cran: SAM | Projects | Ecosyste.ms: Papers

10.1186/s12906-015-0672-x

Uygur Medicine Xipayi Kui Jie’an Affects Gene Expression profiles in intestinal tissue Lesions in a Rat Model of Ulcerative Colitis
Cited by: 6
Author(s): Kurexi Yunusi, Jingping Zhang, Li Zhong, Gulinisha Mosha, Ajiguli Nuermaimaiti, Mairipaiti Abudula, Halmurat Upur
Software Mentions: 1
Published: over 9 years ago

10.1186/s12906-018-2343-1

The effects of yoga and quiet rest on subjective levels of anxiety and physiological correlates: a 2-way crossover randomized trial
Cited by: 12
Author(s): Kembra Albracht‐Schulte, Jacalyn J. Robert-McComb
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-213X-8-21

Expression profiling of circulating non-red blood cells in embryonic blood
Cited by: 18
Author(s): Brendan A.S. McIntyre, Cantas Alev, Hiroshi Tarui, Lars Martin Jakt, Guojun Sheng
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-213X-9-5

Gene expression profiles during early differentiation of mouse embryonic stem cells
Cited by: 46
Author(s): Fiona C. Mansergh, Carl S. Daly, Anna L Hurley, Michael A. Wride, Susan Hunter, Martin Evans
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-213X-7-90

Alterations in transcript abundance of bovine oocytes recovered at growth and dominance phases of the first follicular wave
Cited by: 51
Author(s): Nasser Ghanem, Michael Hölker, F. Rings, Danyel Jennen, Ernst Tholen, Marc‐André Sirard, H. Torner, W. Kanitz, K. Schellander, Dawit Tesfaye
Software Mentions: 1
Published: over 17 years ago

10.1186/s12901-016-0029-1

Tinnitus- related distress: evidence from fMRI of an emotional stroop task
Cited by: 22
Author(s): Dennis Golm, Carsten Schmidt‐Samoa, Peter Dechent, Birgit Kröner‐Herwig
Software Mentions: 1
Published: almost 9 years ago

10.1186/1472-6785-11-5

Wildlife translocation: the conservation implications of pathogen exposure and genetic heterozygosity
Cited by: 22
Author(s): Walter M. Boyce, Mara E. Weisenberger, M. C. T. Penedo, Christine K. Johnson
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12862-021-01801-0

Molecular evolutionary analysis of human primary microcephaly genes
Cited by: 4
Author(s): Nashaiman Pervaiz, Hongen Kang, Yīmíng Bào, Amir Ali Abbasi
Software Mentions: 1
Published: over 3 years ago

10.1186/1472-6823-11-7

Gene-chip studies of adipogenesis-regulated microRNAs in mouse primary adipocytes and human obesity
Cited by: 110
Author(s): Pernille Keller, Valentina Gburcik, Nataša Petrović, Iain J. Gallagher, Jan Nedergaard, Barbara Cannon, James A. Timmons
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2148-7-S1-S12

FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function
Cited by: 48
Author(s): Nandini Krishnamurthy, D. Brown, Kimmen Sjölander
Software Mentions: 1
Published: almost 18 years ago

10.1186/s12862-015-0280-x

Looking for adaptive footprints in the HSP90AA1 ovine gene
Cited by: 9
Author(s): Judit Salces-Ortiz, Claudette Hajaj Gonzalez, Marta Rodriguez Martinez, T. Mayoral, J.H. Calvo, M. Serrano
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12862-015-0439-5

Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953
Cited by: 20
Author(s): Hiba Babiker, Diethard Tautz
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2148-11-113

Altered gene expression and ecological divergence in sibling allopolyploids of Dactylorhiza (Orchidaceae)
Cited by: 60
Author(s): Ovidiu Paun, Richard M. Bateman, Michael F. Fay, Javier A. Luna, Justin Moat, Mikael Hedrén, Mark W. Chase
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2148-9-276

Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)
Cited by: 205
Author(s): Einar Eg Nielsen, Jakob Hemmer‐Hansen, Nina Aagaard Poulsen, Volker Loeschcke, Thomas Moen, Torild Johansen, Christian Mittelholzer, Geir-Lasse Taranger, Rob Ogden, Gary R. Carvalho
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2148-8-313

Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates
Cited by: 33
Author(s): Stefano Campanaro, Laura Treu, Giorgio Valle
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2148-13-160

Localized versus generalist phenotypes in a broadly distributed tropical mammal: how is intraspecific variation distributed across disparate environments?
Cited by: 11
Author(s): Diego F. Alvarado‐Serrano, Lucía Luna, L. Lacey Knowles
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12862-015-0448-4

Past climate change on Sky Islands drives novelty in a core developmental gene network and its phenotype
Cited by: 34
Author(s): Marie-Julie Favé, Robert A. Johnson, Stefan P. Cover, Stephan Handschuh, Brian Metscher, Gerd B. Müller, Shyamalika Gopalan, Ehab Abouheif
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2148-8-190

Evolution of SET-domain protein families in the unicellular and multicellular Ascomycota fungi
Cited by: 39
Author(s): Chendhore S. Veerappan, Zoya Avramova, Etsuko N. Moriyama
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2148-14-147

Adaptive evolution and divergent expression of heat stress transcription factors in grasses
Cited by: 26
Author(s): Zefeng Yang, Yifan Wang, Yun Gao, Yong Zhou, Enying Zhang, Yunyun Hu, Yuan Yuan, Chenwu Xu
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-230X-7-24

Gene expression changes associated with Barrett's esophagus and Barrett's-associated adenocarcinoma cell lines after acid or bile salt exposure
Cited by: 14
Author(s): Hao Ying, Sumita Sood, George Triadafilopoulos, Jong Hyeok Kim, Zheng Wang, Peyman Sahbaie, M. Bishr Omary, Anson W. Lowe
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2156-6-S1-S5

Comparison of single-nucleotide polymorphisms and microsatellites in detecting quantitative trait loci for alcoholism: The Collaborative Study on the Genetics of Alcoholism
Cited by: 4
Author(s): Helen Kim, Carolyn M. Hutter, Stephanie A. Monks, Karen L. Edwards
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2156-10-7

Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean
Cited by: 51
Author(s): Lorraine Pariset, Stéphane Joost, Paolo Ajmone‐Marsan, Alessio Valentini
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12863-017-0546-y

LAIT: a local ancestry inference toolkit
Cited by: 5
Author(s): Daniel Hui, Zhou Fang, Jerome Lin, Qing Duan, Yun Li, Ming Hu, Wei Chen
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2164-6-81

Genome-wide localization of mobile elements: experimental, statistical and biological considerations
Cited by: 4
Author(s): Betsy Martinez‐Vaz, Yang Xie, Wei Pan, Arkady B. Khodursky
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2164-9-506

Changes induced by dietary energy intake and divergent selection for muscle fat content in rainbow trout (Oncorhynchus mykiss), assessed by transcriptome and proteome analysis of the liver
Cited by: 56
Author(s): Catherine Ines Kolditz, Gilles Pabœuf, Maïena Borthaire, Diane Esquerré, Magali SanCristobal, Florence Lefèvre, Françoise Médale
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2164-12-S3-S24

A robust tool for discriminative analysis and feature selection in paired samples impacts the identification of the genes essential for reprogramming lung tissue to adenocarcinoma
Cited by: 15
Author(s): Swee Heng Toh, Philip Prathipati, Efthimios Motakis, Chee Keong Kwoh, Surya Pavan Yenamandra, Vladimir A. Kuznetsov
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-15-849

Stage-specific differential gene expression in Leishmania infantum: from the foregut of Phlebotomus perniciosus to the human phagocyte
Cited by: 24
Author(s): Pedro J. Alcolea, Ana Alonso, Manuel J. Gómez, Marina Postigo, Ricardo Molina, Maribel Jiménez, Vicente Larraga
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-11-526

Comparative transcriptional profiling of the limbal epithelial crypt demonstrates its putative stem cell niche characteristics
Cited by: 72
Author(s): Bina Kulkarni, Patrick J. Tighe, Imran Mohammed, Aaron M. Yeung, Desmond G. Powe, Andrew Hopkinson, Vijay Shanmuganathan, Harminder S Dua
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2164-8-347

Abundance and functional diversity of riboswitches in microbial communities
Cited by: 54
Author(s): Marat D. Kazanov, Alexey G. Vitreschak, Mikhail S. Gelfand
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-13-306

Let-7b regulates the expression of the growth hormone receptor gene in deletion-type dwarf chickens
Cited by: 58
Author(s): Senjie Lin, Hongmei Li, Heping Mu, Wen Luo, Ying Li, Xiaoyun Jia, Sibing Wang, Xiaojun Jia, Qinghua Nie, Yugu Li, Xiquan Zhang
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-6-64

Gene expression profile of cervical tissue compared to exfoliated cells: Impact on biomarker discovery
Cited by: 22
Author(s): Martin Steinau, Daisy R. Lee, Mangalathu S. Rajeevan, Suzanne D. Vernon, Mack T. Ruffin, Elizabeth R. Unger
Software Mentions: 1
Published: over 19 years ago

10.1186/s12864-016-3003-9

De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies
Cited by: 32
Author(s): Mohaddeseh Mousavi, Chunfa Tong, Fenxiang Liu, Shentong Tao, Jiyan Wu, Huogen Li, Jisen Shi
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-017-3995-9

Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of sex-biased miRNA-mRNA pairs in gonad tissue of dark sleeper (Odontobutis potamophila)
Cited by: 29
Author(s): Cheng Zhao, Guosong Zhang, Shaowu Yin, Zecheng Li, Qintao Wang, Shuqiao Chen, Guoqin Zhou
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-019-5440-8

Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal
Cited by: 3
Author(s): David L. J. Vendrami, Jaume Forcada, Joseph I. Hoffman
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-020-07321-3

Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum
Cited by: 23
Author(s): Peng Xu, Qi Guo, Shu Meng, Xianggui Zhang, Zhenzhen Xu, Wangzhen Guo, Xinlian Shen
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2164-11-264

Global transcriptome analysis of spore formation in Myxococcus xanthus reveals a locus necessary for cell differentiation
Cited by: 61
Author(s): Frank-Dietrich Müller, Anke Treuner-Lange, Johann Heider, Stuart Huntley, Penelope I. Higgs
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-10-66

Differential gene expression in ADAM10 and mutant ADAM10 transgenic mice
Cited by: 34
Author(s): Claudia Prinzen, Dietrich Trümbach, Wolfgang Wurst, Kristina Endres, Rolf Postina, Falk Fahrenholz
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-7-47

Identification of rat lung – prominent genes by a parallel DNA microarray hybridization
Cited by: 22
Author(s): Zhongming Chen, Jiwang Chen, Tingting Weng, Nili Jin, Lin Liu
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-14-147

Comparison of the global gene expression of choroid plexus and meninges and associated vasculature under control conditions and after pronounced hyperthermia or amphetamine toxicity
Cited by: 21
Author(s): John F. Bowyer, Tucker A. Patterson, U.T. Saini, Joseph P. Hanig, M. Joy Thomas, Luísa Camacho, Nysia I. George, James J. Chen
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-12-160

Comparative transcriptome profiling of amyloid precursor protein family members in the adult cortex
Cited by: 41
Author(s): Dorothee Aydin, М. А. Филиппов, Jakob Andreas Tschäpe, Norbert Gretz, Marco Prinz, Roland Eils, Benedikt Brors, Ulrike Müller
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-019-5653-x

A cmap-enabled gene expression signature-matching approach identifies small-molecule inducers of accelerated cell senescence
Cited by: 10
Author(s): Duojie Wu, Brett Pepowski, Satoe Takahashi, Stephen J. Kron
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-5445-3

SQUAT: a Sequencing Quality Assessment Tool for data quality assessments of genome assemblies
Cited by: 29
Author(s): Li An Yang, Yu Jung Chang, Shu Hwa Chen, Chung Yen Lin, Jan Ming Ho
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-015-1387-6

Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level
Cited by: 61
Author(s): Christina A. Ahlstrom, Herman W. Barkema, Karen Stevenson, Ruth N. Zadoks, Roman Biek, Rowland R. Kao, Hannah Trewby, Deb Haupstein, D.F. Kelton, Gilles Fecteau, Olivia Labrecque, Greg Keefe, Shawn McKenna, Jeroen De Buck
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-10-482

Widespread variation in transcript abundance within and across developmental stages of Trypanosoma brucei
Cited by: 137
Author(s): Bryan C. Jensen, Dhileep Sivam, Charles T. Kifer, Peter J. Myler, Marilyn Parsons
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2164-7-234

Butyrate induces profound changes in gene expression related to multiple signal pathways in bovine kidney epithelial cells
Cited by: 92
Author(s): Robert W. Li, CongJun Li
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2164-7-231

Discovery and validation of breast cancer subtypes
Cited by: 118
Author(s): Amy V. Kapp, Stefanie S. Jeffrey, Anita Langerød, Anne Lise Børresen-Dale, Wonshik Han, Dong Young Noh, Ida Rashida Khan Bukholm, Monica Nicolau, Patrick O. Brown, Robert Tibshirani
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2164-14-S2-S9

Two-way AIC: detection of differentially expressed genes from large scale microarray meta-dataset
Cited by: 3
Author(s): Koki Tsuyuzaki, Daisuke Tominaga, Yeondae Kwon, Satoru Miyazaki
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-9-115

Arsenic-induced changes in the gene expression of lung epithelial L2 cells: implications in carcinogenesis
Cited by: 13
Author(s): Tisha Posey, Tingting Weng, Zhongming Chen, Narendranath Reddy Chintagari, Pengcheng Wang, Nili Jin, Heidi M. Stricker, Lin Liu
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-11-41

Deletions of Immunoglobulin heavy chain and T cell receptor gene regions are uniquely associated with lymphoid blast transformation of chronic myeloid leukemia
Cited by: 43
Author(s): Elisabeth P. Nacheva, Diana Brazma, Anna Virgili, Julie Howard-Reeves, Anastasios Chanalaris, K Gancheva, Margarita D. Apostolova, Mikel Valgañón, Helen Mazzullo, Colin Grace
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-12-475

Genome-wide examination of the transcriptional response to ecdysteroids 20-hydroxyecdysone and ponasterone A in Drosophila melanogaster
Cited by: 19
Author(s): Sarah E. Gonsalves, Scott J. Neal, Amy S Kehoe, J. Timothy Westwood
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-10-326

A comparison of RNA amplification techniques at sub-nanogram input concentration
Cited by: 28
Author(s): Julie E. Lang, Mark Jesus M. Magbanua, Janet H. Scott, G. Mike Makrigiorgos, Wang Gang, Scot Federman, Laura J. Esserman, John W. Park, Christopher M. Haqq
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-8-55

Microarray-based analysis of fish egg quality after natural or controlled ovulation
Cited by: 104
Author(s): Émilie Bonnet, Alexis Fostier, Julien Bobe
Software Mentions: 1
Published: almost 18 years ago

10.1186/s12864-017-4222-4

Subfunctionalization influences the expansion of bacterial multidrug antibiotic resistance
Cited by: 4
Author(s): Elena Perrin, Marco Fondi, Emanuele Bosi, Alessio Mengoni, Silvia Buroni, Viola Camilla Scoffone, Miguel A. Valvano, Renato Fani
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-018-4748-0

Randomized DNA libraries construction tool: a new 3-bp ‘frequent cutter’ TthHB27I/sinefungin endonuclease with chemically-induced specificity
Cited by: 2
Author(s): Daria Krefft, Aliaksei Papkov, Maciej Prusinowski, Agnieszka Żylicz-Stachula, Piotr M. Skowron
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-8-385

Five distinct biological processes and 14 differentially expressed genes characterize TEL/AML1-positive leukemia
Cited by: 57
Author(s): Virginie Gandemer, Anne-Gaëlle Rio, Marie de Tayrac, Vonnick Sibut, Stéphanie Mottier, Béatrice Ly Sunnaram, Cathérine Henry, Annabelle Monnier, Christian Berthou, E. Le Gall, A. Le Treut, Claudine Schmitt, Jean‐Yves Le Gall, Jean Mosser, Marie‐Dominique Galibert
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-8-25

Exploiting combinatorial cultivation conditions to infer transcriptional regulation
Cited by: 49
Author(s): Theo Knijnenburg, Johannes H. de Winde, Jean-Marc Daran, Pascale Daran‐Lapujade, Jack T. Pronk, Marcel J. T. Reinders, Lodewyk Wessels
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-8-323

Adaptive expression responses in the Pol-γ null strain of S. pombe depleted of mitochondrial genome
Cited by: 19
Author(s): Zhaoqing Chu, Juntao Li, Majid Eshaghi, R. Krishna Murthy Karuturi, Kui Lin, Jianhua Liu
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-8-420

Promoter analysis of intestinal genes induced during iron-deprivation reveals enrichment of conserved SP1-like binding sites
Cited by: 11
Author(s): James F. Collins, Zihua Hu
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-9-154

Comparative transcriptome analysis of Arabidopsis thaliana infested by diamond back moth (Plutella xylostella) larvae reveals signatures of stress response, secondary metabolism, and signalling
Cited by: 93
Author(s): Jürgen Ehlting, Sunita G. Chowrira, Nathalie Mattheus, Dana Aeschliman, Gen Ichiro Arimura, Jörg Bohlmann
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-9-199

Altered gene expression in the superior temporal gyrus in schizophrenia
Cited by: 68
Author(s): Nikola A. Bowden, Rodney J. Scott, Paul A. Tooney
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-12-69

Insights into the innate immunity of the Mediterranean mussel Mytilus galloprovincialis
Cited by: 155
Author(s): Paola Venier, L Varotto, Umberto Rosani, Caterina Millino, Barbara Celegato, Filippo Bernante, Gerolamo Lanfranchi, Beatriz Novoa, Philippe Roch, António Figueras, Alberto Pallavicini
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-11-730

Transcriptome analysis of grain-filling caryopses reveals involvement of multiple regulatory pathways in chalky grain formation in rice
Cited by: 72
Author(s): Xiaolu Liu, Tao Guo, Xiangyuan Wan, Haiyang Wang, Mingzhu Zhu, Aili Li, Ning Su, Yingyue Shen, Bigang Mao, Huqu Zhai, Long Mao, Jianmin Wan
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-15-892

Involvements of PCD and changes in gene expression profile during self-pruning of spring shoots in sweet orange (Citrus sinensis)
Cited by: 22
Author(s): Jin‐Zhi Zhang, Kun Zhao, Xiaoyan Ai, Chun-Gen Hu
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-015-1930-5

An improved genome reference for the African cichlid, Metriaclima zebra
Cited by: 60
Author(s): Matthew A. Conte, Thomas D. Kocher
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-015-1212-2

Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.)
Cited by: 78
Author(s): Rina Kamenetsky, Adi Faigenboim, Einat Shemesh Mayer, Tomer Ben Michael, Chen Gershberg, Sagie Kimhi, I. Esquira, Sarit Rohkin Shalom, Dani Eshel, Haim D. Rabinowitch, Amir Sherman
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-7-289

Gene expression patterns that predict sensitivity to epidermal growth factor receptor tyrosine kinase inhibitors in lung cancer cell lines and human lung tumors
Cited by: 71
Author(s): Justin M. Balko, Anil Potti, Christopher P. Saunders, Arnold J. Stromberg, Eric B. Haura, Esther P. Black
Software Mentions: 1
Published: about 18 years ago

10.1186/s12864-016-2873-1

Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?
Cited by: 15
Author(s): Lea Mette Madsen Sommer, Rasmus Lykke Marvig, Adela M. Luján, Anna Koza, Tacjana Pressler, Søren Molin, Helle Krogh Johansen
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-10-456

Transcriptomic and proteomic analyses of seasonal photoperiodism in the pea aphid
Cited by: 72
Author(s): Gaël Le Trionnaire, Frédéric Francis, Stéphanie Jaubert-Possamai, Joël Bonhomme, Edwin De Pauw, Jean-Pierre Gauthier, Éric Haubruge, Fabrice Legeai, Nathalie Prunier-Leterme, Jean Simon, Sylvie Tanguy, Denis Tagu
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2164-12-419

SAMQA: error classification and validation of high-throughput sequenced read data
Cited by: 14
Author(s): Thomas Robinson, Sarah Killcoyne, Ryan Bressler, John P. Boyle
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-8-296

cis sequence effects on gene expression
Cited by: 8
Author(s): Andrew W. Bergen, Andrea Baccarelli, Timothy K. McDaniel, Kenneth M. Kuhn, Ruth M. Pfeiffer, Jerry Kakol, Patrick K. Bender, Kevin B. Jacobs, Bernice Packer, Stephen J. Chanock, Meredith Yeager
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-7-115

Cell-type specific gene expression profiles of leukocytes in human peripheral blood
Cited by: 272
Author(s): Chana Palmer, Maximilian Diehn, Ash A. Alizadeh, Patrick O. Brown
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-11-272

Microarray analysis of Shigella flexneri-infected epithelial cells identifies host factors important for apoptosis inhibition
Cited by: 16
Author(s): Christina S. Faherty, D. Scott Merrell, Cristina Semino–Mora, A. Dubois, Aishwarya V. Ramaswamy, Anthony T. Maurelli
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-11-S5-S10

Decreasing the number of false positives in sequence classification
Cited by: 3
Author(s): Ariane Machado‐Lima, André Yoshiaki Kashiwabara, Alan Mitchell Durham
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-8-319

A Marfan syndrome gene expression phenotype in cultured skin fibroblasts
Cited by: 22
Author(s): Zizhen Yao, Jochen Jaeger, Walter L. Ruzzo, Cecile Z Morale, Mary J. Emond, Uta Francke, Dianna M. Milewicz, Stephen M. Schwartz, Eileen R. Mulvihill
Software Mentions: 1
Published: about 17 years ago

10.1186/s12864-019-5451-5

A global analysis of CNVs in diverse yak populations using whole-genome resequencing
Cited by: 29
Author(s): Hui Wang, Zhixin Chai, Dan Hu, Qiumei Ji, Jinwei Xin, Chengfu Zhang, Jincheng Zhong
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-15-419

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling
Cited by: 260
Author(s): Wei Zhao, Xiaping He, Katherine A. Hoadley, Joel S. Parker, D. Neil Hayes, Charles M. Perou
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-016-2521-9

Identification of mRNA isoform switching in breast cancer
Cited by: 24
Author(s): Wei Zhao, Katherine A. Hoadley, Joel S. Parker, Charles M. Perou
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-017-4032-8

Essential genome of Campylobacter jejuni
Cited by: 25
Author(s): Rabindra K. Mandal, Tieshan Jiang, Young Min Kwon
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-13-250

Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology
Cited by: 40
Author(s): Aran O’Loughlin, David J. Lynn, M. McGee, Seán Doyle, Matthew S. McCabe, Bernadette Earley
Software Mentions: 1
Published: over 12 years ago

10.1186/s12864-016-2845-5

Exposure to various abscission-promoting treatments suggests substantial ERF subfamily transcription factors involvement in the regulation of cassava leaf abscission
Cited by: 13
Author(s): Wenbin Liao, Yayun Li, Yiling Yang, Gan Wang, Ming Peng
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-13-S6-S8

A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis
Cited by: 24
Author(s): Jamiul Jahid, Jianhua Ruan
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-13-348

Identification of a radiosensitivity signature using integrative metaanalysis of published microarray data for NCI-60 cancer cells
Cited by: 108
Author(s): Han Sang Kim, Sang Cheol Kim, Sun Jeong Kim, Chan Hee Park, Hei‐Cheul Jeung, Yong Bae Kim, Joong Bae Ahn, Hyun Cheol Chung, Sun Young Rha
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-11-288

Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood
Cited by: 142
Author(s): Candida Vaz, Hafiz Ahmad, Pratibha Sharma, Rashi Gupta, Lalit Kumar, Ritu Kulshreshtha, Alok Bhattacharya
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-14-S6-S2

Semantic integration of gene expression analysis tools and data sources using software connectors
Cited by: 4
Author(s): Flavia Akemi Miyazaki, Gabriela D. A. Guardia, Ricardo Zorzetto Nicoliello Vêncio, Cléver Ricardo Guareis de Farias
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-016-2847-3

Genome-wide characterization of non-reference transposons in crops suggests non-random insertion
Cited by: 12
Author(s): Bin Wei, Hanmei Liu, Xin Liu, Qianlin Xiao, Yongbin Wang, Junjie Zhang, Yu‐Feng Hu, Yanping Liu, Guowu Yu, Yubi Huang
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-8-165

Cartilage-selective genes identified in genome-scale analysis of non-cartilage and cartilage gene expression
Cited by: 18
Author(s): Vincent Funari, Allen Day, Deborah Krakow, Zachary A. Cohn, Zugen Chen, Stanley F. Nelson, Daniel H. Cohn
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-8-376

Intrinsic androgen-dependent gene expression patterns revealed by comparison of genital fibroblasts from normal males and individuals with complete and partial androgen insensitivity syndrome
Cited by: 37
Author(s): Paul‐Martin Holterhus, Uta Deppe, Ralf Werner, Annette Richter‐Unruh, Jan-Hendrik Bebermeier, Lutz Wünsch, Susanne Krege, Hans‐Udo Schweikert, János Demeter, Felix G. Riepe, Olaf Hiort, James D. Brooks
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-10-10

A gene expression signature shared by human mature oocytes and embryonic stem cells
Cited by: 109
Author(s): Saïd Assou, Doris Cerecedo, Sylvie Tondeur, Véronique Pantesco, Outi Hovatta, Bernard Klein, S. Hamamah, John De Vos
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-11-31

Temperature increase prevails over acidification in gene expression modulation of amastigote differentiation in Leishmania infantum
Cited by: 57
Author(s): Pedro J. Alcolea, Ana Alonso, Manuel J. Gómez, Alicia Sánchez-Gorostiaga, Mercedes Moreno‐Paz, Eduardo González-Pastor, Alfredo Toraño, Vı́ctor Parro, Vicente Larraga
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-12-605

MicroRNA-mediated gene regulation plays a minor role in the transcriptomic plasticity of cold-acclimated Zebrafish brain tissue
Cited by: 33
Author(s): Ruolin Yang, Zhendong Dai, Shue Chen, Liangbiao Chen
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-5-47

A molecular 'signature' of primary breast cancer cultures; patterns resembling tumor tissue
Cited by: 60
Author(s): Shanaz H. Dairkee, Youngran Ji, Yong Ben, Dan H. Moore, Zhenhang Meng, Stefanie S. Jeffrey
Software Mentions: 1
Published: over 20 years ago

10.1186/1471-2164-15-S3-S2

Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data
Cited by: 56
Author(s): Maria Angela Diroma, Claudia Calabrese, Domenico Simone, Mariangela Santorsola, Francesco Maria Calabrese, Giuseppe Gasparre, Marcella Attimonelli
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-015-1309-7

REDHORSE-REcombination and Double crossover detection in Haploid Organisms using next-geneRation SEquencing data
Cited by: 5
Author(s): Jahangheer Shaik, Asis Khan, Stephen M. Beverley, L. David Sibley
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-11-248

Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum
Cited by: 72
Author(s): Ines Yang, Uwe John, Sára Beszteri, Gernot Glöckner, Bernd Krock, Alexander Goesmann, Allan Cembella
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-13-707

Insights into the regulation of human CNV-miRNAs from the view of their target genes
Cited by: 17
Author(s): Xudong Wu, Dinglin Zhang, Guohui Li
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-015-2120-1

Transcriptome profiling reveals that feeding wild zooplankton to larval Atlantic cod (Gadus morhua) influences suites of genes involved in oxidation-reduction, mitosis, and selenium homeostasis
Cited by: 15
Author(s): Matthew L. Rise, Jennifer R. Hall, Gordon W. Nash, Xi Xue, Marije Booman, Tomer Katan, A. Kurt Gamperl
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-8-438

Dynamic gene expression in fish muscle during recovery growth induced by a fasting-refeeding schedule
Cited by: 96
Author(s): Pierre‐Yves Rescan, Jérôme Montfort, Cécile Rallière, Aurélie Le Cam, Diane Esquerré, Karine Hugot
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-15-S10-S3

Identification of conserved and polymorphic STRs for personal genomes
Cited by: 8
Author(s): Chien‐Ming Chen, Chi Pong Sio, Yu Lu, Hao Teng Chang, Chaofang Hu, Tun‐Wen Pai
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-15-372

Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map
Cited by: 17
Author(s): Qiong Zhang, Leiting Li, Robert VanBuren, Yanling Liu, Mei Yang, Liming Xu, John E. Bowers, Caihong Zhong, Yuepeng Han, Shaohua Li, Ray Ming
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-11-98

Transcriptional profiling of Actinobacillus pleuropneumoniae during the acute phase of a natural infection in pigs
Cited by: 45
Author(s): Vincent Deslandes, Martine Denicourt, Christiane Girard, Josée Harel, John H. E. Nash, Mario Jacques
Software Mentions: 1
Published: almost 15 years ago

Projects: cran: SAM

Papers Mentioning SAM 4,566