.1128/mBio.02495-18

The Transcriptional Cycle Is Suited to Daytime N 2 Fixation in the Unicellular Cyanobacterium “ Candidatus Atelocyanobacterium thalassa” (UCYN-A)
Cited by: 28
Author(s): María del Carmen Muñoz-Marín, Irina N. Shilova, Tianshu Shi, Hanna Farnelid, Ana María Cabello, Jonathan P. Zehr
Software Mentions: 6
Published: almost 6 years ago

10.1038/srep21518

Activation of the TGFβ pathway impairs endothelial to haematopoietic transition
Cited by: 32
Author(s): Özge Vargel, Yang Zhang, Kinga Kosim, Kerstin Ganter, Sophia Föehr, Yannicka Mardenborough, Maya Shvartsman, Anton J. Enright, Jeroen Krijgsveld, Christophe Lancrin
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pone.0150705

Changes in the miRNA-mRNA Regulatory Network Precede Motor Symptoms in a Mouse Model of Multiple System Atrophy: Clinical Implications
Cited by: 26
Author(s): Simon Schafferer, Rimpi Khurana, Violetta Refolo, Serena Venezia, Edith Sturm, Paolo Piatti, Clara Hechenberger, Hubert Hackl, Roman Kessler, Michaela Willi, Ronald Gstir, Anne Krogsdam, Alexandra Lusser, Werner Poewe, Gregor K. Wenning, Alexander Hüttenhofer, Nadia Stefanova
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pone.0180322

Affected pathways and transcriptional regulators in gene expression response to an ultra-marathon trail: Global and independent activity approaches
Cited by: 6
Author(s): María Maqueda, Emma Roca, Daniel Brotons, José Manuel Nieto Soria, Alexandre Perera
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0100052

Mining Gene Expression Data of Multiple Sclerosis
Cited by: 20
Author(s): Pi Guo, Qin Zhang, Zhenli Zhu, Zhengliang Huang, Ké Li
Software Mentions: 5
Published: over 10 years ago

10.1186/s12864-015-1546-9

Activation of defence pathways in Scots pine bark after feeding by pine weevil (Hylobius abietis)
Cited by: 31
Author(s): Andriy Kovalchuk, Tommaso Raffaello, Emad Jaber, Susanna Keriö, Rajendra P. Ghimire, W. Walter Lorenz, Jeffrey F. D. Dean, Jarmo K. Holopainen, Fred O. Asiegbu
Software Mentions: 5
Published: over 9 years ago

10.1038/sdata.2018.136

A merged lung cancer transcriptome dataset for clinical predictive modeling
Cited by: 26
Author(s): Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
Software Mentions: 5
Published: over 6 years ago

10.1186/s12885-020-6533-0

PDAC-ANN: an artificial neural network to predict pancreatic ductal adenocarcinoma based on gene expression
Cited by: 30
Author(s): Palloma Porto Almeida, Cristina Padre Cardoso, Leandro Martins de Freitas
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13072-015-0046-0

Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia
Cited by: 16
Author(s): Jiansheng Wu, Luca Pinello, Elinor Yissachar, Jonathan W. Wischhusen, Guo‐Cheng Yuan, Charles W.M. Roberts
Software Mentions: 5
Published: about 9 years ago

10.1186/s13059-015-0863-2

IL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiation
Cited by: 89
Author(s): Roser Vento‐Tormo, Carlos Company, Javier Rodríguez-Ubreva, Lorenzo de la Rica, José Urquiza, Biola M. Javierre, Radhakrishnan Sabarinathan, Ana Luque, Manel Esteller, Josep M. Aran, Damiana Álvarez-Errico, Esteban Ballestar
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12864-015-2246-1

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants
Cited by: 12
Author(s): Anna Aulicino, Adam M. Dinan, Aleksandra A. Miranda-CasoLuengo, John A. Browne, Kévin Rue-Albrecht, David E. MacHugh, Brendan J. Loftus
Software Mentions: 5
Published: about 9 years ago

10.3390/ijms21218016

Enhancer of Zeste Homolog 2 (EZH2) Mediates Glucolipotoxicity-Induced Apoptosis in β-Cells
Cited by: 3
Author(s): Tina Dahlby, Christian Simon, Marie Balslev Backe, Mattias Salling Dahllöf, Edward B. Holson, Bridget K. Wagner, Marianne Böni-Schnetzler, Michał Marzec, Morten Lundh, Thomas Mandrup‐Poulsen
Software Mentions: 5
Published: about 4 years ago

10.1186/1752-0509-8-56

Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling
Cited by: 0
Author(s): Rosario M. Piro, Stefan Wiesberg, Gunnar Schramm, Nico Rebel, Marcus Oswald, Roland Eils, Gerhard Reinelt, Rainer König
Software Mentions: 5
Published: over 10 years ago

10.3389/fcell.2020.560766

Transcriptome Reveals Multi Pigmentation Genes Affecting Dorsoventral Pattern in Avian Body
Cited by: 6
Author(s): Xi Yang, Hehe Liu, Li Liang, Qian Xu, Yisi Liu, Lei Wang, Shengchao Ma, Jianmei Wang, Lili Bai, Rongping Zhang, Chunchun Han
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0171689

Transcriptomic meta-analysis reveals up-regulation of gene expression functional in osteoclast differentiation in human septic shock
Cited by: 10
Author(s): Samanwoy Mukhopadhyay, Pravat Kumar Thatoi, AK Pandey, B. K. Das, Balachandran Ravindran, Samsiddhi Bhattacharjee, Saroj Kant Mohapatra
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0041066

Transcriptional Response of Peripheral Blood Mononuclear Cells from Cattle Infected with Mycobacterium bovis
Cited by: 25
Author(s): Federico Carlos Blanco, Marcelo Soria, María Verónica Bianco, Fabiana Bigi
Software Mentions: 5
Published: over 12 years ago

10.3389/fimmu.2020.01138

Bioinformatics Analysis of Gut Microbiota and CNS Transcriptome in Virus-Induced Acute Myelitis and Chronic Inflammatory Demyelination; Potential Association of Distinct Bacteria With CNS IgA Upregulation
Cited by: 11
Author(s): Seiichi Omura, Fumitaka Sato, Ah-Mee Park, Mitsugu Fujita, Sundar Khadka, Yumina Nakamura, Aoshi Katsuki, Kenji Nishio, Felicity N. E. Gavins, Ikuo Tsunoda
Software Mentions: 5
Published: over 4 years ago

10.1038/s41398-019-0666-4

Hepatic gene expression explains primary drug toxicity in bipolar disorder
Cited by: 0
Author(s): Anna Maria Birkl-Toeglhofer, Christoph Birkl, Ida C. Llenos, Serge Weis, Johannes Haybaeck
Software Mentions: 5
Published: about 5 years ago

10.3390/microorganisms9040845

Impact of Chronic Exposure to Sublethal Doses of Glyphosate on Honey Bee Immunity, Gut Microbiota and Infection by Pathogens
Cited by: 29
Author(s): Loreley Castelli, Sofía Balbuena, Belén Branchiccela, Pablo Zunino, Joanito Liberti, Philipp Engel, Karina Antúnez
Software Mentions: 5
Published: over 3 years ago

10.1016/j.dib.2016.06.001

Microarray dataset of Jurkat cells following miR-93 over-expression
Cited by: 0
Author(s): Silvia Gioiosa, Lorena Verduci, Gianluca Azzalin, Claudia Carissimi, Valerio Fulci, Giuseppe Macino
Software Mentions: 4
Published: over 8 years ago

10.3390/biom10091230

The Transcriptomic Evidence on the Role of Abdominal Visceral vs. Subcutaneous Adipose Tissue in the Pathophysiology of Diabetes in Asian Indians Indicates the Involvement of Both
Cited by: 6
Author(s): Anshul Kumar, Prabhat Tiwari, Aditya Saxena, Naincy Purwar, Nitin Wahi, Balram Sharma, Sandeep Kumar Mathur
Software Mentions: 4
Published: over 4 years ago

10.1038/s41396-019-0568-8

Gut microbiota structure differs between honeybees in winter and summer
Cited by: 157
Author(s): Lucie Kešnerová, Olivier Emery, Michaël Troilo, Joanito Liberti, Berra Erkoşar, Philipp Engel
Software Mentions: 4
Published: about 5 years ago

10.1155/2013/848952

Integration of Data from Omic Studies with the Literature-Based Discovery towards Identification of Novel Treatments for Neovascularization in Diabetic Retinopathy
Cited by: 4
Author(s): Aleš Maver, Dimitar Hristovski, Thomas C. Rindflesch, Borut Peterlin
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2105-10-37

DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data
Cited by: 11
Author(s): Daniel Glez-Peña, Rodrigo Álvarez, Fernando Díaz, Florentino Fdez-Riverola
Software Mentions: 4
Published: almost 16 years ago

10.1038/s41598-017-05949-y

Enhanced differential expression statistics for data-independent acquisition proteomics
Cited by: 29
Author(s): Tomi Suomi, Laura L. Elo
Software Mentions: 4
Published: over 7 years ago

10.1155/2018/1243858

Characterization of Transcription Termination-Associated RNAs: New Insights into their Biogenesis, Tailing, and Expression in Primary Tumors
Cited by: 4
Author(s): Ilaria Laudadio, Sara Formichetti, Silvia Gioiosa, Filippos Klironomos, Nikolaus Rajewsky, Giuseppe Macino, Claudia Carissimi, Valerio Fulci
Software Mentions: 4
Published: almost 7 years ago

10.1186/1471-2164-10-363

Grapevine cell early activation of specific responses to DIMEB, a resveratrol elicitor
Cited by: 56
Author(s): Anita Zamboni, Pamela Gatto, Alessandro Cestaro, S. Pilati, Roberto Viola, Fulvio Mattivi, C. Moser, Riccardo Velasco
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.ppat.1008066

Linking the effects of helminth infection, diet and the gut microbiota with human whole-blood signatures
Cited by: 25
Author(s): Soo Ching Lee, Mei Tang, Alice V. Easton, Joseph C. Devlin, Ling Ling Chua, Ilseung Cho, Foong Ming Moy, Tsung Fei Khang, Yvonne Ai Lian Lim, P’ng Loke
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0038149

Transcriptional Profiling of Human Brain Endothelial Cells Reveals Key Properties Crucial for Predictive In Vitro Blood-Brain Barrier Models
Cited by: 164
Author(s): Eduard Urich, Stanley E. Lazic, Juliette Molnos, Isabelle Wells, Per Ola Freskgård
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0227193

Transcriptome analysis of early pregnancy vitamin D status and spontaneous preterm birth
Cited by: 22
Author(s): Aishwarya P. Yadama, Hooman Mirzakhani, Thomas F. McElrath, Augusto A. Litonjua, Scott T. Weiss
Software Mentions: 4
Published: almost 5 years ago

10.1111/jcmm.14163

LncRNA-mRNA competing endogenous RNA network depicts transcriptional regulation in ischaemia reperfusion injury
Cited by: 19
Author(s): Hongying Liu, Dan-Ping Xu, Xin Zhong, Dongsheng Xu, Geng Chen, Junbo Ge, Hua Li
Software Mentions: 4
Published: almost 6 years ago

10.3389/fnmol.2019.00293

Identification of lncRNAs Associated With Neuroblastoma in Cross-Sectional Databases: Potential Biomarkers
Cited by: 13
Author(s): Bharat Prajapati, Mena Fatma, Mahar Fatima, Tipu Khan, Subrata Sinha, Prahlad K. Seth
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2164-13-296

ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data
Cited by: 167
Author(s): James R. Perkins, J. D. K. Dawes, Stephen B. McMahon, David L.H. Bennett, Christine A. Orengo, Matthias Kohl
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0250660

System biology and bioinformatics pipeline to identify comorbidities risk association: Neurodegenerative disorder case study
Cited by: 3
Author(s): Utpala Nanda Chowdhury, Shamim Ahmad, M. Babul Islam, Salem A. Alyami, Julian M.W. Quinn, Valsamma Eapen, Mohammad Ali Moni
Software Mentions: 4
Published: over 3 years ago

10.1186/gb-2013-14-9-r99

PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation
Cited by: 164
Author(s): Lorenzo de la Rica, Javier Rodríguez-Ubreva, Mireia García, Abul B.M.M.K. Islam, José Urquiza, Henar Hernando, Jesper Christensen, Kristian Helin, Carmen Gómez-Vaquero, Esteban Ballestar
Software Mentions: 4
Published: almost 12 years ago

10.3390/ijerph17031035

A Network-Based Bioinformatics Approach to Identify Molecular Biomarkers for Type 2 Diabetes that Are Linked to the Progression of Neurological Diseases
Cited by: 48
Author(s): Habibur Rahman, Shou-Li Peng, Xiyuan Hu, Chen Chen, Rezanur Rahman, Shahadat Uddin, Julian M.W. Quinn, Mohammad Ali Moni
Software Mentions: 4
Published: almost 5 years ago

10.1186/jbiol53

Dosage compensation is less effective in birds than in mammals
Cited by: 300
Author(s): Yuichiro Itoh, Esther Melamed, Xia Yang, Kathy Kampf, Susanna Wang, Nadir Yehya, Atila van Nas, Kirstin Replogle, Mark Band, David F. Clayton, Eric E. Schadt, Aldons J. Lusis, Arthur P. Arnold
Software Mentions: 3
Published: almost 18 years ago

10.1186/1471-2105-11-585

Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation
Cited by: 15
Author(s): Andreas Kowarsch, Florian Blöchl, Sebastian Böhl, Maria Saile, Norbert Gretz, Ursula Klingmüller, Fabian J. Theis
Software Mentions: 3
Published: about 14 years ago

10.1186/s12864-015-1644-8

Non-thermal plasma treatment altered gene expression profiling in non-small-cell lung cancer A549 cells
Cited by: 49
Author(s): Jue Hou, Jie Ma, K.N. Yu, Wei Li, Cheng Cheng, Lingzhi Bao, Wei Han
Software Mentions: 3
Published: over 9 years ago

10.1186/s12916-016-0617-3

Human newborn bacille Calmette–Guérin vaccination and risk of tuberculosis disease: a case-control study
Cited by: 47
Author(s): Helen A. Fletcher, Ali Filali‐Mouhim, Elisa Nemes, Anthony Hawkridge, Alana Keyser, Samuel Njikan, Mark Hatherill, Thomas J. Scriba, Brian Abel, Benjamin M. Kagina, Ashley Veldsman, Nancy Marín Agudelo, Gilla Kaplan, Gregory Hussey, Rafick‐Pierre Sékaly, Willem A. Hanekom
Software Mentions: 3
Published: over 8 years ago

10.1186/1755-8794-5-66

Subtypes of primary colorectal tumors correlate with response to targeted treatment in colorectal cell lines
Cited by: 199
Author(s): Andreas Schlicker, Garry Beran, Christine Chresta, Gael McWalter, Alison Pritchard, Susie Weston, Sarah Runswick, Sara Davenport, Kerry Heathcote, D Castro, George M. Orphanides, Tim French, Lodewyk Wessels
Software Mentions: 3
Published: about 12 years ago

10.1186/1471-2180-8-209

Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro
Cited by: 53
Author(s): Philip A. Bronstein, Melanie J. Filiatrault, Christopher R. Myers, Michael Rutzke, David J. Schneider, Samuel Cartinhour
Software Mentions: 3
Published: almost 17 years ago

10.1007/s10522-016-9638-8

The functional consequences of age-related changes in microRNA expression in skeletal muscle
Cited by: 49
Author(s): Ana Soriano‐Arroquia, Louise House, Luke Tregilgas, Elizabeth G. Canty‐Laird, Katarzyna Goljanek‐Whysall
Software Mentions: 3
Published: almost 9 years ago

10.1002/cam4.3842

Subgrouping by gene expression profiles to improve relapse risk prediction in paediatric B‐precursor acute lymphoblastic leukaemia
Cited by: 1
Author(s): Qingsheng Huang, Jiayong Zhong, Huan Gao, Kuanrong Li, Huiying Liang
Software Mentions: 3
Published: over 3 years ago

10.1186/2049-3002-2-13

Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer
Cited by: 27
Author(s): Debarshi Roy, Susmita Mondal, Chen Wang, Xiaoping He, Ashwani Khurana, Shailendra Giri, Robert Hoffmann, Deok‐Beom Jung, Sung Hyun Kim, Eduardo N. Chini, Juliana Camacho Periera, Clifford D.L. Folmes, Andrea Mariani, Sean C. Dowdy, Jamie N. Bakkum-Gamez, Shaun M. Riska, Ann L. Oberg, Edward D. Karoly, Lauren N. Bell, Jeremy Chien, Viji Shridhar
Software Mentions: 3
Published: over 10 years ago

10.1074/mcp.RA120.002345

Mutation-independent Proteomic Signatures of Pathological Progression in Murine Models of Duchenne Muscular Dystrophy
Cited by: 20
Author(s): van Westering Tle., Henrik J. Johansson, Britt Hanson, Anna M.L. Coenen-Stass, Yulia Lomonosova, Jun Tanihata, Norio Matsuki, Toshifumi Yokota, Shin’ichi Takeda, Janne Lehtiö, Matthew J. Wood, Samir El Andaloussi, Yosuke Aoki, Thomas C. Roberts
Software Mentions: 3
Published: about 4 years ago

10.7717/peerj.830

The effect of listening to music on human transcriptome
Cited by: 32
Author(s): Chakravarthi Kanduri, Pirre Raijas, Minna Ahvenainen, Anju K. Philips, Liisa Ukkola-Vuoti, Harri Lähdesmäki, Irma Järvelä
Software Mentions: 3
Published: almost 10 years ago

10.14814/phy2.12538

Deletion of glycerol channel aquaporin-9 (Aqp9 ) impairs long-term blood glucose control in C57BL/6 leptin receptor-deficient (db/db ) obese mice
Cited by: 14
Author(s): Peter Sartipy, Aakash Chawade, Sören Nielsén, Per Kjellbom, Michael Rützler
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0001151

Gene Expression Analysis of In Vivo Fluorescent Cells
Cited by: 35
Author(s): Konstantin Khodosevich, Dragoš Inta, Peter H. Seeburg, Hannah Monyer
Software Mentions: 3
Published: about 17 years ago

10.1371/journal.pone.0016679

Specific Age-Associated DNA Methylation Changes in Human Dermal Fibroblasts
Cited by: 113
Author(s): Carmen M. Koch, Christoph V. Suschek, Qiong Lin, Simone Bork, Maria Goergens, Sylvia Joussen, Norbert Pallua, Anthony D. Ho, Martin Zenke, Wolfgang Wagner
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0067922

Roles for Treg Expansion and HMGB1 Signaling through the TLR1-2-6 Axis in Determining the Magnitude of the Antigen-Specific Immune Response to MVA85A
Cited by: 26
Author(s): Magali Matsumiya, Elena Stylianou, Kristin Griffiths, Zoe Lang, Joel N. Meyer, Stephanie A. Harris, Rosalind Rowland, Angela M. Minassian, Ansar A. Pathan, Helen A. Fletcher, Helen McShane
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0081729

Global Expression Profiling of Low Temperature Induced Genes in the Chilling Tolerant Japonica Rice Jumli Marshi
Cited by: 46
Author(s): Aakash Chawade, Angelica Lindlöf, Björn Olsson, Olof Olsson
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0021825

Formin1 Mediates the Induction of Dendritogenesis and Synaptogenesis by Neurogenin3 in Mouse Hippocampal Neurons
Cited by: 27
Author(s): Julia Simón-Areces, Ana Dopazo, Markus Dettenhofer, Alfredo Rodrı́guez-Tébar, Luis Miguel Garcia-Segura, María Ángeles Arévalo
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0127702

A New Combinatorial Optimization Approach for Integrated Feature Selection Using Different Datasets: A Prostate Cancer Transcriptomic Study
Cited by: 7
Author(s): Nisha Puthiyedth, Carlos Riveros, Regina Berretta, Pablo Moscato
Software Mentions: 3
Published: over 9 years ago

10.1186/s11658-018-0090-4

Essential genes of the macrophage response to Staphylococcus aureus exposure
Cited by: 6
Author(s): Aixia Sun, Hongwei Zhang, Feng Pang, Guifen Niu, Jianzhong Chen, Fei Chen, Jian Zhang
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.602908

Identifying RBM47, HCK, CD53, TYROBP, and HAVCR2 as Hub Genes in Advanced Atherosclerotic Plaques by Network-Based Analysis and Validation
Cited by: 19
Author(s): Chiyu Liu, Haifeng Zhang, Yangxin Chen, Shaohua Wang, Zhiteng Chen, Zhaoyu Liu, Jingfeng Wang
Software Mentions: 3
Published: almost 4 years ago

10.1038/srep26020

The N-end rule pathway regulates pathogen responses in plants
Cited by: 37
Author(s): Rémi de Marchi, Maud Sorel, Brian Mooney, Isabelle Fudal, Kevin Goslin, Kamila Kwaśniewska, Patrick T. Ryan, Marina Pfalz, Juergen Kroymann, Stephan Pollmann, Angela Feechan, Frank Wellmer, Susana Rivas, Emmanuelle Graciet
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-017-07481-5

Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks
Cited by: 32
Author(s): Mehrab Ghanat Bari, Choong Yong Ung, Cheng Zhang, Shizhen Zhu, Li Hu
Software Mentions: 3
Published: over 7 years ago

10.1093/infdis/jiu615

Gene Expression and Cytokine Profile Correlate With Mycobacterial Growth in a Human BCG Challenge Model
Cited by: 29
Author(s): Magali Matsumiya, Iman Satti, Agnieszka Chomka, Stephanie A. Harris, Lisa Stockdale, Joel N. Meyer, Helen A. Fletcher, Helen McShane
Software Mentions: 3
Published: about 10 years ago

10.1007/s10916-021-01718-7

Robust Data Integration Method for Classification of Biomedical Data
Cited by: 0
Author(s): Aneta Polewko-Klim, Krzysztof Mnich, Witold R. Rudnicki
Software Mentions: 3
Published: almost 4 years ago

10.3390/ijms21010317

The Use of PTI-Marker Genes to Identify Novel Compounds that Establish Induced Resistance in Rice
Cited by: 16
Author(s): Jonas De Kesel, Ramsés Gómez-Rodríguez, Eli Bonneure, Sven Mangelinckx, Tina Kyndt
Software Mentions: 3
Published: almost 5 years ago

Projects: bioconductor: genefilter

Papers Mentioning genefilter 142