Scientific Papers with Software Mentions

10.1186/2046-1682-5-4

APM_GUI: analyzing particle movement on the cell membrane and determining confinement
Cited by: 12
Author(s): Silvia Adriana Menchón, María Julia Martín, Carlos G. Dotti
Software Mentions: 1
Published: almost 13 years ago

10.1098/rspb.2017.1059

Offspring genes indirectly influence sibling and maternal behavioural strategies over resource share
Cited by: 19
Author(s): David G. Ashbrook, Naorin Sharmin, Reinmar Hager
Software Mentions: 1
Published: about 7 years ago

10.1186/1472-6750-7-57

Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA
Cited by: 79
Author(s): Karol L. Thompson, P. Scott Pine, Barry A. Rosenzweig, Yaron Turpaz, Jacques D. Retief
Software Mentions: 1
Published: almost 18 years ago

10.1186/s12978-020-01009-3

Looking beyond the numbers: quality assurance procedures in the Global Network for Women’s and Children’s Health Research Maternal Newborn Health Registry
Cited by: 5
Author(s): Ana Garcés, Emily MacGuire, Holly Franklin, Norma Alfaro, Gustavo Arroyo, Lester Figueroa, Shivaprasad S. Goudar, Sarah Saleem, Fabian Esamai, Archana Patel, Elwyn Chomba, Antoinette Tshefu, Rashidul Haque, Jacquelyn Patterson, Edward A. Liechty, Richard Derman, Waldemar A. Carlo, William A. Petri, Elizabeth M McClure, Robert L. Goldenberg, Patricia L. Hibberd, Nancy F. Krebs
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2407-8-19

Suppression subtractive hybridization profiles of radial growth phase and metastatic melanoma cell lines reveal novel potential targets
Cited by: 25
Author(s): Josane F. Sousa, Enilza Maria Espreáfico
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2407-7-64

Gene expression profiles of prostate cancer reveal involvement of multiple molecular pathways in the metastatic process
Cited by: 440
Author(s): Uma Chandran, Changqing Ma, Rajiv Dhir, Michelle Bisceglia, Maureen A. Lyons‐Weiler, Wenjing Liang, George K. Michalopoulos, Michael J. Becich, Federico A. Monzon
Software Mentions: 1
Published: over 17 years ago

10.1038/s41598-017-00587-w

Improving the Efficiency and Effectiveness of Community Detection via Prior-Induced Equivalent Super-Network
Cited by: 11
Author(s): Liang Yang, Di Jin, Dongxiao He, Huazhu Fu, Xiaochun Cao, Françoise Fogelman‐Soulié
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-13925-9

Reference genes validation in Phenacoccus solenopsis under various biotic and abiotic stress conditions
Cited by: 32
Author(s): Shashi Arya, Gourav Jain, Santosh Kumar Upadhyay, . Sarita, Harpal Singh, S. K. Dixit, Praveen Chandra Verma
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2407-6-224

Identification of genes associated with cisplatin resistance in human oral squamous cell carcinoma cell line
Cited by: 72
Author(s): Ping Zhang, Zhiyuan Zhang, Xin Zhou, Weimin Qiu, Fang-An Chen, Wantao Chen
Software Mentions: 1
Published: about 18 years ago

10.1186/s12885-015-1117-0

A functional in vitro model of heterotypic interactions reveals a role for interferon-positive carcinoma associated fibroblasts in breast cancer
Cited by: 13
Author(s): Abdel Hosein, Julie Livingstone, Marguerite Buchanan, James F. Reid, Michael Hallett, Mark Basik
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2407-9-206

Identification of proteins involved in neural progenitor cell targeting of gliomas
Cited by: 26
Author(s): Karin Staflin, Thole Züchner, Gabriella Honeth, Anna Darabi, Cecilia Lundberg
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2407-12-21

Gene expression in tumor cells and stroma in dsRed 4T1 tumors in eGFP-expressing mice with and without enhanced oxygenation
Cited by: 15
Author(s): Ingrid Moen, Charlotte Jevne, Jian Wang, Karl H. Kalland, Martha Chekenya, Lars A. Akslen, Linda Sleire, Per Øyvind Enger, Rolf K. Reed, Anne Margrete Øyan, Linda Elin Birkhaug Stuhr
Software Mentions: 1
Published: almost 13 years ago

10.1155/2014/540679

Gene Network Biological Validity Based on Gene-Gene Interaction Relevance
Cited by: 6
Author(s): Francisco Gómez-Vela, Norberto Díaz–Díaz
Software Mentions: 1
Published: almost 11 years ago

10.3390/s110201489

Estimating Three-Dimensional Orientation of Human Body Parts by Inertial/Magnetic Sensing
Cited by: 258
Author(s): A.M. Sabatini
Software Mentions: 1
Published: almost 14 years ago

10.3390/s20154237

Geometric Nonlinear Model for Prediction of Frequency–Temperature Behavior of SAW Devices for Nanosensor Applications
Cited by: 6
Author(s): Zhenglin Chen, Qiaozhen Zhang, Congcong Li, Sulei Fu, Xiaojun Qiu, Xiaoyu Wang, Haodong Wu
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2407-5-45

Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors
Cited by: 132
Author(s): Uma Chandran, Rajiv Dhir, Changqing Ma, George K. Michalopoulos, Michael J. Becich, John D. Gilbertson
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2407-14-120

A functional proteogenomic analysis of endometrioid and clear cell carcinomas using reverse phase protein array and mutation analysis: protein expression is histotype-specific and loss of ARID1A/BAF250a is associated with AKT phosphorylation
Cited by: 69
Author(s): Kimberly C. Wiegand, Bryan T. Hennessy, Samuel Leung, Yemin Wang, Ju Zhang, Mollianne J. McGahren, Steve E. Kalloger, Sarah Finlayson, Katherine Stemke-Hale, Yiling Lu, Fan Zhang, Michael S. Anglesio, Blake Gilks, Gordon B. Mills, David G. Huntsman, Mark Carey
Software Mentions: 1
Published: almost 11 years ago

10.3390/s21134556

Esophagus Segmentation in CT Images via Spatial Attention Network and STAPLE Algorithm
Cited by: 4
Author(s): Minh-Trieu Tran, Soo-Hyung Kim, Hyung-Jeong Yang, Guee-Sang Lee, Il‐Seok Oh, Sae-Ryung Kang
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2407-14-542

Identification of prognostic inflammatory factors in colorectal liver metastases
Cited by: 34
Author(s): Trevor D. Hamilton, Derek Leugner, Karen Kopciuk, Elijah Dixon, Francis Sutherland, Oliver F. Bathe
Software Mentions: 1
Published: over 10 years ago

10.1155/2021/5528160

Bayesian Fully Convolutional Networks for Brain Image Registration
Cited by: 5
Author(s): Kunpeng Cui, Panpan Fu, Yinghao Li, Yusong Lin
Software Mentions: 1
Published: over 3 years ago

10.1186/s12885-017-3421-3

miRNome landscape analysis reveals a 30 miRNA core in retinoblastoma
Cited by: 31
Author(s): Blanca Elena Castro-Magdonel, Manuela Orjuela, Javier Camacho, Adda Jeanette García-Chéquer, Lourdes Cabrera-Muñóz, Stanislaw Sadowinski-Pine, Noé Durán-Figueroa, María de Jesús Orozco-Romero, Ana Claudia Velázquez-Wong, Adriana Hernández-Ángeles, Claudia Hernández-Galván, Citlali Lara-Molina, M. Verónica Ponce-Castañeda
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.51061

Coordination of tissue cell polarity by auxin transport and signaling
Cited by: 53
Author(s): Carla Verna, Sree Janani Ravichandran, Megan G. Sawchuk, Nguyễn Mạnh Linh, Enrico Scarpella
Software Mentions: 1
Published: almost 5 years ago

10.18632/oncotarget.21243

Near-infrared photothermal therapy using anti-EGFR-gold nanorod conjugates for triple negative breast cancer
Cited by: 29
Author(s): Meihua Zhang, Hoe Suk Kim, Tiefeng Jin, Jisu Woo, Yin Ji Piao, Woo Kyung Moon
Software Mentions: 1
Published: about 7 years ago

10.1177/20556683211021527

Dartanan: Prototype evaluations of a serious game to engage children in the calibration of their hearing aid functionalities
Cited by: 1
Author(s): Madeline Hallewell, Davide Salanitri, Mirabelle D’Cruz, Sue Cobb, Lorenzo Picinali, Emily Frost, Stefano Tamascelli, Harshada Patel
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2407-9-425

Inverse correlation between PDGFC expression and lymphocyte infiltration in human papillary thyroid carcinomas
Cited by: 18
Author(s): Ove Bruland, Øystein Fluge, Lars A. Akslen, Hans Geir Eiken, Johan R. Lillehaug, Jan Erik Varhaug, Per M. Knappskog
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2407-9-365

A 7 gene expression score predicts for radiation response in cancer cervix
Cited by: 26
Author(s): Thangarajan Rajkumar, Neelakantan Vijayalakshmi, K.S. Sabitha, Shirley Sundersingh, Selvaluxmy Ganesarajah, Mayil Vahanan Bose, Lavanya Nambaru
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2407-12-310

Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome
Cited by: 29
Author(s): Manfred Beleut, Philip Zimmermann, Michael Baudis, Nicole Bruni, Peter Bühlmann, Oliver Laule, Van-Duc Luu, Wilhelm Gruissem, Peter Schraml, Holger Moch
Software Mentions: 1
Published: over 12 years ago

10.1002/mnfr.201900927

Mastiha (<i>Pistacia lentiscus</i>) Improves Gut Microbiota Diversity, Hepatic Steatosis, and Disease Activity in a Biopsy‐Confirmed Mouse Model of Advanced Non‐Alcoholic Steatohepatitis and Fibrosis
Cited by: 19
Author(s): Aimo Kannt, Efstathia Papada, Claire Kammermeier, Giuseppe D’Auria, Nuria Jiménez‐Hernández, Martin Stephan, Uwe Schwahn, Andreas Nygaard Madsen, Morten Østergaard, George Dedoussis, M. Pilar Francino
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2407-13-544

Study protocol: rehabilitation including social and physical activity and education in children and teenagers with cancer (RESPECT)
Cited by: 27
Author(s): Troels Thorsteinsson, Anne Sofie Helms, Lis Adamsen, Lars Bo Andersen, Karen Andersen, Karl Bang Christensen, Henrik Hasle, Carsten Heilmann, N Hejgaard, Christoffer Johansen, Mette Madsen, Svend Aage Madsen, Venka Simovska, Birgit Strange, Lone Friis Thing, Peder Skov Wehner, Kjeld Schmiegelow, Hanne Bækgaard Larsen
Software Mentions: 1
Published: about 11 years ago

10.1111/1365-2478.12883

Probing crustal anisotropy by receiver functions at the deep continental drilling site KTB in Southern Germany
Cited by: 4
Author(s): Irene Bianchi, Götz Bokelmann
Software Mentions: 1
Published: about 5 years ago

10.1186/s12885-015-1655-5

Essential role of miR-200c in regulating self-renewal of breast cancer stem cells and their counterparts of mammary epithelium
Cited by: 30
Author(s): Zhong-Ming Feng, Jun Qiu, Xiewan Chen, Rongxia Liao, Xian Liao, Luping Zhang, Chen Xu, Yan Li, Zhengtang Chen, Jianping Sun
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2407-14-648

Erythropoietin suppresses the activation of pro-apoptotic genes in head and neck squamous cell carcinoma xenografts exposed to surgical trauma
Cited by: 4
Author(s): Georg Lindgren, Lars Ekblad, Johan Vallon‐Christersson, Elisabeth Kjellén, Maria Gebre‐Medhin, Johan Wennerberg
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2407-7-84

Global gene expression analysis of the mouse colonic mucosa treated with azoxymethane and dextran sodium sulfate
Cited by: 63
Author(s): Rikako Suzuki, Shingo Miyamoto, Yumiko Yasui, Shigeyuki Sugie, Takuji Tanaka
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2407-8-189

TDAG51 is an ERK signaling target that opposes ERK-mediated HME16C mammary epithelial cell transformation
Cited by: 43
Author(s): Michael Oberst, Stacey J Beberman, Lei Zhao, Juan Juan Yin, Yvona Ward, Kathleen Kelly
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2407-6-105

SSeCKS/Gravin/AKAP12 attenuates expression of proliferative and angiogenic genes during suppression of v-Src-induced oncogenesis
Cited by: 24
Author(s): Yongzhong Liu, Lingqiu Gao, Irwin H. Gelman
Software Mentions: 1
Published: over 18 years ago

10.1186/s12885-015-1067-6

Identification of a novel microRNA signature associated with intrahepatic cholangiocarcinoma (ICC) patient prognosis
Cited by: 31
Author(s): Mei Yin Zhang, Shu Hong Li, Guo Liang Huang, Lin Guo, Ze Yu Shuang, Xiang-Ming Lao, Li Xu, Xiao Jun Lin, Hui Yun Wang, Sheng Ping Li
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12885-018-4993-2

MiR-10a and HOXB4 are overexpressed in atypical myeloproliferative neoplasms
Cited by: 9
Author(s): Pierre‐Yves Dumas, Olivier Mansier, Valérie Prouzet‐Mauléon, Junji Koya, Arnaud Villacreces, Philippe Brunet de la Grange, Damien Luque Paz, Audrey Bidet, Jean‐Max Pasquet, Vincent Perreten, Franck Salin, Mineo Kurokawa, François‐Xavier Mahon, Bruno Cardinaud, Éric Lippert
Software Mentions: 1
Published: about 6 years ago

10.1186/s12885-015-1907-4

Iroquois homeobox 2 suppresses cellular motility and chemokine expression in breast cancer cells
Cited by: 16
Author(s): Stefan Werner, Hauke Stamm, Mutiha Pandjaitan, Dirk Kemming, Benedikt Brors, Klaus Pantel, Harriet Wikman
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2407-13-119

Transcriptional effects of 1,25 dihydroxyvitamin D3physiological and supra-physiological concentrations in breast cancer organotypic culture
Cited by: 34
Author(s): Cíntia Mussi Milani, Maria Lúcia Hirata Katayama, Eduardo Carneiro de Lyra, Jo Ellen Welsh, Laura Tojeiro Campos, Maria Mitzi Brentani, Maria do Socorro Maciel, Rosimeire Aparecida Roela, Paulo Roberto Del Valle, João Carlos Guedes Sampaio Góes, Suely Nonogaki, Rodrigo Esaki Tamura, Maria Aparecida Azevedo Koike Folgueira
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2407-5-66

Differential gene expression profile reveals deregulation of pregnancy specific β1 glycoprotein 9 early during colorectal carcinogenesis
Cited by: 37
Author(s): Sima Salahshor, Jason Gonçalves, Runjan Chetty, Steven Gallinger, James R. Woodgett
Software Mentions: 1
Published: over 19 years ago

10.3390/nu7125523

A Historical Review of Changes in Nutrition Standards of USDA Child Meal Programs Relative to Research Findings on the Nutritional Adequacy of Program Meals and the Diet and Nutritional Health of Participants: Implications for Future Research and the Summer Food Service Program
Cited by: 31
Author(s): Laura Hopkins, Carolyn Gunther
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-9-98

A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy
Cited by: 21
Author(s): Xiangrong Kong, Valeria R. Mas, Kellie J. Archer
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-10-495

Transcriptome analysis of differentiating trypanosomes reveals the existence of multiple post-transcriptional regulons
Cited by: 132
Author(s): Rafael Queiroz, Corinna Benz, Kurt Fellenberg, Jörg D. Hoheisel, Christine Clayton
Software Mentions: 1
Published: about 15 years ago

10.1186/s12864-016-2558-9

A genome-wide expression profile analysis reveals active genes and pathways coping with phosphate starvation in soybean
Cited by: 18
Author(s): Qing Wang, Jiao Wang, Yuming Yang, Wenkai Du, Dan Zhang, Deyue Yu, Hao Cheng
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-8-29

Identification of rat lung-specific microRNAs by microRNA microarray: valuable discoveries for the facilitation of lung research
Cited by: 66
Author(s): Yang Wang, Tingting Weng, Deming Gou, Zhongming Chen, Narendranath Reddy Chintagari, Lin Liu
Software Mentions: 1
Published: almost 18 years ago

10.1186/s13102-021-00241-z

Systemic cross-talk between brain, gut, and peripheral tissues in glucose homeostasis: effects of exercise training (CROSSYS). Exercise training intervention in monozygotic twins discordant for body weight
Cited by: 1
Author(s): Marja A. Heiskanen, Sanna M. Honkala, Jaakko Hentilä, Ronja Ojala, Riikka Lautamäki, Kalle Koskensalo, Martin S. Lietzén, Virva Saunavaara, Jani Saunavaara, Mika Helmiö, Eliisa Löyttyniemi, Lauri Nummenmaa, María Carmen Collado, Tarja Malm, Leo Lahti, Kirsi H. Pietiläinen, Jaakko Kaprio, Juha O. Rinne, Jarna C. Hannukainen
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-16-S9-S2

A computational framework for the prioritization of disease-gene candidates
Cited by: 16
Author(s): Fiona Browne, Haiying Wang, Huiru Zheng
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-8-305

Genome-wide genetic aberrations of thymoma using cDNA microarray based comparative genomic hybridization
Cited by: 31
Author(s): Gui Youn Lee, Woo Ick Yang, Hei Cheul Jeung, Sang Chul Kim, Min Young Seo, Chan Hee Park, Hyun Cheol Chung, Sun Young Rha
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-13-663

Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties
Cited by: 64
Author(s): Ramasamy S Annadurai, Vasanthan Jayakumar, Raja C. Mugasimangalam, Mohan A. V. S. K. Katta, Sanchita Anand, Sreeja Gopinathan, Santosh Prasad Sarma, Sunjay Jude Fernandes, Nandita Mullapudi, M. Senthilkumar, Sudha Rao
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2164-8-384

A systems-biology analysis of isogenic megakaryocytic and granulocytic cultures identifies new molecular components of megakaryocytic apoptosis
Cited by: 19
Author(s): Chi Chen, Peter G. Fuhrken, Li Chi Huang, Pani A. Apostolidis, Min Wang, Carlos J. Paredes, William M. Miller, Eleftherios T. Papoutsakis
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-14-731

Reversible, interrelated mRNA and miRNA expression patterns in the transcriptome of Rasless fibroblasts: functional and mechanistic implications
Cited by: 11
Author(s): Sami Azrak, Alicia Ginel-Picardo, Matthias Drosten, Mariano Barbacid, Eugenio Santos
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2164-7-79

Whitefly (Bemisia tabaci) genome project: analysis of sequenced clones from egg, instar, and adult (viruliferous and non-viruliferous) cDNA libraries
Cited by: 83
Author(s): Dena Leshkowitz, S. Gazit, Eli Reuveni, Murad Ghanim, Henryk Czosnek, Cindy L. McKenzie, Robert G. Shatters, Judith K. Brown
Software Mentions: 1
Published: over 18 years ago

10.1186/s12864-020-06953-9

Physiological and transcriptomic responses of water spinach (Ipomoea aquatica) to prolonged heat stress
Cited by: 12
Author(s): R. S. Guo, Xingru Wang, Xiao Han, Xiao Chen, Gefu Wang‐Pruski
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-10-644

A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum
Cited by: 70
Author(s): Tarun Kumar Bhatt, Charu Kapil, Sameena Khan, Mohamad Aman Jairajpuri, Vinay Sharma, Daniele Santoni, Francesco Silvestrini, Elisabetta Pizzi, Amit Sharma
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-7-118

Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes
Cited by: 191
Author(s): Valerie W. Hu, Bryan Frank, Shannon J. Heine, Norman H. Lee, John Quackenbush
Software Mentions: 1
Published: over 18 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: over 10 years ago

10.3389/fnhum.2014.00825

Uncertainty in perception and the Hierarchical Gaussian Filter
Cited by: 255
Author(s): Christoph Mathys, Ekaterina I. Lomakina, Jean Daunizeau, Sandra Iglesias, Kay H. Brodersen, Karl J. Friston, Klaas Ε. Stephan
Software Mentions: 1
Published: about 10 years ago

10.1186/s13007-017-0172-8

TIPS: a system for automated image-based phenotyping of maize tassels
Cited by: 54
Author(s): Joseph L. Gage, Nathan D. Miller, Edgar P. Spalding, Shawn M. Kaeppler, Natalia de León
Software Mentions: 1
Published: over 7 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 9 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: about 8 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: about 10 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: almost 11 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: almost 12 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: over 18 years ago

10.1186/s12911-015-0236-5

Latitude-based approach for detecting aberrations of hand, foot, and mouth disease epidemics
Cited by: 7
Author(s): Jiahong Tang, Ta‐Chien Chan, Mika Shigematsu, Jing-Shiang Hwang
Software Mentions: 1
Published: almost 9 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 11 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: almost 15 years ago

10.1186/s12867-015-0049-1

Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells
Cited by: 12
Author(s): Yuan Lu, Jilong Li, Jianlin Cheng, Dennis B. Lubahn
Software Mentions: 1
Published: almost 9 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: almost 9 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 17 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: almost 8 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 8 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: almost 13 years ago

10.1038/s41416-018-0221-8

Hierarchical clustering of activated proteins in the PI3K and MAPK pathways in ER-positive, HER2-negative breast cancer with potential therapeutic consequences
Cited by: 15
Author(s): D.T. Kruger, Karin Beelen, Mark Opdam, Joyce Sanders, Vincent van der Noort, Epie Boven, Sabine C. Linn
Software Mentions: 1
Published: about 6 years ago

10.1186/s12934-020-01414-0

Deletion of pgi gene in E. coli increases tolerance to furfural and 5-hydroxymethyl furfural in media containing glucose–xylose mixture
Cited by: 14
Author(s): Syed Bilal Jilani, Chandra Dev, Danish Eqbal, Kamran Jawed, Rajendra Prasad, Syed Shams Yazdani
Software Mentions: 1
Published: over 4 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 3 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: almost 18 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: about 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: almost 12 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: almost 11 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 10 years ago

10.1186/1471-2164-12-405

Transcriptional responses to glucose in Saccharomyces cerevisiae strains lacking a functional protein kinase A
Cited by: 23
Author(s): Daniela Livas, Marinka J. H. Almering, Jean‐Marc Daran, Jack T. Pronk, Juana M. Gancedo
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0080146

Next-Generation Sequencing-Based Transcriptome Analysis of Helicoverpa armigera Larvae Immune-Primed with Photorhabdus luminescens TT01
Cited by: 26
Author(s): Zhen Zhao, Gongqing Wu, Jia Wang, Chunlin Li, Li-hong Qiu
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-10-292

Disorders of sex development expose transcriptional autonomy of genetic sex and androgen-programmed hormonal sex in human blood leukocytes
Cited by: 22
Author(s): Paul‐Martin Holterhus, Jan-Hendrik Bebermeier, Ralf Werner, János Demeter, Annette Richter‐Unruh, Gunnar Cario, Mahesh Appari, Reiner Siebert, Felix G. Riepe, James D. Brooks, Olaf Hiort
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12864-015-1277-y

Characterization of a novel RXR receptor in the salmon louse (Lepeophtheirus salmonis, Copepoda) regulating growth and female reproduction
Cited by: 17
Author(s): Christiane Eichner, Sussie Dalvin, Rasmus Skern‐Mauritzen, Ketil Malde, Heidi Kongshaug, Frank Nilsen
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-15-346

Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars
Cited by: 29
Author(s): Jun‐ichi Yonemaru, Ritsuko Mizobuchi, Hiroshi Katô, Tetsuro Yamamoto, Eiji Yamamoto, Kazuki Matsubara, Hideyuki Hirabayashi, Yoshinobu Takeuchi, Hiroshi Tsunematsu, Takuro Ishii, Hiroto Ohta, Hideo Maeda, Kaworu Ebana, Masahiro Yano
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-11-354

Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity
Cited by: 35
Author(s): Serena Ferraresso, Massimo Milan, Caterina Pellizzari, Nicola Vitulo, Richard Reinhardt, Adelino V.M. Canário, Tomaso Patarnello, Luca Bargelloni
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0240435

Experimental study of hypoxia-induced changes in gene expression in an Asian pika, Ochotona dauurica
Cited by: 5
Author(s): Katherine A. Solari, Elizabeth A. Hadly
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2164-10-404

Streptococcus pneumoniae nasopharyngeal colonization induces type I interferons and interferon-induced gene expression
Cited by: 42
Author(s): Elizabeth A. Joyce, Stephen J. Popper, Stanley Falkow
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0103450

Phytophthora ×stagnum nothosp. nov., a New Hybrid from Irrigation Reservoirs at Ornamental Plant Nurseries in Virginia
Cited by: 28
Author(s): Xiao Yang, Patricia A. Richardson, Chuanxue Hong
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-14-589

Impact of microRNAs on regulatory networks and pathways in human colorectal carcinogenesis and development of metastasis
Cited by: 136
Author(s): Silvia Pizzini, Andrea Bisognin, Susanna Mandruzzato, M. Biasiolo, Arianna Facciolli, Lisa Perilli, Elisabetta Rossi, Giovanni Esposito, Massimo Rugge, Pierluigi Pilati, Simone Mocellin, Donato Nitti, Stefania Bortoluzzi, Paola Zanovello
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0091440

DNA Methylation Biomarkers Predict Progression-Free and Overall Survival of Metastatic Renal Cell Cancer (mRCC) Treated with Antiangiogenic Therapies
Cited by: 42
Author(s): Inga Peters, Natalia Dubrowinskaja, Mahmoud Abbas, Christoph Seidel, Michael Kogosov, Ralph Scherer, Kai Gebauer, Axel S. Merseburger, Markus A. Kuczyk, Viktor Grünwald, Jürgen Serth
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0075963

Progressive Retinal Degeneration and Glial Activation in the CLN6nclf Mouse Model of Neuronal Ceroid Lipofuscinosis: A Beneficial Effect of DHA and Curcumin Supplementation
Cited by: 55
Author(s): Myriam Mirza, Cornelia Volz, Marcus Karlstetter, Monica Langiu, Aleksandra Somogyi, Mika O. Ruonala, Ernst R. Tamm, Herbert Jägle, Thomas Langmann
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2164-13-S8-S9

BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data
Cited by: 6
Author(s): Yuan Yuan, Clift Norris, Yanxun Xu, Kam Wah Tsui, Yuan Ji, Han Liang
Software Mentions: 1
Published: almost 12 years ago

10.1242/dev.148494

A systems level approach reveals new gene regulatory modules in the developing ear
Cited by: 27
Author(s): Jingchen Chen, Monica Tambalo, Meyer Barembaum, Ramya Ranganathan, Marcos Simões-Costa, Marianne Bronner‐Fraser, Andrea Streit
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-8-281

Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis
Cited by: 174
Author(s): Yong‐Mei Bi, Rong-Lin Wang, Tong Zhu, Steven J. Rothstein
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-12-381

Combined analysis of transcriptome and metabolite data reveals extensive differences between black and brown nearly-isogenic soybean (Glycine max) seed coats enabling the identification of pigment isogenes
Cited by: 39
Author(s): Nik Kovinich, Ammar Saleem, John T. Arnason, Brian Miki
Software Mentions: 1
Published: over 13 years ago

10.1289/ehp.1510385

Systems Toxicology of Male Reproductive Development: Profiling 774 Chemicals for Molecular Targets and Adverse Outcomes
Cited by: 49
Author(s): Maxwell C.K. Leung, Jimmy Phuong, Nancy C. Baker, Nisha S. Sipes, Gary R. Klinefelter, Matthew T. Martin, Keith W. McLaurin, R. Woodrow Setzer, Sally Perreault Darney, Richard S. Judson, Thomas B. Knudsen
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-015-1524-2

Microarray: a global analysis of biomineralization-related gene expression profiles during larval development in the pearl oyster, Pinctada fucata
Cited by: 45
Author(s): Jun Li, Dong Yang, Shiting Liu, Shiguo Li, Guangrui Xu, Guilan Zheng, Liping Xie, Rongqing Zhang
Software Mentions: 1
Published: over 9 years ago

10.1186/s13072-017-0168-7

Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads
Cited by: 44
Author(s): Laia Ribas, Konstantinos Vanezis, Marco Antonio Imués, Francesc Piferrer
Software Mentions: 1
Published: almost 7 years ago