cran: SAM | Projects | Ecosyste.ms: Papers

10.1093/bioinformatics/btv098

Sambamba: fast processing of NGS alignment formats
Cited by: 1,278
Author(s): А. В. Тарасов, Albert J. Vilella, Edwin Cuppen, Isaäc J. Nijman, Pjotr Prins
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-016-3402-y

An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.)
Cited by: 24
Author(s): Ye Jiang, Yuhua Yang, Bin Chen, Jiaqin Shi, Meizhong Luo, Jiasui Zhan, Xinfa Wang, Guihua Liu, Hanzhong Wang
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-11-400

Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes
Cited by: 26
Author(s): Amit Zeisel, Amir Almasi‐Hashiani, Wolfgang J. Köstler, Eytan Domany
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2164-11-85

MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori
Cited by: 59
Author(s): Shiping Liu, Song Gao, Danyu Zhang, Jiyun Yin, Xiang Zhang, Qingyou Xia
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-15-S9-S12

ARYANA: Aligning Reads by Yet Another Approach
Cited by: 0
Author(s): Milad Gholami, Aryan Arbabi, Ali Sharifi-Zarchi, Hamidreza Chitsaz, Mehdi Sadeghi
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2105-7-99

Determination of strongly overlapping signaling activity from microarray data
Cited by: 26
Author(s): Ghislain Bidaut, Karsten Suhre, Jean‐Michel Claverie, Michael F. Ochs
Software Mentions: 1
Published: over 20 years ago

10.1186/1471-2164-9-225

Comparative analysis of transcriptional profiling of CD3+, CD4+ and CD8+ T cells identifies novel immune response players in T-Cell activation
Cited by: 84
Author(s): Min Wang, Dirk Windgassen, Eleftherios T. Papoutsakis
Software Mentions: 1
Published: about 18 years ago

10.1186/s12864-015-1544-y

Mutations upstream of fabI in triclosan resistant Staphylococcus aureus strains are associated with elevated fabI gene expression
Cited by: 17
Author(s): Denis Grandgirard, Leonardo Furi, Maria Laura Ciusa, Lucilla Baldassarri, Daniel R. Knight, Ian Morrissey, Carlo R. Largiadèr, Stephen L. Leib, Marco R. Oggioni
Software Mentions: 1
Published: about 11 years ago

10.1093/bioinformatics/bty408

PANDA-view: an easy-to-use tool for statistical analysis and visualization of quantitative proteomics data
Cited by: 25
Author(s): Cheng Chang, Kaikun Xu, Chaoping Guo, Wang Jin-xia, Qi Yan, Jian Zhang, Fuchu He, Yunping Zhu
Software Mentions: 1
Published: about 8 years ago

10.1093/bioinformatics/btu390

The Scramble conversion tool
Cited by: 39
Author(s): James K. Bonfield
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2164-9-54

Glioma cells on the run – the migratory transcriptome of 10 human glioma cell lines
Cited by: 59
Author(s): Tim Demuth, Jessica L. Rennert, Dominique B. Hoelzinger, Linsey B. Reavie, Mitsutoshi Nakada, Christian Beaudry, Satoko Nakada, Eric M. Anderson, Amanda Henrichs, Wendy S. McDonough, David R. Holz, Anna Joy, Richard Lin, Kuang Hung Pan, Chih Jian Lih, Stan N Cohen, Michael E. Berens
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-8-85

Gene function in early mouse embryonic stem cell differentiation
Cited by: 129
Author(s): Kagnew Hailesellasse Sene, Christopher J. Porter, Gareth Palidwor, Carolina Perez‐Iratxeta, Enrique M. Muro, Pearl A. Campbell, Michael A. Rudnicki, Miguel A. Andrade‐Navarro
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2105-16-S18-S5

Analysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data
Cited by: 7
Author(s): Kouichi Kimura, Atsushi Koike
Software Mentions: 1
Published: over 10 years ago

10.1038/srep33297

Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development
Cited by: 63
Author(s): Niraj Khemka, Vikash Singh, Rohini Garg, Mukesh Jain
Software Mentions: 1
Published: almost 10 years ago

10.1093/bioinformatics/btt601

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop
Cited by: 82
Author(s): André Schumacher, Luca Pireddu, Matti Niemenmaa, Aleksi Kallio, Eija Korpelainen, Gianluigi Zanetti, Keijo Heljanko
Software Mentions: 1
Published: almost 13 years ago

10.3390/ijms21103661

Synthetic Strategies and Computational Inhibition Activity Study for Triazinyl-Substituted Benzenesulfonamide Conjugates with Polar and Hydrophobic Amino Acids as Inhibitors of Carbonic Anhydrases
Cited by: 8
Author(s): Mária Bodnár Mikulová, Dáša Kružlicová, Daniel Pecher, Claudiu T. Supuran, Peter Mikuš
Software Mentions: 1
Published: about 6 years ago

10.1111/acel.13029

Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice
Cited by: 16
Author(s): Jaime M. Ross, Giuseppe Coppotelli, Rui M. Branca, Kyung Mi Kim, Janne Lehtiö, David Sinclair, Lar̀s Olson
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-8-94

Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation
Cited by: 40
Author(s): Carl Trygve Stansberg, Audun Osland Vik‐Mo, Rita Holdhus, Harald Breilid, Boleslaw Srebro, Kjell Petersen, Hugo A. Jørgensen, Inge Jonassen, Vidar M. Steen
Software Mentions: 1
Published: over 19 years ago

10.1038/srep34941

Genome scans for divergent selection in natural populations of the widespread hardwood species Eucalyptus grandis (Myrtaceae) using microsatellites
Cited by: 15
Author(s): Zexing Song, Miaomiao Zhang, Fagen Li, Qijie Weng, Chanpin Zhou, Li Mei, Jie Li, Huanhua Huang, Xiaoyong Mo, Gan Shen
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-14-504

REACTIN: Regulatory activity inference of transcription factors underlying human diseases with application to breast cancer
Cited by: 20
Author(s): Mingzhu Zhu, Chun-Chi Liu, Chao Cheng
Software Mentions: 1
Published: about 13 years ago

10.1093/bioinformatics/bts456

YAHA: fast and flexible long-read alignment with optimal breakpoint detection
Cited by: 63
Author(s): Gregory G. Faust, Ira M. Hall
Software Mentions: 1
Published: about 14 years ago

10.1186/s12864-018-4445-z

EOGD: the Euplotes octocarinatus genome database
Cited by: 13
Author(s): Ruanlin Wang, Wei Miao, Wei Wang, Jie Xiong, Aihua Liang
Software Mentions: 1
Published: over 8 years ago

10.1007/s00422-013-0574-2

Revealing instances of coordination among multiple cortical areas
Cited by: 10
Author(s): Moshe Abeles
Software Mentions: 1
Published: over 12 years ago

10.1038/srep35664

HER2-encoded mir-4728 forms a receptor-independent circuit with miR-21-5p through the non-canonical poly(A) polymerase PAPD5
Cited by: 16
Author(s): Inga Newie, Rolf Søkilde, Helena Persson, Thiago Jacomasso, Andrej Gorbatenko, Åke Borg, Michiel de Hoon, Stine Falsig Pedersen, Carlos Rovira
Software Mentions: 1
Published: almost 10 years ago

10.1186/1745-6150-6-50

Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome
Cited by: 46
Author(s): Manfredo J. Seufferheld, Kyung Mo Kim, James B. Whitfield, Alejandro A. Valerio, Gustavo Caetano‐Anollés
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-7-69

Specific age related signatures in Drosophila body parts transcriptome
Cited by: 97
Author(s): Fabrice Girardot, Christelle Lasbleiz, Véronique Monnier, Hervé Tricoire
Software Mentions: 1
Published: over 20 years ago

10.1186/1471-2164-12-37

The sex-biased brain: sexual dimorphism in gene expression in two species of songbirds
Cited by: 60
Author(s): Sara Naurin, Bengt Hansson, Dennis Hasselquist, Yong Hwan Kim, Staffan Bensch
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-10-398

Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress
Cited by: 47
Author(s): Harkamal Walia, Clyde Wilson, Abdelbagi M. Ismail, Timothy J. Close, Xinping Cui
Software Mentions: 1
Published: over 17 years ago

10.1038/srep35936

The use of targeted genomic capture and massively parallel sequencing in diagnosis of Chinese Leukoencephalopathies
Cited by: 13
Author(s): Xiaole Wang, Fang He, Fei Yin, Chao Chen, Liwen Wu, Lei Yang, Jing Peng
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep35284

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions
Cited by: 67
Author(s): Joana C. Silva, Emmanuel Cornillot, Carrie McCracken, Sahar Usmani‐Brown, Ankit Dwivedi, Olukemi O. Ifeonu, Jonathan Crabtree, Hanzel T. Gotia, Azan Z. Virji, Christelle Reynès, Jacques Colinge, Vidya P. Kumar, Lauren Lawres, Joseph E. Pazzi, Jozelyn Pablo, Christopher Hung, Jana Brancato, Priti Kumari, Joshua Orvis, Kyle Tretina, Marcus C. Chibucos, Sandy Ott, Lisa Sadzewicz, Naomi Sengamalay, Amol C. Shetty, Qi Su, Luke J. Tallon, Claire M. Fraser, Roger Frutos, Douglas M. Molina, Peter J. Krause, Choukri Ben Mamoun
Software Mentions: 1
Published: almost 10 years ago

10.1186/s40659-019-0216-9

Intestinal transcriptional profiling reveals fava bean-induced immune response in DBA/1 mice
Cited by: 1
Author(s): Guankui Du, Mochao Xiao, Quangang Zhu, Chen Zhou, Ao Wang, Wei Cai
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-14-195

5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea
Cited by: 60
Author(s): Chi Keung Cheng, Chun Hang Au, Sarah K. Wilke, Jason E. Stajich, Miriam E. Zolan, Patricia J. Pukkila, Hoi Shan Kwan
Software Mentions: 1
Published: over 13 years ago

10.3390/biology1010005

Biomarker Gene Signature Discovery Integrating Network Knowledge
Cited by: 27
Author(s): Yupeng Cun, Holger Fröhlich
Software Mentions: 1
Published: over 14 years ago

10.1038/srep36227

Identifying reproducible cancer-associated highly expressed genes with important functional significances using multiple datasets
Cited by: 2
Author(s): Haiyan Huang, Xiangyu Li, You Guo, Yuncong Zhang, Xusheng Deng, Lufei Chen, Jiahui Zhang, Zheng Guo, Lu Ao
Software Mentions: 1
Published: over 9 years ago

10.3390/biology10070578

Influence of Varying Dietary ω6 to ω3 Fatty Acid Ratios on the Hepatic Transcriptome, and Association with Phenotypic Traits (Growth, Somatic Indices, and Tissue Lipid Composition), in Atlantic Salmon (Salmo salar)
Cited by: 2
Author(s): Tomer Katan, Xi Xue, Albert Caballero‐Solares, Richard G. Taylor, Christopher C. Parrish, Matthew L. Rise
Software Mentions: 1
Published: about 5 years ago

10.3390/biology6010014

MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data
Cited by: 2
Author(s): Christopher Noune, Caroline Hauxwell
Software Mentions: 1
Published: over 9 years ago

10.1186/s40364-021-00303-x

LncRNAs serve as novel biomarkers for diagnosis and prognosis of childhood ALL
Cited by: 9
Author(s): Xuanmei Huang, Libin Huang, Qing Xie, Ling Zhang, Shaohui Huang, Mingye Hong, Jiangbin Li, Zunnan Huang, Hua Zhang
Software Mentions: 1
Published: about 5 years ago

10.1186/s12938-021-00930-3

Extended classifier system with continuous real-coded variables for feature extraction of instantaneous pulse-rate variability and respiration of individuals with gaming disorder
Cited by: 1
Author(s): Hung Ming, Tzu Chien Hsiao
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12938-021-00882-8

Event-related EEG oscillatory responses elicited by dynamic facial expression
Cited by: 1
Author(s): Tuba Aktürk, Tom A. de Graaf, Yasemin Abra, Sevilay Şahoğlu-Göktaş, Dilek Özkan, Aysun Kula, Bahar Güntekin
Software Mentions: 1
Published: over 5 years ago

10.1186/1475-925X-13-81

The influence of emotion on keyboard typing: an experimental study using visual stimuli
Cited by: 12
Author(s): Po-Ming Lee, Wei-Hsuan Tsui, Tzu‐Chien Hsiao
Software Mentions: 1
Published: about 12 years ago

10.1186/1475-925X-3-34

Review and standardization of cell phone exposure calculations using the SAM phantom and anatomically correct head models
Cited by: 24
Author(s): Brian B. Beard, Wolfgang Kainz
Software Mentions: 1
Published: almost 22 years ago

10.1186/s12938-021-00848-w

Attention-based multi-scale features fusion for unobtrusive atrial fibrillation detection using ballistocardiogram signal
Cited by: 7
Author(s): Fangfang Jiang, Chuhang Hong, Tianqing Cheng, Haoqian Wang, Bowen Xu, Biyong Zhang
Software Mentions: 1
Published: over 5 years ago

10.2349/biij.3.1.e25

Using magnetoencephalography to investigate brain activity during high frequency deep brain stimulation in a cluster headache patient
Cited by: 18
Author(s): NJ Ray, Morten L. Kringelbach, Ned Jenkinson, Owen Slf., Paul Davies, S Wang, Nick de Pennington, PC Hansen, John Stein, TZ Aziz
Software Mentions: 1
Published: over 19 years ago

10.1155/2015/492395

Transcriptomic Analysis of mRNAs in Human Monocytic Cells Expressing the HIV-1 Nef Protein and Their Exosomes
Cited by: 31
Author(s): Madeeha Aqil, Saurav Mallik, Sanghamitra Bandyopadhyay, Ujjwal Maulik, Shahid Jameel
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-8-72

Transcriptional profiling of Actinobacillus pleuropneumoniae under iron-restricted conditions
Cited by: 59
Author(s): Vincent Deslandes, John H. E. Nash, Josée Harel, James W. Coulton, Mario Jacques
Software Mentions: 1
Published: over 19 years ago

10.1155/2018/8475463

Siji Antiviral Mixture Protects against CA16 Induced Brain Injury through Inhibiting PERK/STAT3/NF-κB Pathway
Cited by: 1
Author(s): Huimin Xiao, Ruiyang Zhao, Yue He, Yang Liu, Qin He, Siwang Wang, Fei Chen
Software Mentions: 1
Published: almost 8 years ago

10.1155/2020/8595473

Contributions of Gene Modules Regulated by Essential Noncoding RNA in Colon Adenocarcinoma Progression
Cited by: 0
Author(s): Chunhua Li, Xihe Yu, Jianping Lu, Lei Zheng, Dahua Xu, Zelong Xu, Liqiang Wang, Ying Cui, Yeshuang Li, Hong Wang, Jiankai Xu, Kongning Li
Software Mentions: 1
Published: over 6 years ago

10.1155/2013/317926

Profiling of Hepatocellular Carcinoma Cell Cycle Regulating Genes Targeted by Calycosin
Cited by: 14
Author(s): Dongqing Zhang, Shufang Wang, Li Zhu, Yao Tian, Haibao Wang, Yuan Zhuang, Yu Li, Deqing Wang
Software Mentions: 1
Published: over 13 years ago

10.1155/2015/625192

Age-Specific Gene Expression Profiles of Rhesus Monkey Ovaries Detected by Microarray Analysis
Cited by: 8
Author(s): Hengxi Wei, Xiangjie Liu, Jihong Yuan, Li Li, Dongdong Zhang, Xiaolong Guo, Lin Liu, Shouquan Zhang
Software Mentions: 1
Published: over 11 years ago

10.1155/2015/949624

Transcriptional Changes Associated with Long-Term Left Ventricle Volume Overload in Rats: Impact on Enzymes Related to Myocardial Energy Metabolism
Cited by: 9
Author(s): Élise Roussel, Marie‐Claude Drolet, Élisabeth Walsh-Wilkinson, Wahiba Dhahri, Dominic Lachance, Suzanne Gascon, Otman Sarrhini, Jacques Rousseau, Roger Lecomte, Jacques Couët, Marie Arsenault
Software Mentions: 1
Published: over 11 years ago

10.1155/2019/3843295

Breast Tumor Detection and Classification Using Intravoxel Incoherent Motion Hyperspectral Imaging Techniques
Cited by: 6
Author(s): Si-Wa Chan, Yung-Chieh Chang, Po-Chiun Huang, Yen-Chieh Ouyang, Yu-Tzu Chang, Ruey-Feng Chang, Jyh‐Wen Chai, Clayton Chi‐Chang Chen, Hsian‐Min Chen, Chein‐I Chang, Chia-Chieh Lin
Software Mentions: 1
Published: almost 7 years ago

10.1038/srep35860

Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling
Cited by: 27
Author(s): Martin T. Jahn, Sebastian M. Markert, Tae Woo Ryu, Timothy Ravasi, Christian Stigloher, Ute Hentschel, Lucas Moitinho‐Silva
Software Mentions: 1
Published: over 9 years ago

10.1155/2014/543673

Complex Network-Driven View of Genomic Mechanisms Underlying Parkinson’s Disease: Analyses in Dorsal Motor Vagal Nucleus, Locus Coeruleus, and Substantia Nigra
Cited by: 22
Author(s): Beatriz Raposo Corradini, Priscila Iamashita, Edilaine Tampellini, José Marcelo Farfel, Lea T. Grinberg, Carlos Alberto Moreira-Filho
Software Mentions: 1
Published: over 12 years ago

10.1155/2018/5895628

Global, Survival, and Apoptotic Transcriptome during Mouse and Human Early Embryonic Development
Cited by: 9
Author(s): D. Haouzi, I. Boumela, Karim Chébli, S. Hamamah
Software Mentions: 1
Published: over 7 years ago

10.1155/2015/561819

Targeted Next-Generation Sequencing Reveals Hot Spots and Doubly Heterozygous Mutations in Chinese Patients with Familial Cardiomyopathy
Cited by: 9
Author(s): Yue Zhao, Yue Feng, Yunmei Zhang, Xiaoqing Ding, Yuzhu Song, A-Mei Zhang, Li Liu, Hong Zhang, Jindong Ding, Xueshan Xia
Software Mentions: 1
Published: over 11 years ago

10.1155/2017/6423021

Bioinformatics Genes and Pathway Analysis for Chronic Neuropathic Pain after Spinal Cord Injury
Cited by: 36
Author(s): Guan Zhang, Ping Yang
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-8-264

Genomic expression during human myelopoiesis
Cited by: 30
Author(s): Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Dario Basso, Silvio Bicciato, Roberta Zini, Claudia Gemelli, Gian Antonio Danieli, Sérgio Ferrari
Software Mentions: 1
Published: over 19 years ago

10.1155/2016/6125204

Structural and Histochemical Alterations in the Aortic Valves of Elderly Patients: A Comparative Study of Aortic Stenosis, Aortic Regurgitation, and Normal Valves
Cited by: 19
Author(s): Katsutoshi Miura, Hideki Katoh
Software Mentions: 1
Published: over 10 years ago

10.1155/2014/171487

Alteration of Interictal Brain Activity in Patients with Temporal Lobe Epilepsy in the Left Dominant Hemisphere: A Resting-State MEG Study
Cited by: 4
Author(s): Haitao Zhu, Jing Zhu, Tiezhu Zhao, Yong Wu, Hongyi Liu, Ting Wu, Lu Yang, Yuanjie Zou, Rui Zhang, Gang Zheng
Software Mentions: 1
Published: over 12 years ago

10.1155/2014/527029

Survey of Network-Based Approaches to Research of Cardiovascular Diseases
Cited by: 8
Author(s): Anida Sarajlić, Nataša Pržulj
Software Mentions: 1
Published: over 12 years ago

10.1155/2014/850802

ECR-MAPK Regulation in Liver Early Development
Cited by: 4
Author(s): Xiu-Ju Zhao, Hexian Zhuo
Software Mentions: 1
Published: over 12 years ago

10.1155/2013/354582

Comparative Gene Expression Profiling in Human Cumulus Cells according to Ovarian Gonadotropin Treatments
Cited by: 33
Author(s): Saïd Assou, D. Haouzi, H. Déchaud, Anna Gala, A. Ferrières, S. Hamamah
Software Mentions: 1
Published: over 13 years ago

10.1155/2014/651751

Microarray-Based RNA Profiling of Breast Cancer: Batch Effect Removal Improves Cross-Platform Consistency
Cited by: 19
Author(s): Martin Jakob Larsen, Mads Thomassen, Qihua Tan, Kristina Pilekær Sørensen, Torben A. Kruse
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-9-369

Peripheral arterial occlusive disease: Global gene expression analyses suggest a major role for immune and inflammatory responses
Cited by: 57
Author(s): Shijun Fu, Hulin Zhao, Jiantao Shi, Arhat Abzhanov, Keith Crawford, Lucila Ohno-Machado, Jianqin Zhou, Yanzhi Du, Winston Patrick Kuo, Ji Zhang, Mier Jiang, Jiamin Jin
Software Mentions: 1
Published: almost 18 years ago

10.1155/2014/951937

Endometrial Receptivity Profile in Patients with Premature Progesterone Elevation on the Day of hCG Administration
Cited by: 46
Author(s): D. Haouzi, Laurence Bissonnette, Anna Gala, Saïd Assou, Frida Entezami, Hélène Perrochia, H. Déchaud, Jean‐Noël Hugues, S. Hamamah
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-6-122

Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains
Cited by: 87
Author(s): Stefano Campanaro, Alessandro Vezzi, Nicola Vitulo, Federico M. Lauro, Michela D’Angelo, Francesca Simonato, Alessandro Cestaro, G Malacrida, Giulio Bertoloni, Giorgio Valle, Douglas H. Bartlett
Software Mentions: 1
Published: almost 21 years ago

10.1155/2013/317912

Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis
Cited by: 13
Author(s): Shuo Feng, Tong HeLin, Chun‐Xiang You, Jingyi Wang, Yeyuan Chen, Guangming Sun, Jun He, Yan Wu
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-13-177

Improving the performance of true single molecule sequencing for ancient DNA
Cited by: 39
Author(s): Aurélien Ginolhac, Julia T. Vilstrup, Jesper Stenderup, Morten Rasmussen, Mathias Stiller, Beth Shapiro, Grant D. Zazula, Duane G. Froese, Kathleen E. Steinmann, John F. Thompson, Khaled A. S. Al-Rasheid, M. Thomas P. Gilbert, Eske Willerslev, Ludovic Orlando
Software Mentions: 1
Published: about 14 years ago

10.1155/2014/536591

Computational Analysis of mRNA Expression Profiles Identifies theITGFamily andPIK3R3as Crucial Genes for Regulating Triple Negative Breast Cancer Cell Migration
Cited by: 13
Author(s): Sukhontip Klahan, Mei-Shin Wu, Edward Hsi, Chi‐Cheng Huang, Ming‐Feng Hou, Wei Chiao Chang
Software Mentions: 1
Published: over 12 years ago

10.1038/srep36877

Transcriptome analysis of follicles reveals the importance of autophagy and hormones in regulating broodiness of Zhedong white goose
Cited by: 31
Author(s): Jing Yu, Ya‐Ping Lou, Ayong Zhao
Software Mentions: 1
Published: over 9 years ago

10.1155/2016/8208904

Expression of Migration-Related Genes in Human Colorectal Cancer and Activity of a Disintegrin and Metalloproteinase 17
Cited by: 19
Author(s): Katarzyna Walkiewicz, Paweł Kozieł, Martyna Bednarczyk, Adam Błażelonis, Urszula Mazurek, Małgorzata Muc-Wierzgoń
Software Mentions: 1
Published: over 10 years ago

10.1155/2014/138410

msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks
Cited by: 4
Author(s): Yuan Zhang, Nan Du, Kang Li, Jinchao Feng, Kebin Jia, Aidong Zhang
Software Mentions: 1
Published: over 12 years ago

10.7603/s40681-014-0010-5

Coronary artery aneurysms occurrence risk analysis between Kawasaki disease and LRP1B gene in Taiwanese children
Cited by: 8
Author(s): Ying Lin, Xiang Liu, Jen‐Ping Chang, Wen Kuei Chien, Jin Hua Chen, Hsinyi Tsang, Chien Hui Hung, Ting Hsu Lin, Shaohui Huang, Chien-Chang Liao, Cheng Wen Lin, Tsung Jung Ho, Fuu Jen Tsai
Software Mentions: 1
Published: about 12 years ago

10.3390/biomedicines9091258

Master Regulators of Epithelial-Mesenchymal Transition and WNT Signaling Pathways in Juvenile Nasopharyngeal Angiofibromas
Cited by: 2
Author(s): Naiade Calanca, Sara Martoreli Silveira Binato, Sabrina Daniela da Silva, Helena Brentani, Luiz Ubirajara Sennes, Clóvis Antônio Lopes Pinto, Maria Aparecida Custódio Domingues, Carlos Eduardo Fonseca-Alves, Cláudia Aparecida Rainho, Sílvia Regina Rogatto
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2164-8-63

Target genes of myostatin loss-of-function in muscles of late bovine fetuses
Cited by: 69
Author(s): Isabelle Cassar-Malek, Florent Passelaigue, Carine Bernard, Jean J. Léger, Jean-François Hocquette
Software Mentions: 1
Published: over 19 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 11 years ago

10.1038/srep37061

Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions
Cited by: 5
Author(s): Nilofer Husain, Nikhil Kumar Tulsian, Wang Loo Chien, Sushant Suresh, Ganesh S. Anand, J. Sivaraman
Software Mentions: 1
Published: over 9 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: almost 15 years ago

10.3390/ijms21145032

Nutri-Epigenetics and Gut Microbiota: How Birth Care, Bonding and Breastfeeding Can Influence and Be Influenced?
Cited by: 15
Author(s): Rosita Gabbianelli, Laura Bordoni, Sandra Morano, Jean Calleja‐Agius, Joan Lalor
Software Mentions: 1
Published: about 6 years ago

10.3390/biom6040042

CoverageAnalyzer (CAn): A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles
Cited by: 16
Author(s): Ralf Hauenschild, Stephan Werner, Lyudmil Tserovski, Andreas Hildebrandt, Yuri Motorin, Mark Helm
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-10-5

Bayesian optimal discovery procedure for simultaneous significance testing
Cited by: 22
Author(s): Jing Cao, Xian-Jin Xie, Song Zhang, Angelique W. Whitehurst, Michael A. White
Software Mentions: 1
Published: over 17 years ago

10.3390/biom7010003

DNA Methylation Targeting: The DNMT/HMT Crosstalk Challenge
Cited by: 93
Author(s): Omar Castillo-Aguilera, Patrick Depreux, Ludovic Halby, Paola B. Arimondo, Laurence Goossens
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-11-65

Tungsten carbide cobalt nanoparticles exert hypoxia-like effects on the gene expression level in human keratinocytes
Cited by: 41
Author(s): Wibke Busch, Dana Kühnel, Kristin Schirmer, Stefan Scholz
Software Mentions: 1
Published: over 16 years ago

10.1042/BSR20181016

The effect of HMGB1 on the clinicopathological and prognostic features of cervical cancer
Cited by: 12
Author(s): Li Pan, Meng-Fei Xu, Hongwei Cai, Niresh Thapa, Cancan He, Zhen Song
Software Mentions: 1
Published: about 7 years ago

10.1038/srep37840

Two novel mutations in PRPF3 causing autosomal dominant retinitis pigmentosa
Cited by: 11
Author(s): Zaimin Zhong, Ming Yan, Wan Sun, Zehua Wu, Liyun Han, Zheng Zhou, Fang Zheng, Jianjun Chen
Software Mentions: 1
Published: over 9 years ago

10.3390/bios10110162

Carbon-Based Quantum Dots for Electrochemical Detection of Monoamine Neurotransmitters—Review
Cited by: 15
Author(s): Saheed E. Elugoke, Abolanle S. Adekunle, Omolola E. Fayemi, Bhekie B. Mamba, El‐Sayed M. Sherif, Eno E. Ebenso
Software Mentions: 1
Published: over 5 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: almost 19 years ago

10.1186/1471-2164-10-275

7TMRmine: a Web server for hierarchical mining of 7TMR proteins
Cited by: 21
Author(s): Guoquing Lu, Zhifang Wang, Alan M. Jones, Etsuko N. Moriyama
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2105-7-49

Effects of filtering by Present call on analysis of microarray experiments
Cited by: 235
Author(s): Jeanette N. McClintick, Howard J. Edenberg
Software Mentions: 1
Published: over 20 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: over 13 years ago

10.1038/srep38493

Identification of BnaYUCCA6 as a candidate gene for branch angle in Brassica napus by QTL-seq
Cited by: 44
Author(s): Hui Wang, Hongyan Cheng, Wenxiang Wang, Jia Liu, Ming Hao, Desheng Mei, Rijin Zhou, Fu Li, Qiong Hu
Software Mentions: 1
Published: over 9 years ago

10.1186/s13068-015-0415-8

SorGSD: a sorghum genome SNP database
Cited by: 41
Author(s): Hong Luo, Wenming Zhao, Yanqing Wang, Yan Xia, Xiaoyuan Wu, Limin Zhang, Bixia Tang, Junwei Zhu, Fang Lü, Zhenglin Du, Wubishet A. Bekele, Shuaishuai Tai, David R. Jordan, Ian D. Godwin, Rod J. Snowdon, Emma Mace, Hai‐Chun Jing, Jianxun Luo
Software Mentions: 1
Published: over 10 years ago

10.1186/s13068-015-0260-9

Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum
Cited by: 30
Author(s): Keerthi P. Venkataramanan, Lie Min, Shuyu Hou, Shawn W. Jones, Matthew T. Ralston, Kelvin H. Lee, Eleftherios T. Papoutsakis
Software Mentions: 1
Published: about 11 years ago

10.1186/s13068-019-1554-0

Metabolic engineering of Bacillus amyloliquefaciens for enhanced production of S-adenosylmethionine by coupling of an engineered S-adenosylmethionine pathway and the tricarboxylic acid cycle
Cited by: 15
Author(s): Liying Ruan, Lü Li, Dian Zou, Cong Jiang, Zhiyou Wen, Shouwen Chen, Yu Deng, Xuetuan Wei
Software Mentions: 1
Published: almost 7 years ago

10.1186/1754-6834-7-31

Transcriptional comparison of the filamentous fungus Neurospora crassagrowing on three major monosaccharides D-glucose, D-xylose and L-arabinose
Cited by: 53
Author(s): Jingen Li, Liangcai Lin, Yong Li, Chaoguang Tian, Yanhe Ma
Software Mentions: 1
Published: over 12 years ago

10.1038/srep38769

Aerosol effect on the evolution of the thermodynamic properties of warm convective cloud fields
Cited by: 24
Author(s): Guy Dagan, Ilan Koren, Orit Altaratz, Reuven H. Heiblum
Software Mentions: 1
Published: over 9 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: almost 13 years ago

10.1038/boneres.2017.30

New insights into the vitamin D requirements during pregnancy
Cited by: 84
Author(s): Bruce W. Hollis, Carol L. Wagner
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41416-019-0725-x

Anti-VEGF therapy resistance in ovarian cancer is caused by GM-CSF-induced myeloid-derived suppressor cell recruitment
Cited by: 57
Author(s): Naoki Horikawa, Kaoru Abiko, Noriomi Matsumura, Tsukasa Baba, Junzo Hamanishi, Ken Yamaguchi, Ryusuke Murakami, Mana Taki, Masao Ukita, Yuko Hosoe, Masafumi Koshiyama, Ikuo Konishi, Masaki Mandai
Software Mentions: 1
Published: over 6 years ago

10.1038/s41416-021-01377-y

The circulating soluble form of the CD40 costimulatory immune checkpoint receptor and liver metastasis risk in rectal cancer
Cited by: 7
Author(s): Sebastian Meltzer, Annette Torgunrud, Hanna Abrahamsson, Arne M. Solbakken, Kjersti Flatmark, Svein Dueland, Kine Mari Bakke, Paula A. Bousquet, Anne Negård, Christin Johansen, Lars Gustav Lyckander, Finn Ole Larsen, Jesper Sølver Schou, Kathrine Røe Redalen, Anne Hansen Ree
Software Mentions: 1
Published: over 5 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566