cran: SAM | Projects | Ecosyste.ms: Papers

10.1186/1756-0500-6-43

Intra-platform comparison of 25-mer and 60-mer oligonucleotide Nimblegen DNA microarrays
Cited by: 3
Author(s): Stéphane Fénart, Malika Chabi, Sophie Gallina, Rudy Huis, Godfrey Neutelings, Nathalie Rivière, Brigitte Thomasset, Simon Hawkins, Anca Lucau-Danila
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-15-273

SNP Discovery for mapping alien introgressions in wheat
Cited by: 78
Author(s): Vijay K. Tiwari, Shichen Wang, Sunish K. Sehgal, Jan Vrána, Bernd Friebe, Marie Kubaláková, Praveen Chhuneja, Jaroslav Doležel, Eduard Akhunov, Bhanu Kalia, Jamal S. M. Sabir, Bikram S. Gill
Software Mentions: 1
Published: over 12 years ago

10.1186/s13104-016-2113-4

Thermodynamically optimal whole-genome tiling microarray design and validation
Cited by: 6
Author(s): Hyejin Cho, Hui‐Hsien Chou
Software Mentions: 1
Published: over 10 years ago

10.1186/1756-0500-7-360

Application of next generation sequencing to CEPH cell lines to discover variants associated with FDA approved chemotherapeutics
Cited by: 5
Author(s): Gunjan Hariani, Ernest J. Lam, Tammy M. Havener, Pui Yan Kwok, Howard L. McLeod, Michael J. Wagner, Alison A. Motsinger‐Reif
Software Mentions: 1
Published: over 12 years ago

10.1186/1756-0500-3-39

Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation
Cited by: 26
Author(s): Elizabeth A. Tindall, Desiree C. Petersen, Stina Nikolaysen, Webb Miller, Stephan C. Schuster, Vanessa M. Hayes
Software Mentions: 1
Published: over 16 years ago

10.1186/s12864-018-4636-7

Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423
Cited by: 24
Author(s): Hadrien Máté de Gérando, François Wasels, Angélique Bisson, Benjamin Clément, Frédérique Bidard, Etienne Jourdier, Ana M. López-Contreras, Nicolas Lopes Ferreira
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-15-180

Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution
Cited by: 38
Author(s): Biao Wang, Robert Ekblom, Ignas Bunikis, Heli Siitari, Jacob Höglund
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-14-315

Exploring the larval transcriptome of the common sole (Solea solea L.)
Cited by: 42
Author(s): Serena Ferraresso, Alessio Bonaldo, Luca Parma, Stefano Cinotti, Paola Massi, Luca Bargelloni, Pier Paolo Gatta
Software Mentions: 1
Published: over 13 years ago

10.1186/1756-0500-3-158

Animal Ca2+ release-activated Ca2+ (CRAC) channels appear to be homologous to and derived from the ubiquitous cation diffusion facilitators
Cited by: 18
Author(s): Madeleine Matias, Kenny M. Gomolplitinant, Dorjee G. Tamang, Milton H. Saier
Software Mentions: 1
Published: over 16 years ago

10.1038/srep17252

Impacts of IOD, ENSO and ENSO Modoki on the Australian Winter Wheat Yields in Recent Decades
Cited by: 64
Author(s): Chaoxia Yuan, Toshio Yamagata
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep18405

Identification of a highly efficient stationary phase promoter in Bacillus subtilis
Cited by: 49
Author(s): Xiaoxia Yu, XU Jiang-tao, Xiaoqing Liu, Xiaoyu Chu, Ping Wang, Jian Tian, Ningfeng Wu, Yanting Fan
Software Mentions: 1
Published: over 10 years ago

10.1038/srep17749

Comparative transcriptome analysis of grapevine in response to copper stress
Cited by: 96
Author(s): Xiangpeng Leng, Haifeng Jia, Xin Sun, Lingfei Shangguan, Qian Mei, Baoju Wang, Jinggui Fang
Software Mentions: 1
Published: over 10 years ago

10.1186/1756-0500-3-24

Non-coding RNAs change their expression profile after Retinoid induced differentiation of the promyelocytic cell line NB4
Cited by: 28
Author(s): Annalisa Rossi, Oscar Fernando D’Urso, Graziana Gatto, Palmiro Poltronieri, Manuela Ferracin, Paolo Remondelli, Massimo Negrini, Maria Gabriella Caporaso, Stefano Bonatti, Massimo Mallardo
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-13-500

Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing
Cited by: 22
Author(s): Abdou ElSharawy, Jason Warner, Jeff Olson, Michael Förster, Markus B. Schilhabel, Darren R. Link, Stefan Rose-John, Stefan Schreiber, Philip Rosenstiel, James Brayer, André Franke
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-8-87

Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise
Cited by: 40
Author(s): Harkamal Walia, Clyde Wilson, Pascal Condamine, Abdelbagi M. Ismail, Jin Xu, Xinping Cui, Timothy J. Close
Software Mentions: 1
Published: over 19 years ago

10.1186/s13104-019-4764-4

Reliability of crowdsourcing as a method for collecting emotions labels on pictures
Cited by: 6
Author(s): Olga Korovina, Marcos Báez, Fabio Casati
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13104-016-2296-8

Immunoassay of S-adenosylmethionine and S-adenosylhomocysteine: the methylation index as a biomarker for disease and health status
Cited by: 22
Author(s): Xiujuan Hao, Yan Huang, Ming Qiu, Chunlin Yin, Haiyan Ren, Hongjie Gan, Huijun Li, Yaxia Zhou, Jiazhi Xia, Wenting Li, Lijuan Guo, Isaac Angres
Software Mentions: 1
Published: almost 10 years ago

10.1523/ENEURO.0531-19.2020

The Neural Dynamics of Individual Differences in Episodic Autobiographical Memory
Cited by: 10
Author(s): Raluca Petrican, Daniela J. Palombo, Signy Sheldon, Brian Levine
Software Mentions: 1
Published: over 6 years ago

10.1186/2052-1847-6-6

Cardiac performance, biomarkers and gene expression studies in previously sedentary men participating in half-marathon training
Cited by: 8
Author(s): Danica D. Vance, Gordon L. Chen, Mark Stoutenberg, Robert J. Myerburg, Kevin A. Jacobs, Lubov Nathanson, Arlette C. Perry, David Seo, Pascal J. Goldschmidt‐Clermont, Evadnie Rampersaud
Software Mentions: 1
Published: over 12 years ago

10.1186/1472-6807-10-S1-S2

Prediction of protein long-range contacts using an ensemble of genetic algorithm classifiers with sequence profile centers
Cited by: 16
Author(s): Peng Chen, Jinyan Li
Software Mentions: 1
Published: over 16 years ago

10.1038/srep18775

Ultrasound-aided Multi-parametric Photoacoustic Microscopy of the Mouse Brain
Cited by: 70
Author(s): Bo Ning, Naidi Sun, Rui Cao, Ruimin Chen, K. Kirk Shung, John A. Hossack, Lee J, Qifa Zhou, Song Hu
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-021-07772-2

A two-way rectification method for identifying differentially expressed genes by maximizing the co-function relationship
Cited by: 0
Author(s): Bolin Chen, Li Gao, Xuequn Shang
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-13-S2-S4

Haplotype and minimum-chimerism consensus determination using short sequence data
Cited by: 19
Author(s): Shawn T. O’Neil, Scott J. Emrich
Software Mentions: 1
Published: over 14 years ago

10.1186/s12864-016-3377-8

Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency
Cited by: 9
Author(s): Desalegn D. Serba, Srinivasa Rao Uppalapati, Nick Krom, Shreyartha Mukherjee, Yuhong Tang, Kirankumar S. Mysore, Malay C. Saha
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep18796

Characterization of vegetative inflorescence (mc-vin) mutant provides new insight into the role of MACROCALYX in regulating inflorescence development of tomato
Cited by: 35
Author(s): Fernando J. Yuste‐Lisbona, Muriel Quinet, Antonia Fernández-Lozano, Benito Pineda, Vicente Moreno, Trinidad Angosto, Rafael Lozano
Software Mentions: 1
Published: over 10 years ago

10.1038/srep19264

Psmir: a database of potential associations between small molecules and miRNAs
Cited by: 17
Author(s): Fengyan Meng, Jing Wang, Erfu Dai, Feng Yang, Xiaowen Chen, Shuyuan Wang, Xuexin Yu, Dianming Liu, Wei Jiang
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2482-14-18

Use of human fibrin glue (Ti sseel) versus sta ples for mesh fixation in laparoscopic transabdominal preperitoneal hernioplasty (TISTA): a randomized controlled trial (NCT01641718)
Cited by: 2
Author(s): Sascha Müller, René Warschkow, Ulrich Beutner, Cornelia Lüthi, Kristjan Ukegjini, Bruno M. Schmied, Ignazio Tarantino
Software Mentions: 1
Published: over 12 years ago

10.1186/s12893-016-0126-5

Emergency radiological examination of the externally stabilized pelvis – there is a catch to it: lessons learned from two cases with symphyseal disruption despite initial inconspicuous computed tomography
Cited by: 3
Author(s): Jörg Bayer, Thorsten Hammer, Dirk Maier, Norbert P. Südkamp, Oliver Hauschild
Software Mentions: 1
Published: over 10 years ago

10.1186/1752-0509-5-2

Models of sequestration and receptor cross-talk for explaining multiple mutants in plant stem cell regulation
Cited by: 7
Author(s): Patrik Sahlin, Pontus Melke, Henrik Jönsson
Software Mentions: 1
Published: over 15 years ago

10.1186/1752-0509-5-52

A computational framework for gene regulatory network inference that combines multiple methods and datasets
Cited by: 33
Author(s): R. Gupta, Anna Stincone, Philipp Antczak, Sarah M. Durant, Roy Bicknell, Andréas Bikfalvi, Francesco Falciani
Software Mentions: 1
Published: over 15 years ago

10.1186/1752-0509-3-20

Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation
Cited by: 32
Author(s): Albert C. Huang, Limei Hu, Stuart Kauffman, Wei Zhang, Ilya Shmulevich
Software Mentions: 1
Published: over 17 years ago

10.1038/srep19260

Analysis of a four generation family reveals the widespread sequence-dependent maintenance of allelic DNA methylation in somatic and germ cells
Cited by: 12
Author(s): Aifa Tang, Yi Huang, Zesong Li, Shengqing Wan, Lisha Mou, Guangliang Yin, Ning Li, Jun Xie, Yudong Xia, Xianxin Li, Liya Luo, Junwen Zhang, Shen Chen, Song Wu, Jihua Sun, Xiaojuan Sun, Ziyu Jiang, Jing Chen, Yingrui Li, Jian Wang, Jun Wang, Zhiming Cai, Yaoting Gui
Software Mentions: 1
Published: over 10 years ago

10.1186/1752-0509-6-112

Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study
Cited by: 13
Author(s): Mohammed Alshalalfa, Gary D. Bader, Anna Goldenberg, Quaid Morris, Reda Alhajj
Software Mentions: 1
Published: over 14 years ago

10.1186/s12864-016-3405-8

Genome-wide expression profiling in muscle and subcutaneous fat of lambs in response to the intake of concentrate supplemented with vitamin E
Cited by: 20
Author(s): L. González-Calvo, Elda Dervishi, M. Joy, P. Sarto, Roberto Martín‐Hernández, M. Serrano, José M. Ordovás, J.H. Calvo
Software Mentions: 1
Published: over 9 years ago

10.1186/s12918-015-0215-6

Mathematical analysis of the regulation of competing methyltransferases
Cited by: 21
Author(s): Michael C. Reed, Mary V. Gamble, Megan N. Hall, H. Frederik Nijhout
Software Mentions: 1
Published: almost 11 years ago

10.1186/1752-0509-3-11

A Drosophila systems model of pentylenetetrazole induced locomotor plasticity responsive to antiepileptic drugs
Cited by: 26
Author(s): Farhan Mohammad, Priyanka Singh, Abhay Sharma
Software Mentions: 1
Published: over 17 years ago

10.1038/srep19272

Exposure to Polycyclic Aromatic Hydrocarbons, Plasma Cytokines and Heart Rate Variability
Cited by: 24
Author(s): Binyao Yang, Qifei Deng, Wangzhen Zhang, Yingying Feng, Xiayun Dai, Wei Feng, Xiaosheng He, Suli Huang, X Zhang, Xiaohai Li, Dafeng Lin, Meian He, Huan Guo, Huizhen Sun, Jing Yuan, Jiachun Lü, Frank B. Hu, Xiaomin Zhang, Tangchun Wu
Software Mentions: 1
Published: over 10 years ago

10.1186/1752-0509-7-S4-S1

A novel approach to minimize false discovery rate in genome-wide data analysis
Cited by: 2
Author(s): Yuanzhe Bei, Pengyu Hong
Software Mentions: 1
Published: over 13 years ago

10.1186/1752-0509-6-68

Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis
Cited by: 116
Author(s): Jihong Fu, Wentao Tang, Peng Du, Guanghui Wang, Wei Chen, Jingming Li, Yunxiang Zhu, Jun Gao, Long Cui
Software Mentions: 1
Published: about 14 years ago

10.1186/1752-0509-6-152

Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach
Cited by: 32
Author(s): Shengjun Fan, Qiang Geng, Zhenyu Pan, Xin Li, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 1
Published: almost 14 years ago

10.1038/srep19199

Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean
Cited by: 141
Author(s): Gunvant Patil, Tuyen Do, Tri D. Vuong, Babu Valliyodan, Jeong Dong Lee, Juhi Chaudhary, J. Grover Shannon, Henry T. Nguyen
Software Mentions: 1
Published: over 10 years ago

10.1038/srep19763

Phenotypic Characterization Analysis of Human Hepatocarcinoma by Urine Metabolomics Approach
Cited by: 34
Author(s): Qun Li, Han Liu, Cong Wang, Binbing Li
Software Mentions: 1
Published: over 10 years ago

10.1186/1752-0509-4-177

Individual vs. combinatorial effect of elevated CO2 conditions and salinity stress on Arabidopsis thaliana liquid cultures: Comparing the early molecular response using time-series transcriptomic and metabolomic analyses
Cited by: 52
Author(s): Harin Kanani, Bhaskar Dutta, Maria I. Klapa
Software Mentions: 1
Published: almost 16 years ago

10.1186/1752-0509-5-158

Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network
Cited by: 22
Author(s): Liu Hui, Jianzhong Su, Junhua Li, Hongbo Liu, Jie Lv, Boyan Li, Hong Qiao, Yan Zhang
Software Mentions: 1
Published: almost 15 years ago

10.1038/srep19616

The role of motility and chemotaxis in the bacterial colonization of protected surfaces
Cited by: 41
Author(s): Einat Shaer Tamar, Moriah Koler, Ady Vaknin
Software Mentions: 1
Published: over 10 years ago

10.1186/1752-0509-7-120

Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress
Cited by: 65
Author(s): Qinghua Wang, Keerthi P. Venkataramanan, Hongzhan Huang, Eleftherios T. Papoutsakis, Cathy H. Wu
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-8-153

Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates
Cited by: 67
Author(s): Fang Liu, Tor Kristian Jenssen, Jeffrey M. Trimarchi, Claudio Punzo, Connie Cepko, Lucila Ohno-Machado, Eivind Hovig, Winston Patrick Kuo
Software Mentions: 1
Published: over 19 years ago

10.1186/1752-0509-4-51

Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma
Cited by: 229
Author(s): Huiqing Liu, A. Rose Brannon, Anupama Reddy, Gabriela Alexe, Michael Seiler, Alexandra Arreola, Jay Oza, Ming Yao, David Juan, Louis S. Liou, Shridar Ganesan, Arnold J. Levine, W. Kimryn Rathmell, Gyan Bhanot
Software Mentions: 1
Published: over 16 years ago

10.1186/1752-0509-5-99

Integrative network analysis reveals active microRNAs and their functions in gastric cancer
Cited by: 79
Author(s): Chien Wei Tseng, Lin Chen, Chiung Nien Chen, Hsuan‐Cheng Huang, Hsueh‐Fen Juan
Software Mentions: 1
Published: about 15 years ago

10.18632/aging.100900

Altered lipid metabolism in the aging kidney identified by three layered omic analysis
Cited by: 45
Author(s): Fabian Braun, Markus M. Rinschen, Valerie Bartels, Peter Frommolt, Bianca Habermann, Jan H.J. Hoeijmakers, Björn Schumacher, Martijn E.T. Dollé, Roman‐Ulrich Müller, Thomas Benzing, Bernhard Schermer, Christine Kurschat
Software Mentions: 1
Published: over 10 years ago

10.1186/1752-0509-7-S2-S10

HSA: A Heuristic Splice Alignment Tool
Cited by: 7
Author(s): Jingde Bu, Xuebin Chi, Zhong Jin
Software Mentions: 1
Published: almost 13 years ago

10.1038/srep21542

Reactive oxygen species regulate leaf pulvinus abscission zone cell separation in response to water-deficit stress in cassava
Cited by: 49
Author(s): Wenbin Liao, Gan Wang, Yayun Li, Bin Wang, Peng Zhang, Ming Peng
Software Mentions: 1
Published: over 10 years ago

10.1186/1752-0509-8-S2-S8

A diVIsive Shuffling Approach (VIStA) for gene expression analysis to identify subtypes in Chronic Obstructive Pulmonary Disease
Cited by: 23
Author(s): Jörg Menche, Amitabh Sharma, Michael H. Cho, Ruth Mayer, Stephen I. Rennard, Bartolomé R. Celli, Bruce E. Miller, Nick Locantore, Ruth Tal‐Singer, Soumitra Ghosh, Chris Larminie, Glyn Bradley, John Riley, Àlvar Agustí, Edwin K. Silverman, Albert‐László Barabási
Software Mentions: 1
Published: over 12 years ago

10.1186/s12864-016-2416-9

Comparative transcriptome analysis of wheat embryo and endosperm responses to ABA and H2O2 stresses during seed germination
Cited by: 23
Author(s): Yonglong Yu, Shoumin Zhen, Wang Shu, Yaping Wang, Hui Cao, Yanzhen Zhang, Jiarui Li, Yueming Yan
Software Mentions: 1
Published: over 10 years ago

10.1038/srep22599

MiR-708 promotes steroid-induced osteonecrosis of femoral head, suppresses osteogenic differentiation by targeting SMAD3
Cited by: 79
Author(s): Hao Cheng, Shuai Yang, Weihua Xu, Jacson K. Shen, Shunan Ye, Xianzhe Liu, Zhe Dong, Bokui Xiao, Yong Feng
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-018-4582-4

Combining QTL-seq and linkage mapping to fine map a wild soybean allele characteristic of greater plant height
Cited by: 47
Author(s): Xiaoli Zhang, Wubin Wang, Na Guo, Youyi Zhang, Yuanpeng Bu, Jinming Zhao
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-11-265

Chronic activation of the epithelial immune system of the fruit fly's salivary glands has a negative effect on organismal growth and induces a peculiar set of target genes
Cited by: 14
Author(s): Ahmed Abdelsadik, Thomas Roeder
Software Mentions: 1
Published: over 16 years ago

10.1186/s12917-016-0904-4

A frameshift mutation in MOCOS is associated with familial renal syndrome (xanthinuria) in Tyrolean Grey cattle
Cited by: 12
Author(s): Leonardo Murgiano, Vidhya Jagannathan, Christian Piffer, Inmaculada Diez-Prieto, Marilena Bolcato, Arcangelo Gentile, Cord Drögemüller
Software Mentions: 1
Published: almost 10 years ago

10.1186/1746-6148-6-49

Ovine serum biomarkers of early and late phase scrapie
Cited by: 14
Author(s): Isabelle Batxelli-Molina, Nicolas Salvetat, Olivier Andréoletti, Luc Guerrier, Guillaume Vicat, Franck Molina, Chantal Mourton-Gilles
Software Mentions: 1
Published: over 16 years ago

10.1186/1746-6148-8-205

Transcriptomic markers meet the real world: finding diagnostic signatures of corticosteroid treatment in commercial beef samples
Cited by: 10
Author(s): Sara Pegolo, Guglielmo Gallina, Clara Montesissa, Francesca Capolongo, Serena Ferraresso, Caterina Pellizzari, Lisa Poppi, Massimo Castagnaro, Luca Bargelloni
Software Mentions: 1
Published: almost 14 years ago

10.1186/1746-6148-8-65

Evaluating observer agreement of scoring systems for foot integrity and footrot lesions in sheep
Cited by: 23
Author(s): Alessandro Foddai, Laura Green, Sarah Mason, Jasmeet Kaler
Software Mentions: 1
Published: over 14 years ago

10.1136/bmjgh-2020-002613

Long-term outcomes for children with disability and severe acute malnutrition in Malawi
Cited by: 8
Author(s): Natasha Lelijveld, Nora Groce, Seema Patel, Theresa Nnensa, Emmanuel Chimwezi, Melissa Gladstone, Macpherson Mallewa, Jonathan C. K. Wells, Andrew Seal, Marko Kerac
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-14-378

Transcriptional adaptation of pneumococci and human pharyngeal cells in the presence of a virus infection
Cited by: 13
Author(s): Sheila Z. Kimaro Mlacha, Teresa C. T. Peret, Nikhil Kumar, Sandra Romero-Steiner, Julie C. Dunning Hotopp, Nadeeza Ishmael, Valerie Grinblat-Huse, David R. Riley, Dean D. Erdman, George M. Carlone, Jacquelyn S. Sampson, J. Anthony G. Scott, Hervé Tettelin
Software Mentions: 1
Published: over 13 years ago

10.1038/srep23113

The importance of interacting climate modes on Australia’s contribution to global carbon cycle extremes
Cited by: 63
Author(s): James Cleverly, Derek Eamus, Qunying Luo, Natalia Restrepo‐Coupe, Natascha Kljun, Xuanlong Ma, Cäcilia Ewenz, Longhui Li, Qiang Yu, Alfredo Huete
Software Mentions: 1
Published: over 10 years ago

10.1186/bcr2913

Reversal of endocrine resistance in breast cancer: interrelationships among 14-3-3ζ, FOXM1, and a gene signature associated with mitosis
Cited by: 72
Author(s): Anna Bergamaschi, Barbara L. Christensen, Benita S. Katzenellenbogen
Software Mentions: 1
Published: over 15 years ago

10.1038/srep23083

Hemodynamic (fNIRS) and EEG (N200) correlates of emotional inter-species interactions modulated by visual and auditory stimulation
Cited by: 20
Author(s): Michela Balconi, Maria Elide Vanutelli
Software Mentions: 1
Published: over 10 years ago

10.1186/bcr3152

Gene expression in extratumoral microenvironment predicts clinical outcome in breast cancer patients
Cited by: 76
Author(s): Erick Román-Pérez, Patricia Casbas-Hernández, Jason R. Pirone, Jessica Rein, Lisa A. Carey, Ronald A. Lubet, Sendurai A. Mani, Keith D. Amos, Melissa A. Troester
Software Mentions: 1
Published: over 14 years ago

10.1186/bcr1506

The effect of the stromal component of breast tumours on prediction of clinical outcome using gene expression microarray analysis
Cited by: 66
Author(s): Susan Cleator, Trevor J. Powles, Tim Dexter, Laura Fulford, Alan Mackay, Ian Smith, Haukur Valgeirsson, Alan Ashworth, Mitch Dowsett
Software Mentions: 1
Published: over 20 years ago

10.1186/s12864-016-3136-x

Distinct transcriptome responses to water limitation in isohydric and anisohydric grapevine cultivars
Cited by: 43
Author(s): Silvia Dal Santo, Alberto Palliotti, Sara Zenoni, Giovanni Battista Tornielli, Marianna Fasoli, Paola Paci, Sergio Tombesi, Tommaso Frioni, O. Silvestroni, Andrea Bellincontro, Claudio D’Onofrio, Fabiola Matarese, Matteo Gatti, Stefano Poni, Mario Pezzotti
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-7-208

Cell organisation, sulphur metabolism and ion transport-related genes are differentially expressed in Paracoccidioides brasiliensis mycelium and yeast cells
Cited by: 17
Author(s): Rosângela Viana Andrade, Hugo Costa Paes, André Moraes Nicola, Maria José A. Carvalho, Ana Lúcia Fachin, Renato Cardoso, Simoneide S. Silva, Larissa Fernandes, Silvana P. Silva, Eduardo Antônio Donadi, Elza T. Sakamoto-Hojo, Geraldo A. S. Passos, C. M. A. Soares, Marcelo M. Brígido, Maria Sueli Soares Felipe
Software Mentions: 1
Published: about 20 years ago

10.1186/1471-2164-14-104

A highly expressed miR-101 isomiR is a functional silencing small RNA
Cited by: 93
Author(s): Franc Llorens, Mónica Báñez-Coronel, Lorena Pantano, José Antonio del Rı́o, Isidre Ferrer, Xavier Estivill, Eulàlia Martı́
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-15-1145

Genomic and transcriptomic differences in community acquired methicillin resistant Staphylococcus aureus USA300 and USA400 strains
Cited by: 18
Author(s): Marcus B. Jones, Christopher P. Montgomery, Susan Boyle-Vavra, Kenneth Shatzkes, Rosslyn Maybank, Bryan Frank, Scott N. Peterson, Robert S. Daum
Software Mentions: 1
Published: over 12 years ago

10.1038/srep23384

Higher-order Multivariable Polynomial Regression to Estimate Human Affective States
Cited by: 18
Author(s): Wei Jie, Tong Chen, Guangyuan Liu, Jiemin Yang
Software Mentions: 1
Published: over 10 years ago

10.1038/srep24052

Degradation Physics of High Power LEDs in Outdoor Environment and the Role of Phosphor in the degradation process
Cited by: 54
Author(s): Preetpal Singh, Cher Ming Tan
Software Mentions: 1
Published: over 10 years ago

10.1186/bcr3035

A clinically relevant gene signature in triple negative and basal-like breast cancer
Cited by: 283
Author(s): Achim Rody, Thomas Karn, Cornelia Liedtke, Lajos Pusztai, Eugen Ruckhaeberle, Lars Hanker, R. Gaetje, Christine Solbach, A. Ahr, Dirk Metzler, Marcus Schmidt, Volkmar Müller, Uwe Holtrich, M. Kaufmann
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-14-15

Saccharopolyspora erythraea’sgenome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch
Cited by: 25
Author(s): Esteban Marcellin, Tim R. Mercer, Cuauhtémoc Licona-Cassani, Robin W. Palfreyman, Marcel E. Dinger, Jennifer A. Steen, John S. Mattick, Lars K. Nielsen
Software Mentions: 1
Published: over 13 years ago

10.1186/s13058-021-01392-0

Molecular analyses of triple-negative breast cancer in the young and elderly
Cited by: 23
Author(s): Mattias Aine, Ceren Boyacı, Johan Hartman, Jari Häkkinen, Shamik Mitra, Ana Bosch Campos, Emma Niméus, Anna Ehinger, Johan Vallon‐Christersson, Åke Borg, Johan Staaf
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-1016

Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells
Cited by: 15
Author(s): Masahiro Tokunaga, Chikara Kokubu, Yusuke Maeda, Jun Sese, Kyoji Horie, Nakaba Sugimoto, Taroh Kinoshita, Kosuke Yusa, Junji Takeda
Software Mentions: 1
Published: almost 12 years ago

10.1186/bcr3344

Selective gene-expression profiling of migratory tumor cells in vivo predicts clinical outcome in breast cancer patients
Cited by: 124
Author(s): Antonia Patsialou, Yarong Wang, Juan Lin, Kathleen D. Whitney, Sumanta Goswami, Paraic A. Kenny, John S. Condeelis
Software Mentions: 1
Published: almost 14 years ago

10.1038/srep24236

Transcriptome Variability in Keratocystic Odontogenic Tumor Suggests Distinct Molecular Subtypes
Cited by: 7
Author(s): Shijia Hu, Kimon Divaris, Joel S. Parker, Ricardo Padilla, Valerie A. Murrah, J. Timothy Wright
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-016-3147-7

Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences
Cited by: 19
Author(s): Damarius S. Fleming, James E. Koltes, Eric R. Fritz-Waters, Max F. Rothschild, Carl J. Schmidt, C. M. Ashwell, Michael E. Persia, James M. Reecy, Susan J. Lamont
Software Mentions: 1
Published: almost 10 years ago

10.1186/bcr1771

Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas
Cited by: 531
Author(s): Bas Kreike, Marieke van Kouwenhove, Hugo M. Horlings, Britta Weigelt, Hans Peterse, Harry Bartelink, Marc J. van de Vijver
Software Mentions: 1
Published: almost 19 years ago

10.18632/aging.103441

Ovarian aging increases small extracellular vesicle CD81+ release in human follicular fluid and influences miRNA profiles
Cited by: 25
Author(s): Rosalia Battaglia, Paolo Musumeci, Marco Ragusa, Davide Barbagallo, Marina Scalia, Massimo Zimbone, Maria José Lo Faro, Placido Borzì, Paolo Scollo, Michele Purrello, Elena Maria Vento, Cinzia Di Pietro
Software Mentions: 1
Published: about 6 years ago

10.1186/bcr2142

The functional loss of the retinoblastoma tumour suppressor is a common event in basal-like and luminal B breast carcinomas
Cited by: 215
Author(s): Jason I. Herschkowitz, Xiaping He, Cheng Fan, Charles M. Perou
Software Mentions: 1
Published: about 18 years ago

10.1038/srep25274

Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth
Cited by: 12
Author(s): Patrícia Pečnerová, David Díez-del-Molino, Sergey Vartanyan, Love Dalén
Software Mentions: 1
Published: over 10 years ago

10.1007/s10549-021-06193-9

Clinical and genomic assessment of PD-L1 SP142 expression in triple-negative breast cancer
Cited by: 12
Author(s): Sung Gwe Ahn, Seon‐Kyu Kim, Jonathan H. Shepherd, Yoon Jin, Soong June Bae, Chungyeul Kim, Jeong Eon Lee, Charles M. Perou
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-015-2256-z

De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.)
Cited by: 29
Author(s): Liwu Zhang, Ray Ming, Jisen Zhang, Aifen Tao, Pingping Fang, Jianmin Qi
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-10-370

The steady-state transcriptome of the four major life-cycle stages of Trypanosoma cruzi
Cited by: 119
Author(s): Todd Minning, D. Brent Weatherly, James Atwood, Ron Orlando, Rick L. Tarleton
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-15-708

Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly
Cited by: 97
Author(s): Amit Deokar, Larissa Ramsay, Andrew Sharpe, Marwan Diapari, Anoop Sindhu, Kirstin E. Bett, Thomas D. Warkentin, Bunyamin Tar’an
Software Mentions: 1
Published: about 12 years ago

10.1093/bib/bbt045

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability
Cited by: 6
Author(s): Jing‐Woei Li, Dan Bolser, Magnus Manske, Federico M. Giorgi, Nikolay Vyahhi, Björn Usadel, Bernardo Clavijo, Ting‐Fung Chan, Nathalie Wong, Daniel R. Zerbino, Maria Victoria Schneider
Software Mentions: 1
Published: about 13 years ago

10.1038/srep25543

Evolved resistance to colistin and its loss due to genetic reversion in Pseudomonas aeruginosa
Cited by: 58
Author(s): Jiyoung Lee, Young Kyoung Park, Eun Seon Chung, In Young Na, Kwan Soo Ko
Software Mentions: 1
Published: over 10 years ago

10.1089/crispr.2018.0009

Three-Component Repurposed Technology for Enhanced Expression: Highly Accumulable Transcriptional Activators via Branched Tag Arrays
Cited by: 27
Author(s): Atsushi Kunii, Yoshihiro Hara, Mitsumasa Takenaga, Naoko Hattori, Takuya Fukazawa, Toshikazu Ushijima, Takashi Yamamoto, Tetsushi Sakuma
Software Mentions: 1
Published: almost 8 years ago

10.1155/2021/9936932

Whole Exome Sequencing Identifies Two Novel Mutations in a Patient with UC Associated with PSC and SSA
Cited by: 2
Author(s): Dong Wu, Dan Chen, Wen Shi, Wei Liu, Weixun Zhou, Jiaming Qian
Software Mentions: 1
Published: about 5 years ago

10.1155/2017/2945282

Readability and Suitability of COPD Consumer Information
Cited by: 3
Author(s): Kathryn Fullmann, David Blackburn, Mark Fenton, Holly Mansell
Software Mentions: 1
Published: over 9 years ago

10.1016/j.ccr.2007.02.015

The Differentiation and Stress Response Factor XBP-1 Drives Multiple Myeloma Pathogenesis
Cited by: 354
Author(s): Daniel R. Carrasco, Kumar Sukhdeo, Marina Protopopova, Raktim Sinha, Miriam Enos, Daniel E. Carrasco, Zheng Ma, Mala Mani, Joel M. Henderson, Geraldine S. Pinkus, Nikhil C. Munshi, James W. Horner, Elena Ivanova, Alexei Protopopov, Kenneth C. Anderson, Giovanni Tonon, Ronald A. DePinho
Software Mentions: 1
Published: over 19 years ago

10.1038/srep25397

Identification of side- and shear-dependent microRNAs regulating porcine aortic valve pathogenesis
Cited by: 40
Author(s): Swetha Rathan, Casey Jane Ankeny, Sivakkumar Arjunon, Zannatul Ferdous, Sandeep Kumar, Joan Fernández Esmerats, Jonathon Heath, Robert M. Nerem, Ajit P. Yoganathan, Hanjoong Jo
Software Mentions: 1
Published: over 10 years ago

10.1186/1475-2867-11-9

A 6-gene signature identifies four molecular subgroups of neuroblastoma
Cited by: 27
Author(s): Frida Abel, Daniel Dalevi, Maria Nethander, Rebecka Jörnsten, Katleen De Preter, Joëlle Vermeulen, Raymond L. Stallings, Per Kogner, John M. Maris, Staffan Nilsson
Software Mentions: 1
Published: over 15 years ago

10.1186/s12935-018-0547-6

Identification of four differentially methylated genes as prognostic signatures for stage I lung adenocarcinoma
Cited by: 15
Author(s): Weiming Luo, Zheng-Yu Wang, Zhang Xin
Software Mentions: 1
Published: over 8 years ago

10.1186/s12935-021-02127-z

Allele frequency deviation (AFD) as a new prognostic model to predict overall survival in lung adenocarcinoma (LUAD)
Cited by: 3
Author(s): Aisha Al-Dherasi, Yuwei Liao, Sultan Al-Mosaib, Rulin Hua, Yichen Wang, Ying Yu, Yu Zhang, Xuehong Zhang, Raeda Jalayta, Haithm Mousa, Abdullah Al-Danakh, Fawze Alnadari, Marwan Almoiliqy, Salem Baldi, Leming Shi, Dekang Lv, Chi Kong Li, Quentin Liu
Software Mentions: 1
Published: about 5 years ago

10.1002/cam4.1672

Molecular profiles of tumor contrast enhancement: A radiogenomic analysis in anaplastic gliomas
Cited by: 9
Author(s): Xing Liu, Yiming Li, Zimin Sun, Shaowu Li, Kai Wang, Xing Fan, Yuqing Liu, Lei Wang, Yinyan Wang, Tao Jiang
Software Mentions: 1
Published: about 8 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566