10.1186/s12864-019-5915-7

Integrated application of multi-omics provides insights into cold stress responses in pufferfish Takifugu fasciatus
Cited by: 46
Author(s): Xintian Wen, Yadong Hu, Xinyu Zhang, Xiaozhen Wei, Tao Wang, Shaowu Yin
Software Mentions: 2
Published: about 7 years ago

10.1155/2008/892927

Bayesian Mixture Model Analysis for Detecting Differentially Expressed Genes
Cited by: 4
Author(s): Zhenyu Jia, Shizhong Xu
Software Mentions: 2
Published: over 18 years ago

10.1155/2012/831460

SNP Discovery through Next-Generation Sequencing and Its Applications
Cited by: 211
Author(s): Santosh Kumar, Travis Banks, Sylvie Cloutier
Software Mentions: 2
Published: over 13 years ago

10.1186/2041-2223-5-9

Validation of high throughput sequencing and microbial forensics applications
Cited by: 56
Author(s): Bruce Budowle, Nancy Connell, Anna Bielecka-Oder, Rita R. Colwell, Cindi R. Corbett, Jacqueline Fletcher, Mats Forsman, Dana R Kadavy, Alemka Markotić, Stephen Morse, Randall S. Murch, Antti Sajantila, Sarah E. Schmedes, Krista Ternus, Stephen D. Turner, Samuel S. Minot
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0017163

Gene Expression Profiles from Formalin Fixed Paraffin Embedded Breast Cancer Tissue Are Largely Comparable to Fresh Frozen Matched Tissue
Cited by: 136
Author(s): Lorenza Mittempergher, Jorma J. de Ronde, Marja Nieuwland, Ron Kerkhoven, Iris Simón, Emiel J. T. Rutgers, Lodewyk Wessels, Laura J. van’t Veer
Software Mentions: 2
Published: over 15 years ago

10.1186/s12890-015-0142-8

A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis
Cited by: 36
Author(s): Yong Huang, Shwu Fan, Rekha Vij, Justin M. Oldham, Jose D. Herazo‐Maya, Steven M. Broderick, Mary E. Strek, Steven R. White, D. Kyle Hogarth, Nathan Sandbo, Yves A. Lussier, Kevin F. Gibson, Naftali Kaminski, Joe G.N. Garcia, Imre Noth
Software Mentions: 2
Published: over 10 years ago

10.1186/s13104-015-1382-7

cFinder: definition and quantification of multiple haplotypes in a mixed sample
Cited by: 6
Author(s): Norbert Niklas, Julia Hafenscher, Agnes Barna, Karin Wiesinger, Johannes Pröll, Stephan Dreiseitl, Sandra Preuner-Stix, Peter Valent, Thomas Lion, Christian Gabriel
Software Mentions: 2
Published: almost 11 years ago

10.2196/mental.4984

Mental Health Smartphone Apps: Review and Evidence-Based Recommendations for Future Developments
Cited by: 619
Author(s): David Bakker, Nikolaos Kazantzis, Debra Rickwood, Nikki Rickard
Software Mentions: 2
Published: over 10 years ago

10.3390/ijerph10104836

Estimating the Public Health Impact of Setting Targets at the European Level for the Reduction of Zoonotic Salmonella in Certain Poultry Populations
Cited by: 15
Author(s): Winy Messens, Luis Vivas-Alegre, Saghir Bashir, Giusi Amore, Pablo Romero-Barrios, Marta Hugas
Software Mentions: 2
Published: almost 13 years ago

10.1186/1756-0500-7-483

HMM-ModE: implementation, benchmarking and validation with HMMER3
Cited by: 11
Author(s): Swati Sinha, Andrew M. Lynn
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-13-62

Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter
Cited by: 108
Author(s): Bridget M. Barker, Kristin Kroll, Martin Vödisch, Aurélien Mazurie, Olaf Kniemeyer, Robert A. Cramer
Software Mentions: 2
Published: over 14 years ago

10.3390/ijerph15091941

A Hybrid Forecasting Approach to Air Quality Time Series Based on Endpoint Condition and Combined Forecasting Model
Cited by: 27
Author(s): Jiaming Zhu, Peng Wu, Huayou Chen, Ligang Zhou
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijerph16245102

PM2.5 Pollution: Health and Economic Effect Assessment Based on a Recursive Dynamic Computable General Equilibrium Model
Cited by: 6
Author(s): Keyao Chen, Guizhi Wang, Lingyan Wu, Jibo Chen, Shuai Yuan, Qi Liu, Xiaodong Liu
Software Mentions: 2
Published: over 6 years ago

10.3390/ijerph17030933

Comparative Analysis of the Reproduction Accuracy of Main Methods for Finding the Mandible Position in the Centric Relation Using Digital Research Method. Comparison between Analog-to-Digital and Digital Methods: A Preliminary Report
Cited by: 3
Author(s): А А Stafeev, A N Ryakhovsky, P Petrov, Sergey Chikunov, A V Khizhuk, Marina Bykova, Nataliya Vuraki
Software Mentions: 2
Published: over 6 years ago

10.3390/ijerph17155576

Dissociable Effects of Executive Load on Perceived Exertion and Emotional Valence during Submaximal Cycling
Cited by: 5
Author(s): Vicente Ávila-Gandía, Francisco Alarcón, José C. Perales, Francisco Javier López-Román, Antonio J. Luque-Rubia, David Cárdenas Vélez
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0015271

The Prevalence and Regulation of Antisense Transcripts in Schizosaccharomyces pombe
Cited by: 52
Author(s): Ting Ni, Kang Tu, Zhong Wang, Shen Song, Han Wu, Bin Xie, Kristin C. Scott, Shiv I. S. Grewal, Yuan Gao, Jun Zhu
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0087836

Deciphering the Adjustment between Environment and Life History in Annuals: Lessons from a Geographically-Explicit Approach in Arabidopsis thaliana
Cited by: 53
Author(s): Esperanza Manzano-Piedras, Arnald Marcer, Carlos Alonso‐Blanco, F. Xavier Picó
Software Mentions: 2
Published: over 12 years ago

10.3390/ijerph18179228

Evidence for the Crash Avoidance Effectiveness of Intelligent and Connected Vehicle Technologies
Cited by: 9
Author(s): Hong Tan, Fuquan Zhao, Han Hao, Zongwei Liu
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2105-16-S18-S11

Light-RCV: a lightweight read coverage viewer for next generation sequencing data
Cited by: 1
Author(s): Chih Ching Chang, Wen Bin Lee, An Chen-Deng, Tsunglin Liu, Joseph T. Tseng, Darby Tien Hao Chang
Software Mentions: 2
Published: over 10 years ago

10.1186/s12859-017-1810-x

Robust gene selection methods using weighting schemes for microarray data analysis
Cited by: 14
Author(s): Seok Kang, Jongwoo Song
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0152468

Disentangling the Role of Climate, Topography and Vegetation in Species Richness Gradients
Cited by: 60
Author(s): Mario R. Moura, Fabricio Villalobos, Gabriel C. Costa, Paulo Christiano de Anchieta Garcia
Software Mentions: 2
Published: over 10 years ago

10.1136/jitc-2020-001717

Differential and longitudinal immune gene patterns associated with reprogrammed microenvironment and viral mimicry in response to neoadjuvant radiotherapy in rectal cancer
Cited by: 14
Author(s): Anna Wilkins, Elisa Fontana, Gift Nyamundanda, Chanthirika Ragulan, Yatish Patil, David Mansfield, Jennifer Kingston, Fiona Errington-Mais, Daniel Bottomley, Katharina von Loga, Hannah Bye, Paul Carter, Emma Tinkler-Hundal, Arish Noshirwani, Jessica A. Downs, Magnus T. Dillon, Sandra Demaria, David Sebag‐Montefiore, Kevin Harrington, Nicholas P. West, Alan Melcher, Anguraj Sadanandam
Software Mentions: 2
Published: over 5 years ago

10.1136/jitc-2020-002223

Genomic profiling of advanced cervical cancer to predict response to programmed death-1 inhibitor combination therapy: a secondary analysis of the CLAP trial
Cited by: 21
Author(s): Xin Huang, Minke He, Hongyu Peng, Chongjie Tong, Zhimin Liu, Xiaolong Zhang, Yang Shao, Dongqin Zhu, Junli Zhang, Jiani C. Yin, Fan Yang, C. Y. Lan
Software Mentions: 2
Published: about 5 years ago

10.1177/1753495X20929502

Provision of acute medicine services for pregnant women in UK hospitals: Data from the Society for Acute Medicine Benchmarking Audit 2019
Cited by: 1
Author(s): Catherine Atkin, Paarul Prinja, Anita Banerjee, Mark Holland, Daniel Lasserson
Software Mentions: 2
Published: about 6 years ago

10.18632/aging.202888

Genetic landscape of breast cancer and mutation tracking with circulating tumor DNA in Chinese women
Cited by: 6
Author(s): Yinghao Wang, Lizhi Lin, Linhong Li, Jialiang Wen, Yili Chi, Rutian Hao, Xuanxuan Dai, Yizuo Chen, Du-Ping Huang, Yi-Li Zhou, Jie You, Zhiqiang Ye, Hao Chen, Liping Jin, Danxiang Chen, Fan Yang, Erjie Xia, Xueyan Ma, Fengyu Guo, Yunguang Tong, Min Zheng, Ouchen Wang
Software Mentions: 2
Published: over 5 years ago

10.1186/1756-0500-6-365

Variable selection methods for developing a biomarker panel for prediction of dengue hemorrhagic fever
Cited by: 17
Author(s): Huangxian Ju, Allan R. Brasier
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0213040

Metabolic and physiological changes induced by plant growth regulators and plant growth promoting rhizobacteria and their impact on drought tolerance in Cicer arietinum L.
Cited by: 72
Author(s): Naeem Khan, Asghari Bano, Ali Babar
Software Mentions: 2
Published: over 7 years ago

10.1186/s13104-016-1847-3

SeqTools: visual tools for manual analysis of sequence alignments
Cited by: 22
Author(s): Gemma Barson, Ed Griffiths
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0019651

Platelets Alter Gene Expression Profile in Human Brain Endothelial Cells in an In Vitro Model of Cerebral Malaria
Cited by: 35
Author(s): Mathieu Barbier, Dorothée Faille, Béatrice Loriod, Julien Textoris, Claire Camus, Denis Puthier, Laurence Flori, Samuel C. Wassmer, Geneviève Victoréro, Marie‐Christine Alessi, Thierry Fusaı̈, Catherine Nguyen, Georges E. Grau, Pascal Rihet
Software Mentions: 2
Published: about 15 years ago

10.1186/1756-0500-6-334

De novo likelihood-based measures for comparing genome assemblies
Cited by: 46
Author(s): Mohammadreza Ghodsi, Curtis Hill, Irina Astrovskaya, Henry Lin, Dan Sommer, Sergey Koren, Mihai Pop
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2105-8-S7-S24

ProtQuant: a tool for the label-free quantification of MudPIT proteomics data
Cited by: 47
Author(s): Susan M. Bridges, G Bryce Magee, Nan Wang, W. Paul Williams, Shane C. Burgess, Bindu Nanduri
Software Mentions: 2
Published: over 18 years ago

10.1186/s12864-021-07610-5

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs
Cited by: 13
Author(s): Adéla Nosková, Meenu Bhati, Naveen Kumar Kadri, Danang Crysnanto, Stefan Neuenschwander, Andreas Höfer, Hubert Pausch
Software Mentions: 2
Published: over 5 years ago

10.1186/1756-0500-7-157

In silico prediction of protein-protein interactions in human macrophages
Cited by: 4
Author(s): Oussema Souiai, Fatma Z. Guerfali, Slimane Ben Miled, Catherine Brun, Alia Benkahla
Software Mentions: 2
Published: over 12 years ago

10.7554/eLife.20640

Modularity and determinants of a (bi-)polarization control system from free-living and obligate intracellular bacteria
Cited by: 26
Author(s): Matthieu Bergé, Sébastien Campagne, Johann Mignolet, Séamus Holden, Laurence Théraulaz, Suliana Manley, Frédéric H.‐T. Allain, Patrick H. Viollier
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.43101

Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae
Cited by: 39
Author(s): Alok Arun, Susana M. Coelho, Akira F. Peters, Simon Bourdareau, Laurent Pérès, Delphine Scornet, Martina Strittmatter, Agnieszka P. Lipinska, Haiqin Yao, Olivier Godfroy, Gabriel J Montecinos, Komlan Avia, Nicolas Macaisne, Christelle Troadec, Abdelhafid Bendahmane, J. Mark Cock
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-14-S7-S11

WEP: a high-performance analysis pipeline for whole-exome data
Cited by: 42
Author(s): Mattia D’Antonio, Paolo D’Onorio De Meo, Daniele Paoletti, B Elmi, Matteo Pallocca, Nico Sanna, Ernesto Picardi, Graziano Pesole, Tiziana Castrignanò
Software Mentions: 2
Published: over 13 years ago

10.7554/eLife.54536

Vestigial auriculomotor activity indicates the direction of auditory attention in humans
Cited by: 15
Author(s): Daniel J. Strauß, Farah I. Corona-Strauss, Andreas Schroeer, Philipp Flotho, Ronny Hannemann, Steven A. Hackley
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.37545

Tuned polymerization of the transcription factor Yan limits off-DNA sequestration to confer context-specific repression
Cited by: 3
Author(s): Charlene Hope, Jemma L. Webber, Sherzod A Tokamov, Ilaria Rebay
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.30135

Control of plant cell fate transitions by transcriptional and hormonal signals
Cited by: 36
Author(s): Christophe Gaillochet, Thomas Stiehl, Christian Wenzl, Juan-José Ripoll, Lindsay J. Bailey-Steinitz, Lanxin Li, Anne Pfeiffer, Andrej Miotk, Jana P. Hakenjos, Joachim Forner, Martin F. Yanofsky, Anna Marciniak‐Czochra, Jan U. Lohmann
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.50109

Two roles for the yeast transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA
Cited by: 71
Author(s): Rafał Donczew, Linda Warfield, Derek Pacheco, Ariel Erijman, Steven Hahn
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.00569

The genome sequence of the colonial chordate, Botryllus schlosseri
Cited by: 209
Author(s): Ayelet Voskoboynik, Norma Neff, Debashis Sahoo, Aaron M. Newman, Dmitry Pushkarev, Winston Koh, Benedetto Passarelli, Hai-Wei Fan, Gary L. Mantalas, Karla J. Palmeri, Katherine J. Ishizuka, Carmela Gissi, Francesca Griggio, Rachel Ben‐Shlomo, Daniel Corey, Lolita Penland, Richard Allen White, Irving L. Weissman, Stephen R. Quake
Software Mentions: 2
Published: about 13 years ago

10.1186/1472-6807-6-24

Cited by: 26
Author(s): Rudra P. Saha, Pinak Chakrabarti
Software Mentions: 2
Published: over 20 years ago

10.7554/eLife.62021

Structural basis for SARM1 inhibition and activation under energetic stress
Cited by: 77
Author(s): Michael Sporny, Julia Guez-Haddad, Tami Khazma, Avraham Yaron, Moshe Dessau, Yoel Shkolnisky, Carsten Mim, Michail N. Isupov, Ran Zalk, Michael Hons, Yarden Opatowsky
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.27421

Cell type boundaries organize plant development
Cited by: 96
Author(s): Monica Pia Caggiano, Xiulian Yu, Neha Bhatia, Anna-Maria Larsson, Hasthi Ram, Carolyn Ohno, Pia G. Sappl, Elliot M. Meyerowitz, Henrik Jönsson, Marcus G. Heisler
Software Mentions: 2
Published: almost 9 years ago

10.1186/1472-6807-13-6

Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach
Cited by: 37
Author(s): Rajaram Gana, Shruti Rao, Hongzhan Huang, Cathy H. Wu, Sona Vasudevan
Software Mentions: 2
Published: over 13 years ago

10.1186/1472-6807-6-9

Fold-recognition and comparative modeling of human α2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni
Cited by: 8
Author(s): Sujatha, Petety V. Balaji
Software Mentions: 2
Published: over 20 years ago

10.1371/journal.pone.0093462

Arabidopsis Transcriptome Analysis Reveals Key Roles of Melatonin in Plant Defense Systems
Cited by: 262
Author(s): Sarah Weeda, Na Zhang, Xiaolei Zhao, Grace Ndip, Yang‐Dong Guo, Gregory A. Buck, Conggui Fu, Shuxin Ren
Software Mentions: 2
Published: over 12 years ago

10.7554/eLife.47864

Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID
Cited by: 141
Author(s): Andrea Mair, Shan-Mei Xu, Tess C Branon, Alice Y. Ting, Dominique C. Bergmann
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12859-018-2579-2

NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors
Cited by: 119
Author(s): John Gaspar
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-8-452

Gene expression analysis reveals early changes in several molecular pathways in cerebral malaria-susceptible mice versus cerebral malaria-resistant mice
Cited by: 55
Author(s): Nicolas Nf Delahaye, Nicolas Coltel, Denis Puthier, Mathieu Barbier, P. Benech, Florence Joly, Fuad Fa Iraqi, Georges E. Grau, Catherine Nguyen, Pascal Rihet
Software Mentions: 2
Published: over 18 years ago

10.1186/s12864-018-4475-6

Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome
Cited by: 6
Author(s): Fedor Naumenko, Irina Abnizova, Nathan Beka, Mikhail A. Genaev, Yuriy L. Orlov
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0111581

MiRNA Expression May Account for Chronic but Not for Acute Regulation of mRNA Expression in Human Thyroid Tumor Models
Cited by: 9
Author(s): Sébastien Floor, Aline Hébrant, Jaime Miguel Gomes Pita, Manuel Saiselet, Christophe Trésallet, Frédérick Libert, Guy Andry, Jacques Emile Dumont, Wilma Van Staveren, Carine Maenhaut
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0067142

Layered Signaling Regulatory Networks Analysis of Gene Expression Involved in Malignant Tumorigenesis of Non-Resolving Ulcerative Colitis via Integration of Cross-Study Microarray Profiles
Cited by: 13
Author(s): Shengjun Fan, Zhenyu Pan, Qiang Geng, Xin Li, Yefan Wang, Yu An, Yan Xu, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 2
Published: about 13 years ago

10.1186/1752-0509-5-46

Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells
Cited by: 8
Author(s): Francisco Azuaje, Haiying Wang, Huiru Zheng, Frédérique Léonard, Magali Rolland-Turner, Lu Zhang, Yvan Devaux, Daniel R. Wagner
Software Mentions: 2
Published: over 15 years ago

10.18632/oncotarget.22131

<i>CD24</i>, <i>CD27</i>, <i>CD36</i> and <i>CD302</i> gene expression for outcome prediction in patients with multiple myeloma
Cited by: 20
Author(s): Elina Alaterre, Sébastien Raimbault, Hartmut Goldschmidt, Salahedine Bouhya, Guilhem Requirand, Robert Naeije, Stéphanie Boireau, Anja Seckinger, Dirk Hose, Bernard Klein, Jérôme Moreaux
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0091869

Upland Cotton Gene GhFPF1 Confers Promotion of Flowering Time and Shade-Avoidance Responses in Arabidopsis thaliana
Cited by: 21
Author(s): Xiaoyan Wang, Shuli Fan, Meizhen Song, Chaoyou Pang, Hengling Wei, Jie-Ae Yu, Qin Ma, Shuang Yu
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-14-310

A method to identify differential expression profiles of time-course gene data with Fourier transformation
Cited by: 12
Author(s): Jaehee Kim, R. Todd Ogden, Haseong Kim
Software Mentions: 2
Published: almost 13 years ago

10.1186/1752-0509-4-134

Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche
Cited by: 58
Author(s): Eugenio Azpeitia, Mariana Benítez, Iliusi Vega, Cuauhtémoc Calderón Villarreal, Elena Alvarez–Buylla
Software Mentions: 2
Published: almost 16 years ago

10.18632/oncotarget.27142

Development and analytical validation of a next-generation sequencing based microsatellite instability (MSI) assay
Cited by: 13
Author(s): Sarabjot Pabla, Jonathan Andreas, Felicia L. Lenzo, Blake Burgher, Jacob Hagen, Vincent Giamo, Mary Nesline, Yirong Wang, Mark Gardner, Jeffrey M. Conroy, Antonios Papanicolau‐Sengos, Carl Morrison, Sean T. Glenn
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2164-12-384

Temperature stress differentially modulates transcription in meiotic anthers of heat-tolerant and heat-sensitive tomato plants
Cited by: 96
Author(s): Craita E. Bita, Sara Zenoni, Wim H. Vriezen, Celestina Mariani, Mario Pezzotti, Tom Geräts
Software Mentions: 2
Published: almost 15 years ago

10.1111/jns.12228

Clinical and genetic diversities of Charcot-Marie-Tooth disease with<i>MFN2</i>mutations in a large case study
Cited by: 31
Author(s): Masahiro Ando, Akihiro Hashiguchi, Yuji Okamoto, Akinobu Yoshimura, Yoshihiro Hiramatsu, Jun‐Hui Yuan, Yujiro Higuchi, Jun Mitsui, Hiroyuki Ishiura, Atsushi Umemura, Koichi Maruyama, Takeshi Matsushige, Shinichi Morishita, Masanori Nakagawa, Shoji Tsuji, Hiroshi Takashima
Software Mentions: 2
Published: almost 9 years ago

10.3390/jpm4020282

Differential Transcriptome Profile of Peripheral White Cells to Identify Biomarkers Involved in Oxaliplatin Induced Neuropathy
Cited by: 9
Author(s): Manuel Morales, Julio Ávila, Rebeca González-Fernández, Laia Boronat, M L Soriano, Pablo Martín‐Vasallo
Software Mentions: 2
Published: about 12 years ago

10.1186/s12918-018-0653-z

Reframing gene essentiality in terms of adaptive flexibility
Cited by: 11
Author(s): Gabriela I. Guzmán, Connor A. Olson, Ying Hefner, Patrick V. Phaneuf, Edward Catoiu, Lais B. Crepaldi, Lucas Goldschmidt Micas, Bernhard Ø. Palsson, Adam M. Feist
Software Mentions: 2
Published: over 7 years ago

10.1186/1752-0509-7-14

Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties
Cited by: 51
Author(s): Yuanhua Liu, Valentina Devescovi, Suning Chen, Christine Nardini
Software Mentions: 2
Published: over 13 years ago

10.4172/jpb.1000384

Proteome Dynamics of the Specialist Oxalate Degrader Oxalobacter formigenes
Cited by: 13
Author(s): Mellissa L Ellis, James A. Mobley, Ross P. Holmes, John Knight
Software Mentions: 2
Published: over 10 years ago

10.4172/jpb.S9-001

Predicting Protein Model Quality from Sequence Alignments by Support Vector Machines
Cited by: 6
Author(s): Xin Deng, Jilong Li, Jianlin Cheng
Software Mentions: 2
Published: over 12 years ago

10.1016/j.jpsychores.2019.01.011

A longitudinal study on the effects of psychological stress on proteinuria in childhood steroid-sensitive nephrotic syndrome
Cited by: 10
Author(s): Lianne Bakkum, A.M. Willemen, Lydia Zoetebier, Antonia H. Bouts
Software Mentions: 2
Published: about 7 years ago

10.1186/s12859-020-3428-7

LCQS: an efficient lossless compression tool of quality scores with random access functionality
Cited by: 2
Author(s): Jiabing Fu, Bixin Ke, Sujun Dong
Software Mentions: 2
Published: over 6 years ago

10.1098/rsif.2014.1111

Micro- and nano-structural details of a spider's filter for substrate vibrations: relevance for low-frequency signal transmission
Cited by: 32
Author(s): Maxim Erko, Osnat Younes‐Metzler, Alexander Rack, Paul Zaslansky, Seth L. Young, Garrett Milliron, Marius Chyasnavichyus, Friedrich G. Barth, Peter Fratzl, Vladimir V. Tsukruk, Igor Zlotnikov, Yael Politi
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0092202

A Microarray-Based Analysis of Gametogenesis in Two Portuguese Populations of the European Clam Ruditapes decussatus
Cited by: 14
Author(s): Joana Sousa, Massimo Milan, Luca Bargelloni, Marianna Pauletto, Domitília Matias, Sandra Joaquim, Ana Margarete Matias, Virgile Quillien, Alexandra Leitão, Arnaud Huvet
Software Mentions: 2
Published: over 12 years ago

10.1186/1752-0509-7-S6-S12

Missing value imputation for microarray data: a comprehensive comparison study and a web tool
Cited by: 34
Author(s): Chia Chun Chiu, Shih Yao Chan, Chung Ching Wang, Wei Wu
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0000145

Heterologous Tissue Culture Expression Signature Predicts Human Breast Cancer Prognosis
Cited by: 8
Author(s): Eun Sung Park, Ju Seog Lee, Hyun Goo Woo, Fenghuang Zhan, Joanna H. Shih, John D. Shaughnessy, J. Frederic Mushinski
Software Mentions: 2
Published: over 19 years ago

10.1186/s12859-015-0705-y

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data
Cited by: 7
Author(s): Gregory K. Farrant, Mark Hoebeke, Frédéric Partensky, Gwendoline Andres, Matthieu Le Corre, Laurence Garczarek
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0091353

Natural Antisense Transcripts and Long Non-Coding RNA in Neurospora crassa
Cited by: 41
Author(s): Yamini Arthanari, Christian Heintzen, Sam Griffiths-Jones, Susan K. Crosthwaite
Software Mentions: 2
Published: over 12 years ago

10.1186/1479-5876-6-79

Aurora kinase inhibitors synergize with paclitaxel to induce apoptosis in ovarian cancer cells
Cited by: 61
Author(s): Christopher D. Scharer, Noelani Laycock, Adeboye O. Osunkoya, Sanjay Logani, John F. McDonald, Benedict B. Benigno, Carlos S. Moreno
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2105-10-198

A Bayesian approach to efficient differential allocation for resampling-based significance testing
Cited by: 6
Author(s): Shane T. Jensen, Sameer Soi, Li-San Wang
Software Mentions: 2
Published: about 17 years ago

10.1186/1752-0509-4-S2-S5

Shrunken methodology to genome-wide SNPs selection and construction of SNPs networks
Cited by: 7
Author(s): Yang Liu, Michael K. Ng
Software Mentions: 2
Published: almost 16 years ago

10.1186/1479-5876-4-29

Gene expression in acute Stanford type A dissection: a comparative microarray study
Cited by: 44
Author(s): Barbara Theresia Weis-Müller, Olga Modlich, Irina Drobinskaya, Derya Unay, Rita Huber, Hans Bojar, Jochen D. Schipke, P. Feindt, E. Gams, Wolfram Müller, Timm O. Goecke, W. Sandmann
Software Mentions: 2
Published: about 20 years ago

10.1186/1471-2105-7-106

A simple method for assessing sample sizes in microarray experiments
Cited by: 94
Author(s): Robert Tibshirani
Software Mentions: 2
Published: over 20 years ago

10.1186/s12918-018-0656-9

Analysis of significant protein abundance from multiple reaction-monitoring data
Cited by: 0
Author(s): Jongsu Jun, Jungsoo Gim, Yongkang Kim, Hyunsoo Kim, Su Jong Yu, Injun Yeo, Jiyoung Park, Jeong‐Ju Yoo, Young Youn Cho, Dong Hoon Lee, Eun Ju Cho, Jeong Hoon Lee, Yoon Jun Kim, Seungyeoun Lee, Jung Hwan Yoon, Youngsoo Kim, Taesung Park
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0215405

Large cortical bone pores in the tibia are associated with proximal femur strength
Cited by: 17
Author(s): Gianluca Iori, Johannes Schneider, Andreas Reisinger, Frans Heyer, Laura Peralta, Caroline E. Wyers, Melanie Gräsel, Reinhard Barkmann, Claus C. Glüer, Joop van den Bergh, Dieter H. Pahr, Kay Raum
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0006146

Molecular Profiling of Breast Cancer Cell Lines Defines Relevant Tumor Models and Provides a Resource for Cancer Gene Discovery
Cited by: 647
Author(s): Jennifer L. Kao, Keyan Salari, Melanie Bocanegra, Yoon‐La Choi, Luc Girard, Jeet Gandhi, Kevin Kwei, Tina Hernandez‐Boussard, Pei Wang, Adi F. Gazdar, John D. Minna, Jonathan R. Pollack
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0197539

Terrestrial mammal responses to oil palm dominated landscapes in Colombia
Cited by: 27
Author(s): Lain E. Pardo, Mason J. Campbell, Will Edwards, Gopalasamy Reuben Clements, William F. Laurance
Software Mentions: 2
Published: about 8 years ago

10.1186/1752-0509-4-136

Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks
Cited by: 77
Author(s): Monika Ray, Weixiong Zhang
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12937-018-0382-6

Severely malnourished children with a low weight-for-height have a higher mortality than those with a low mid-upper-arm-circumference: III. Effect of case-load on malnutrition related mortality– policy implications
Cited by: 9
Author(s): Emmanuel Grellety, Michael Golden
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12937-018-0384-4

Severely malnourished children with a low weight-for-height have a higher mortality than those with a low mid-upper-arm-circumference: I. Empirical data demonstrates Simpson’s paradox
Cited by: 23
Author(s): Emmanuel Grellety, Michael Golden
Software Mentions: 2
Published: almost 8 years ago

10.1007/s10456-016-9527-4

Identification of HIF-2α-regulated genes that play a role in human microvascular endothelial sprouting during prolonged hypoxia in vitro
Cited by: 40
Author(s): Tessa D. Nauta, Marloes van den Broek, S. Gibbs, Tineke C. T. M. van der Pouw‐Kraan, Cees B.M. Oudejans, Victor W.M. van Hinsbergh, Pieter Koolwijk
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-13-187

Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit
Cited by: 32
Author(s): Viviana Lima-Silva, Abel Rosado, Vítor Amorim‐Silva, Antonio Muñoz‐Mérida, Clara Pons, Aureliano Bombarely, Oswaldo Trelles, Rafael Fernández-Muñoz, Antonio Granell, Victoriano Valpuesta, Miguel A. Botella
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0012362

Profiling and Functional Analyses of MicroRNAs and Their Target Gene Products in Human Uterine Leiomyomas
Cited by: 65
Author(s): Jiří Zavadil, Huihui Ye, Zhaojian Liu, Jingjing Wu, Peng Lee, Eva Hernando, Patricia Soteropoulos, Gokce Toruner, Jian Jun Wei
Software Mentions: 2
Published: almost 16 years ago

10.3390/nu10091255

Lactobacillus acidophilus DDS-1 Modulates the Gut Microbiota and Improves Metabolic Profiles in Aging Mice
Cited by: 57
Author(s): Ravichandra Vemuri, Rajaraman Eri, Rohit Gundamaraju, Shakuntla Gondalia, Avinash V. Karpe, David J. Beale, Christopher Martoni, Rajaraman Eri
Software Mentions: 2
Published: almost 8 years ago

10.3390/nu9040390

Novel Genetic Variants Associated with Child Refractory Esophageal Stricture with Food Allergy by Exome Sequencing
Cited by: 1
Author(s): Min Yang, Min Xiong, Huan Chen, Lanlan Geng, Peiyu Chen, Jing Xie, Shui Qing Ye, Ding‐You Li, Sitang Gong
Software Mentions: 2
Published: over 9 years ago

10.3390/nu13062120

Untargeted Plasma Metabolomics Unravels a Metabolic Signature for Tissue Sensitivity to Glucocorticoids in Healthy Subjects: Its Implications in Dietary Planning for a Healthy Lifestyle
Cited by: 4
Author(s): Nicolas C. Nicolaides, Maria-Konstantina Ioannidi, Eleni Koniari, Ifigeneia Papageorgiou, Αnastasia Bartzeliotou, Amalia Sertedaki, Maria I. Klapa, Evangelia Charmandari
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0064829

Transcriptome Analysis Reveals New Insights into the Modulation of Endometrial Stromal Cell Receptive Phenotype by Embryo-Derived Signals Interleukin-1 and Human Chorionic Gonadotropin: Possible Involvement in Early Embryo Implantation
Cited by: 35
Author(s): Amélie Bourdiec, Ézéquiel Calvo, Ch.V. Rao, Ali Akoum
Software Mentions: 2
Published: about 13 years ago

10.18632/oncotarget.11754

A characteristic biosignature for discrimination of gastric cancer from healthy population by high throughput GC-MS analysis
Cited by: 42
Author(s): Yinan Chen, Jun Zhang, Li Guo, Lei Liu, Jingran Wen, Lu Xu, Min Yan, Zuofeng Li, Xiaoyan Zhang, Nan Peng, Jinling Jiang, Jun Ji, Jianian Zhang, Wei Cai, Huisheng Zhuang, Yan Wang, Zhenggang Zhu, Yingyan Yu
Software Mentions: 2
Published: almost 10 years ago

10.18632/oncotarget.13718

DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival
Cited by: 15
Author(s): Thomas Fleischer, Jovana Klajic, Miriam Ragle Aure, Riku Louhimo, Arne V. Pladsen, Lars Ottestad, Nizar Touleimat, Marko Laakso, Ann Rita Halvorsen, Grethe I.G. Alnæs, Margit Riis, Åslaug Helland, Sampsa Hautaniemi, Per Eystein Lønning, Bjørn Naume, Anne‐Lise Børresen‐Dale, Jörg Tost, Vessela N. Kristensen
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.1784

A<i>de novo</i>transcriptome of the Malpighian tubules in non-blood-fed and blood-fed Asian tiger mosquitoes<i>Aedes albopictus</i>: insights into diuresis, detoxification, and blood meal processing
Cited by: 45
Author(s): Carlos J. Esquivel, Bryan J. Cassone, Peter M. Piermarini
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.11931

A highly invasive subpopulation of MDA-MB-231 breast cancer cells shows accelerated growth, differential chemoresistance, features of apocrine tumors and reduced tumorigenicity<i>in vivo</i>
Cited by: 26
Author(s): Adriana Amaro, Giovanna Ángelini, Valentina Mirisola, Alba Esposito, Daniele Reverberi, Serena Matis, Massimo Maffei, Walter Giaretti, Maurizio Viale, Rosaria Gangemi, Laura Emionite, Simonetta Astigiano, Michele Cilli, Beatrice E. Bachmeier, Peter H. Killian, Adriana Albini, Ulrich Pfeffer
Software Mentions: 2
Published: almost 10 years ago

10.18632/oncotarget.11996

Differential expression analysis for individual cancer samples based on robust within-sample relative gene expression orderings across multiple profiling platforms
Cited by: 41
Author(s): Qingzhou Guan, Rou Chen, Haidan Yan, Hao Cai, You Guo, Mengyao Li, Xiangyu Li, Man‐Li Tong, Lu Ao, Hongdong Li, Hong Guan, Zheng Guo
Software Mentions: 2
Published: almost 10 years ago

10.18632/oncotarget.12624

LncRNA profile study reveals four-lncRNA signature associated with the prognosis of patients with anaplastic gliomas
Cited by: 57
Author(s): Wen Wang, Fan Yang, Lu Zhang, Jing Chen, Zheng Zhao, Haoyuan Wang, Fan Wu, Tingyu Liang, Xiaoyan Yan, Jiye Li, Qing Lan, Jiangfei Wang, Jizong Zhao
Software Mentions: 2
Published: almost 10 years ago

10.3390/ph4010007

GPCR Conformations: Implications for Rational Drug Design
Cited by: 16
Author(s): Abby L. Parrill, Debra L. Bautista
Software Mentions: 2
Published: over 15 years ago