cran: SAM | Projects | Ecosyste.ms: Papers

10.1186/gb-2008-9-1-r14

Adipose tissue transcriptomic signature highlights the pathological relevance of extracellular matrix in human obesity
Cited by: 379
Author(s): Corneliu Hénégar, Joan Tordjman, Vincent Achard, Danièle Lacasa, Isabelle Cremer, Michèle Guerre-Millo, Christine Poitou, Arnaud Basdevant, Vladimír Štich, Nathalie Viguerie, Dominique Langin, Pierre Bédossa, Jean-Daniel Zucker, Karine Clément
Software Mentions: 2
Published: over 18 years ago

10.1186/s12859-018-2579-2

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

10.1186/s12864-021-07610-5

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

10.1534/g3.118.200417

Development of Diagnostic SNP Markers To Monitor Hybridization Between Sika Deer (Cervus nippon) and Wapiti (Cervus elaphus)
Cited by: 3
Author(s): Hengxing Ba, Zhipeng Li, Yumei Yang, Chunyi Li
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2105-14-S7-S11

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

10.1534/g3.115.017921

Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon
Cited by: 33
Author(s): Yizhou Wang, Kristina M. Smith, John W. Taylor, Michael Freitag, Jason E. Stajich
Software Mentions: 2
Published: almost 11 years ago

10.1534/g3.118.200481

Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes
Cited by: 12
Author(s): Yingpeng Hua, Ting Zhou, Qiong Liao, Haixing Song, Chunyun Guan, Zhenhua Zhang
Software Mentions: 2
Published: almost 8 years ago

10.3389/fvets.2021.732129

Identification of Multiple Blastocystis Subtypes in Domestic Animals From Colombia Using Amplicon-Based Next Generation Sequencing
Cited by: 49
Author(s): Adriana Higuera, Giovanny Herrera, Paula Andrea Jiménez, Diego García-Corredor, Martín Orlando Pulido-Medellín, Diana María Bulla-Castañeda, Juan Carlos Pinilla, Darwin A. Moreno-Pérez, Jenny G. Maloney, Mónica Santı́n, Juan David Ramírez
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2229-11-114

Resistance to Plasmopara viticola in a grapevine segregating population is associated with stilbenoid accumulation and with specific host transcriptional responses
Cited by: 89
Author(s): G. Malacarne, Urška Vrhovšek, L. Zulini, Alessandro Cestaro, M. Stefanini, Fulvio Mattivi, Massimo Delledonne, Riccardo Velasco, C. Moser
Software Mentions: 2
Published: over 15 years ago

10.1186/1742-9994-10-9

Habitat productivity constrains the distribution of social spiders across continents – case study of the genus Stegodyphus
Cited by: 26
Author(s): Marija Majer, Jens‐Christian Svenning, Trine Bilde
Software Mentions: 2
Published: over 13 years ago

10.1186/s40478-021-01118-5

Molecular analysis of pediatric CNS-PNET revealed nosologic heterogeneity and potent diagnostic markers for CNS neuroblastoma with FOXR2-activation
Cited by: 19
Author(s): Andrey Korshunov, Konstantin Okonechnikov, Felix Schmitt-Hoffner, Marina Ryzhova, Felix Sahm, Damian Stichel, Daniel Schrimpf, David Reuß, Philipp Sievers, Abigail K Suwala, Ella Kumirova, Olga Zheludkova, Andrey Golanov, David Jones, Stefan M. Pfister, Marcel Kool, Andreas von Deimling
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2229-10-273

Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees
Cited by: 37
Author(s): Caroline Côté, Francis Boileau, Vicky Roy, Mario Ouellet, Caroline Levasseur, Marie-Josée Morency, Janice E. K. Cooke, Armand Séguin, John Mackay
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2105-8-S7-S24

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

10.3389/fonc.2021.631056

Development of a Gene-Based Prediction Model for Recurrence of Colorectal Cancer Using an Ensemble Learning Algorithm
Cited by: 10
Author(s): Han-Ching Chan, Amrita Chattopadhyay, Eric Y. Chuang, Tzu-Pin Lu
Software Mentions: 2
Published: over 5 years ago

10.1534/g3.118.200171

RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding
Cited by: 28
Author(s): Emily Humble, Kanchon K. Dasmahapatra, Alvaro Martinez-Barrio, Inês Gregório, Jaume Forcada, Ann-Christin Polikeit, Simon Goldsworthy, Michael E. Goebel, Jörn Kalinowski, Jochen B. W. Wolf, Joseph I. Hoffman
Software Mentions: 2
Published: almost 8 years ago

10.3389/fnins.2016.00601

Variation in Gene Expression in Autism Spectrum Disorders: An Extensive Review of Transcriptomic Studies
Cited by: 62
Author(s): Ashley Ansel, Joshua P. Rosenzweig, Philip D. Zisman, Michal L. Melamed, Benjamin Gesundheit
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-13-62

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

10.3389/fnins.2020.616802

A Sextuple Knockout Cell Line System to Study the Differential Roles of CRY, PER, and NR1D in the Transcription-Translation Feedback Loop of the Circadian Clock
Cited by: 4
Author(s): Yi Ying Chiou, Tzu-Ying Li, Yanyan Yang, Aziz Sancar
Software Mentions: 2
Published: over 5 years ago

10.3389/fnmol.2017.00248

Translational Identification of Transcriptional Signatures of Major Depression and Antidepressant Response
Cited by: 26
Author(s): Mylène Hervé, Aurélie Bergon, Anne-Marie Le Guisquet, Samuel Leman, Julia-Lou Consoloni, Nicolas Fernandez-Nunez, Marie-Noëlle Lefebvre, Wissam El‐Hage, Raoul Belzeaux, Catherine Belzung, El Chérif Ibrahim
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2431-13-17

Optimising Ankle Foot Orthoses for children with Cerebral Palsy walking with excessive knee flexion to improve their mobility and participation; protocol of the AFO-CP study
Cited by: 14
Author(s): Yvette L. Kerkum, Jaap Harlaar, Annemieke I. Buizer, Josien C. van den Noort, Jules G. Becher, Merel-Anne Brehm
Software Mentions: 2
Published: over 13 years ago

10.3389/fninf.2019.00066

Exploring EEG Effective Connectivity Network in Estimating Influence of Color on Emotion and Memory
Cited by: 25
Author(s): Meei Tyng Chai, Hafeez Ullah Amin, Lila Iznita Izhar, Mohamad Naufal Mohamad Saad, Mohammad Abdul Rahman, Aamir Saeed Malik, Tong Boon Tang
Software Mentions: 2
Published: almost 7 years ago

10.3389/fnins.2020.580970

Expected Valence Predicts Choice in a Recurrent Decision Task
Cited by: 1
Author(s): Daniel Thomas Jäger, Melanie Boltzmann, Jens D. Rollnik, Jascha Rüsseler
Software Mentions: 2
Published: over 5 years ago

10.3389/fnmol.2021.651355

Single-Nucleus Chromatin Accessibility Landscape Reveals Diversity in Regulatory Regions Across Distinct Adult Rat Cortex
Cited by: 7
Author(s): Yeya Yu, Xiaoyü Wei, Qiuting Deng, Qing Lan, Yiping Guo, Lei Han, Yue Yuan, Peng Fan, Peng Wu, Shuncheng Shangguan, Yang Liu, Yiwei Lai, Giacomo Volpe, Miguel A. Esteban, Chuanyu Liu, Yong Hou, Longqi Liu
Software Mentions: 2
Published: about 5 years ago

10.3389/fnmol.2018.00290

Salivary MicroRNAs: Diagnostic Markers of Mild Traumatic Brain Injury in Contact-Sport
Cited by: 68
Author(s): Valentina Di Pietro, Edoardo Porto, Marco Ragusa, Cristina Barbagallo, David Davies, Mario Forcione, Ann Logan, Cinzia Di Pietro, Michele Purrello, Michael J. Grey, Douglas Hammond, Vijay Sawlani, Aron K. Barbey, Antonio Belli
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-017-1810-x

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

10.3389/fmicb.2018.02827

BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes
Cited by: 12
Author(s): Irina Garanina, Gleb Y. Fisunov, Vadim M. Govorun
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2017.01672

Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698
Cited by: 0
Author(s): Elena Ferrari, Mathias C. Walter, Christopher Huptas, Siegfried Scherer, Stefanie Müller-Herbst
Software Mentions: 2
Published: almost 9 years ago

10.1186/gb-2008-9-7-r108

Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers
Cited by: 59
Author(s): Kamila Naxerova, Carol J. Bult, Anne Peaston, Karen Fancher, Barbara B. Knowles, Simon Kasif, Isaac S. Kohane
Software Mentions: 2
Published: over 18 years ago

10.3389/fmicb.2014.00530

Perturbations in small molecule synthesis uncovers an iron-responsive secondary metabolite network in Aspergillus fumigatus
Cited by: 44
Author(s): Philipp Wiemann, Beatrix E. Lechner, Joshua A. Baccile, Thomas Velk, Wen‐Bing Yin, Jin Woo Bok, Suman B. Pakala, Liliana Losada, William C. Nierman, Frank C. Schroeder, Hubertus Haas, Nancy P. Keller
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2202-8-95

Gene expression profiling in a mouse model of infantile neuronal ceroid lipofuscinosis reveals upregulation of immediate early genes and mediators of the inflammatory response
Cited by: 28
Author(s): Xingwen Qiao, Jui Yun Lu, Sandra L. Hofmann
Software Mentions: 2
Published: over 18 years ago

10.3389/fmicb.2020.00202

Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
Cited by: 11
Author(s): José Manuel Rubio-Gómez, Carlos Molina-Santiago, Zulema Udaondo, Mireia Tena-Garitaonaindia, Tino Krell, Juan L. Ramos, Abdelali Daddaoua
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2019.00107

Survival Mechanisms of Campylobacter hepaticus Identified by Genomic Analysis and Comparative Transcriptomic Analysis of in vivo and in vitro Derived Bacteria
Cited by: 19
Author(s): Thi Thu Hao Van, Jake A. Lacey, Ben Vezina, Canh Phung, Arif Anwar, Peter C. Scott, Robert J. Moore
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2020.00863

The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes
Cited by: 14
Author(s): Nan Song, Yuehua Geng, Xinghao Li
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2017.02394

Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici
Cited by: 25
Author(s): Chongjing Xia, Meinan Wang, Omar E. Cornejo, Derick Jiwan, Deven R. See, Xianming Chen
Software Mentions: 2
Published: over 8 years ago

10.3389/fimmu.2019.00468

CD117 (c-Kit) Is Expressed During CD8+ T Cell Priming and Stratifies Sensitivity to Apoptosis According to Strength of TCR Engagement
Cited by: 19
Author(s): Guido Frumento, Jianmin Zuo, Kriti Verma, Wayne Croft, Pradeep Ramagiri, Frederick Chen, Paul Moss
Software Mentions: 2
Published: over 7 years ago

10.1186/s12883-018-1044-1

Protocol for promoting recovery optimization of walking activity in stroke (PROWALKS): a randomized controlled trial
Cited by: 16
Author(s): Henry Wright, Tamara Wright, Ryan T. Pohlig, Scott E. Kasner, Jonathan Raser-Schramm, Darcy S. Reisman
Software Mentions: 2
Published: over 8 years ago

10.3389/fimmu.2017.01288

Helicobacter pylori Affects the Antigen Presentation Activity of Macrophages Modulating the Expression of the Immune Receptor CD300E through miR-4270
Cited by: 34
Author(s): Matteo Pagliari, Fabio Munari, Marta Toffoletto, Silvia Lonardi, Francesco Chemello, Gaia Codolo, Caterina Millino, Chiara Della Bella, Beniamina Pacchioni, William Vermi, Matteo Fassan, Marina de Bernard, Stefano Cagnin
Software Mentions: 2
Published: almost 9 years ago

10.3813/AAA.919239

Pitch of Harmonic Complex Tones: Rate Coding of Envelope Repetition Rate in the Auditory Midbrain
Cited by: 1
Author(s): Yaqing Su, Bertrand Delgutte
Software Mentions: 2
Published: almost 8 years ago

10.3389/fimmu.2021.625586

The Effects of Helicobacter pylori Infection on Microbiota Associated With Gastric Mucosa and Immune Factors in Children
Cited by: 9
Author(s): Wei Zheng, Miao Jin, Lingling Luo, Long Gao, Bin Chen, Xiaoli Shu, Weizhong Gu, Kui Peng, Fubang Li, Hong Zhao, Benson O. A. Botchway, Marong Fang, Mizu Jiang
Software Mentions: 2
Published: over 5 years ago

10.3389/fnint.2012.00113

The Interplay between Emotion and Cognition in Autism Spectrum Disorder: Implications for Developmental Theory
Cited by: 91
Author(s): Sebastian Gaigg
Software Mentions: 2
Published: over 14 years ago

10.3389/fmicb.2021.640054

Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data
Cited by: 4
Author(s): Katerina Jureckova, Hana Raschmanová, Jan Kolek, Maryna Vasylkivska, Barbora Branská, Petra Patáková, Ivo Provazník, Karel Sedlář
Software Mentions: 2
Published: over 5 years ago

10.3389/fnhum.2018.00322

Mapping the Spatiotemporal Evolution of Emotional Processing: An MEG Study Across Arousal and Valence Dimensions
Cited by: 11
Author(s): Charis Styliadis, Andreas A. Ioannides, Panagiotis D. Bamidis, Christos Papadelis
Software Mentions: 2
Published: almost 8 years ago

10.3389/fgene.2015.00163

Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways
Cited by: 12
Author(s): Adrián Mosquera Orgueira
Software Mentions: 2
Published: about 11 years ago

10.1186/s12862-015-0378-1

Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)8 isomerase evolutionary intermediates from a diverse metagenome
Cited by: 16
Author(s): Lianet Noda‐Garcia, Ana Lilia Juárez-Vázquez, María C. Ávila-Arcos, E.A. Verduzco-Castro, Gabriela M. Montero-Morán, Paul Gaytán, Mauricio Carrillo‐Tripp, Francisco Barona‐Gómez
Software Mentions: 2
Published: about 11 years ago

10.3389/fgene.2020.00406

Analysis of the Mouse Y Chromosome by Single-Molecule Sequencing With Y Chromosome Enrichment
Cited by: 9
Author(s): Yuki Yano, Tomoki Chiba, Hiroshi Asahara
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2148-8-74

Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans
Cited by: 52
Author(s): Santos Alonso, Neskuts Izagirre, Isabel Smith Zubiaga, Jesús Gardeazábal, José Luís Díaz-Ramón, J.L. Díaz‐Pérez, Diana Zélénika, María Dolores Boyano, Nico P.M. Smit, Concepción de la Rúa
Software Mentions: 2
Published: over 18 years ago

10.1186/s12866-019-1663-8

Thymol tolerance in Escherichia coli induces morphological, metabolic and genetic changes
Cited by: 9
Author(s): Fatemah Al-Kandari, Rabeah Al-Temaimi, Arnoud H. M. van Vliet, Martin J. Woodward
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2180-12-22

A comparison of two distinct murine macrophage gene expression profiles in response to Leishmania amazonensisinfection
Cited by: 24
Author(s): Christian M. Probst, Rodrigo A Silva, Juliana Perrone Bezerra de Menezes, Taís Fontoura de Almeida, Ivana Nunes Gomes, Andreia Cristine Dallabona, Luiz Shozo Ozaki, Gregory A. Buck, Daniela Parada Pavoni, Marco Aurélio Krieger, Patrícia Sampaio Tavares Veras
Software Mentions: 2
Published: over 14 years ago

10.3389/fgene.2020.00113

FBXW4 Acts as a Protector of FOLFOX-Based Chemotherapy in Metastatic Colorectal Cancer Identified by Co-Expression Network Analysis
Cited by: 6
Author(s): Yiyi Zhang, Lijun Sun, Xiaojie Wang, Yanwu Sun, Ying Chen, Meifang Xu, Pan Chi, Xingrong Lu, Zongbin Xu
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-11-483

Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types
Cited by: 14
Author(s): Noor Dawany, Aydın Tözeren
Software Mentions: 2
Published: almost 16 years ago

10.3389/fgene.2020.00830

Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead, Channa argus Through Histological and Transcriptome Analyses
Cited by: 2
Author(s): Aiguo Zhou, Shaolin Xie, Feng Yuan, Dan Sun, Shulin Liu, Zhuolin Sun, Mingzhi Li, Chaonan Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-14-S11-S3

Efficient digest of high-throughput sequencing data in a reproducible report
Cited by: 4
Author(s): Zhe Zhang, Jeremy Leipzig, Ariella Sasson, Angela M Yu, Juan C. Perín, Hongbo Xie, Mahdi Sarmady, Patrick V. Warren, Peter S. White
Software Mentions: 2
Published: almost 13 years ago

10.3389/fgene.2019.01190

Whole Genome Resequencing Reveals Selection Signatures Associated With Important Traits in Ethiopian Indigenous Goat Populations
Cited by: 6
Author(s): Haile Berihulay, Yefang Li, Berihu Gebrekidan, Gebremedhin Gebreselassie, Xuexue Liu, Lin Jiang, Yue Ma
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-14-358

Fragment assignment in the cloud with eXpress-D
Cited by: 24
Author(s): Anjeanette Roberts, Harvey Feng, Lior Pachter
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-13-S15-S4

Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213
Cited by: 12
Author(s): Joseph S. Reddy, Ranjit Kumar, James Watt, Mark L. Lawrence, Shane C. Burgess, Bindu Nanduri
Software Mentions: 2
Published: almost 14 years ago

10.3389/fgene.2021.634635

Research on the Mechanism of Soybean Resistance to Phytophthora Infection Using Machine Learning Methods
Cited by: 5
Author(s): Junxia Chi, Shizeng Song, Hao Zhang, Yuanning Liu, Hengyi Zhao, Liyan Dong
Software Mentions: 2
Published: over 5 years ago

10.3389/fendo.2012.00133

Thyroid cancer cell lines: an overview
Cited by: 104
Author(s): Manuel Saiselet, Sébastien Floor, Maxime Tarabichi, Geert Dom, Aline Hébrant, Wilma C.G. van Staveren, Carine Maenhaut
Software Mentions: 2
Published: over 14 years ago

10.1111/anec.12840

Young and early‐onset dilated cardiomyopathy with malignant ventricular arrhythmia and sudden cardiac death induced by the heterozygous LDB3, MYH6, and SYNE1 missense mutations
Cited by: 9
Author(s): Ting Zhao, Yuting Ma, Zuoquan Zhang, Jing Xian, Xiaojing Geng, Feng Wang, Jiana Huang, Zhe Yang, Yi Luo, Yenn‐Jiang Lin
Software Mentions: 2
Published: about 5 years ago

10.3389/fcell.2020.628222

Structural and Biochemical Characterization of EFhd1/Swiprosin-2, an Actin-Binding Protein in Mitochondria
Cited by: 6
Author(s): Sang A Mun, Jongseo Park, Kyoung Ryoung Park, Youngjin Lee, Jung Youn Kang, Tae‐In Park, Minho Jin, Jamie O. Yang, Chang‐Duk Jun, Soo Hyun Eom
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-14-S2-S7

Discovery and analysis of consistent active sub-networks in cancers
Cited by: 12
Author(s): Raj Gaire, Lorey Smith, Patrick O. Humbert, James E. Bailey, Peter J. Stuckey, Izhak Haviv
Software Mentions: 2
Published: over 13 years ago

10.3389/fgene.2017.00231

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools
Cited by: 29
Author(s): Deborah Antunes, Natasha Andressa Nogueira Jorge, Ernesto R. Caffarena, Fábio Passetti
Software Mentions: 2
Published: over 8 years ago

10.3389/fcell.2020.00242

Detection of Allosteric Effects of lncRNA Secondary Structures Altered by SNPs in Human Diseases
Cited by: 7
Author(s): Xiaoyan Lu, Yu Ding, Yu Bai, Jing Li, Guosi Zhang, Siyu Wang, Wenyan Gao, Liangde Xu, Hong Wang
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-015-0101-5

Molecular subtypes of urothelial carcinoma are defined by specific gene regulatory systems
Cited by: 55
Author(s): Pontus Eriksson, Mattias Aine, Srinivas Veerla, Fredrik Liedberg, Gottfrid Sjödahl, Mattias Höglund
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2105-12-S14-S7

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information
Cited by: 42
Author(s): Shin Suzuki, Tomohiro Yasuda, Yuichi Shiraishi, Satoru Miyano, Masao Nagasaki
Software Mentions: 2
Published: over 14 years ago

10.1186/s12920-018-0415-1

Distributed gene clinical decision support system based on cloud computing
Cited by: 2
Author(s): Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Chao Wang, Xuehai Zhou
Software Mentions: 2
Published: over 7 years ago

10.1186/s12920-015-0090-4

BMP2 response pattern in human lung fibroblasts predicts outcome in lung adenocarcinomas
Cited by: 15
Author(s): Michal Rajski, Annika Sääf, Martin Buess
Software Mentions: 2
Published: about 11 years ago

10.1186/s12862-019-1531-z

Geographic body size variation of a tropical anuran: effects of water deficit and precipitation seasonality on Asian common toad from southern Asia
Cited by: 6
Author(s): Guo Cheng, Shuai Gao, Ali Krzton, Long Zhang
Software Mentions: 2
Published: over 6 years ago

10.3389/fcell.2021.715275

Identification of Somatic Mutation-Driven Immune Cells by Integrating Genomic and Transcriptome Data
Cited by: 2
Author(s): Ying Jiang, Buhong Zheng, Yang Yang, Xiangmei Li, Junwei Han
Software Mentions: 2
Published: about 5 years ago

10.3389/fbioe.2021.731247

Rapid Enabling of Gluconobacter oxydans Resistance to High D-Sorbitol Concentration and High Temperature by Microdroplet-Aided Adaptive Evolution
Cited by: 3
Author(s): Li Liu, Weizhu Zeng, Shiqin Yu, Jianghua Li, Jingwen Zhou
Software Mentions: 2
Published: almost 5 years ago

10.3389/fbioe.2020.00882

Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation Systems
Cited by: 26
Author(s): K. M. Shakirova, Viktoriia Y. Ovchinnikova, Э. Б. Дашинимаев
Software Mentions: 2
Published: about 6 years ago

10.3389/fbioe.2020.00711

Development and Application of CRISPR/Cas in Microbial Biotechnology
Cited by: 36
Author(s): Wentao Ding, Zhipeng Yang, Shuobo Shi
Software Mentions: 2
Published: about 6 years ago

10.1186/s12862-021-01825-6

A comparative genomic approach using mouse and fruit fly data to discover genes involved in testis function in hymenopterans with a focus on Nasonia vitripennis
Cited by: 0
Author(s): Charlotte Lécureuil, Sophie Fouchécourt, Rémi Eliautout, Vanessa Guérin, Kévin Hidalgo, Dorian Neutre, Géraldine Roux, Philippe Monget
Software Mentions: 2
Published: about 5 years ago

10.1186/1755-8794-5-48

Integrative analysis of neuroblastoma and pheochromocytoma genomics data
Cited by: 15
Author(s): Péter M. Szabó, Miklós Pintér, Dorottya Szabó, Adrienn Zsippai, Attila Patócs, András Falus, Kàroly Rácz, Péter Igaz
Software Mentions: 2
Published: over 13 years ago

10.1186/1472-6785-10-2

Tracing the origins of rescued chimpanzees reveals widespread chimpanzee hunting in Cameroon
Cited by: 66
Author(s): Lora Ghobrial, Felix Lankester, John Kiyang, Akih E Akih, Simone de Vries, Roger Fotso, Elizabeth L. Gadsby, P. D. Jenkins, Mary Katherine Gonder
Software Mentions: 2
Published: over 16 years ago

10.12688/f1000research.22954.3

QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing
Cited by: 3
Author(s): Frédéric Jarlier, Nicolas Joly, Nicolas Fedy, Thomas Magalhaes, Leonor Sirotti, Paul Paganiban, F. Elizabeth Martin, Michael T. McManus, Philippe Hupé
Software Mentions: 2
Published: almost 6 years ago

10.3389/fcell.2021.607782

Hypermethylation and Downregulation of UTP6 Are Associated With Stemness Properties, Chemoradiotherapy Resistance, and Prognosis in Rectal Cancer: A Co-expression Network Analysis
Cited by: 1
Author(s): Yiyi Zhang, Qun Gao, Yong Wu, Yong Peng, Jinfu Zhuang, Yuanfeng Yang, Weizhong Jiang, Xing Liu, Guoxian Guan
Software Mentions: 2
Published: almost 5 years ago

10.3389/fgene.2020.603093

Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing Data
Cited by: 0
Author(s): Huijing Zhao, Shuang Wang, Xiguo Yuan
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2020.591778

Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi’s Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins
Cited by: 5
Author(s): Rishikesh Lotke, Ulrike Schneeweiß, Marcel Pietrek, Thomas Guenther, Adam Grundhoff, Magdalena Weidner-Glunde, Thomas F. Schulz
Software Mentions: 2
Published: almost 6 years ago

10.12688/f1000research.2-217.v2

MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data
Cited by: 16
Author(s): Guillermo Barturen, Antonio Rueda, José Luis Tejera Oliver, Michael Hackenberg
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-11-156

Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization
Cited by: 4
Author(s): Marc Hulsman, Anouk Mentink, Eugene P. van Someren, Koen J. Dechering, Jan de Boer, Marcel J. T. Reinders
Software Mentions: 2
Published: over 16 years ago

10.12688/f1000research.8382.2

Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping
Cited by: 12
Author(s): Ben Busby, Matthew Lesko, August, January Hackathon participants, Lisa Federer
Software Mentions: 2
Published: about 10 years ago

10.1002/evl3.39

Male-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture
Cited by: 62
Author(s): Alison E. Wright, Matteo Fumagalli, Christopher R. Cooney, Natasha I. Bloch, Filipe Garrett Vieira, Séverine D. Buechel, Niclas Kolm, Judith E. Mank
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-15-165

Cache-Oblivious parallel SIMD Viterbi decoding for sequence search in HMMER
Cited by: 11
Author(s): Miguel Ferreira, Nuno Roma, Luís M. S.Russo
Software Mentions: 2
Published: about 12 years ago

10.1186/1755-8794-2-57

Evaluation of a new high-dimensional miRNA profiling platform
Cited by: 24
Author(s): Julie M. Cunningham, Ann L. Oberg, Pedro M. Borralho, Betsy T. Kren, Amy J. French, Liang Wang, Brian M. Bot, Bruce W. Morlan, Kevin A.T. Silverstein, Rod Staggs, Yan Zeng, Anne Françoise Lamblin, Christopher A. Hilker, Jie Fan, Clifford J. Steer, Stephen N. Thibodeau
Software Mentions: 2
Published: almost 17 years ago

10.1186/s40001-014-0052-x

RETRACTED ARTICLE: Ranking candidate genes of esophageal squamous cell carcinomas based on differentially expressed genes and the topological properties of the co-expression network
Cited by: 3
Author(s): Yi Shen, Jicheng Tantai, Heng Zhao
Software Mentions: 2
Published: over 11 years ago

10.1002/eji.200838232

Fibroblasts from different sites may promote or inhibit recruitment of flowing lymphocytes by endothelial cells
Cited by: 81
Author(s): Helen M. McGettrick, Emily Smith, Andrew Filer, Stephen Kissane, M Salmon, Christopher D. Buckley, G. Ed Rainger, Gerard B. Nash
Software Mentions: 2
Published: over 17 years ago

10.1111/eva.12890

Restoration‐mediated secondary contact leads to introgression of alewife ecotypes separated by a colonial‐era dam
Cited by: 10
Author(s): Kerry Reid, John Carlos Garza, Steven R. Gephard, Adalgisa Caccone, David M. Post, Eric P. Palkovacs
Software Mentions: 2
Published: over 6 years ago

10.1007/s11356-017-0515-z

Transcriptional changes measured in rice roots after exposure to arsenite-contaminated sediments
Cited by: 7
Author(s): Alexandra Brinke, Georg Reifferscheid, Roland Klein, Ute Feiler, Sebastian Buchinger
Software Mentions: 2
Published: over 8 years ago

10.1186/1755-8794-1-10

Identification of differentially expressed genes in fibroblasts derived from patients with Dupuytren's Contracture
Cited by: 56
Author(s): Latha Satish, William A. LaFramboise, David B. O’Gorman, Sharon L. Johnson, Benjamin Janto, Bing Siang Gan, Mark E. Baratz, Fang Hu, J. Christopher Post, Garth D. Ehrlich, Sandeep Kathju
Software Mentions: 2
Published: over 18 years ago

10.1186/s12920-015-0088-y

Gene expression network analysis reveals new transcriptional regulators as novel factors in human ischemic cardiomyopathy
Cited by: 19
Author(s): Isabel Herrer, Esther Roselló‐Lletí, Ana Ortega, Estefanía Tarazón, Maria Micaela Molina‐Navarro, Juan Carlos Triviño, Luis Martínez‐Dolz, Luís Almenar, Francisca Lago, Ignacio Sánchez‐Lázaro, José Ramón González-Juanatey, Antonio Salvador, Manuel Portolés, Miguel Rivera
Software Mentions: 2
Published: over 11 years ago

10.1186/1756-8935-4-10

Genome-wide mapping of imprinted differentially methylated regions by DNA methylation profiling of human placentas from triploidies
Cited by: 74
Author(s): Ryan K. C. Yuen, Ruiwei Jiang, Maria S. Peñaherrera, Deborah E. McFadden, Wendy P. Robinson
Software Mentions: 2
Published: about 15 years ago

10.1289/ehp.10216

Nanosize Titanium Dioxide Stimulates Reactive Oxygen Species in Brain Microglia and Damages Neurons in Vitro
Cited by: 399
Author(s): Thomas Long, Julianne Tajuba, Preethi Sama, Navid B. Saleh, Carol D. Swartz, Joel Parker, Susan Hester, Gregory V. Lowry, Bellina Veronesi
Software Mentions: 2
Published: over 18 years ago

10.1186/1471-2105-15-S15-S10

Compression of next-generation sequencing quality scores using memetic algorithm
Cited by: 12
Author(s): Jian Zhou, Zhen Ji, Zexuan Zhu, Shan He
Software Mentions: 2
Published: over 11 years ago

10.1289/ehp.10861

Drinking-Water Arsenic Exposure Modulates Gene Expression in Human Lymphocytes from a U.S. Population
Cited by: 128
Author(s): Angeline S. Andrew, Dianne V. Jewell, Rebecca A. Mason, Michael L. Whitfield, Jason H. Moore, Margaret R. Karagas
Software Mentions: 2
Published: over 18 years ago

10.1016/j.tcsw.2020.100043

Biofilms of the non-tuberculous Mycobacterium chelonae form an extracellular matrix and display distinct expression patterns
Cited by: 8
Author(s): Perla Jazmín Vega-Domínguez, Eliza J.R. Peterson, Min Pan, Alessandro Di Maio, Saumya Singh, Siva Umapathy, Deepak Kumar Saini, Nitin S. Baliga, Apoorva Bhatt
Software Mentions: 2
Published: over 5 years ago

10.1016/j.tcsw.2021.100051

Mycobacterium abscessus biofilms produce an extracellular matrix and have a distinct mycolic acid profile
Cited by: 20
Author(s): Anja Dokic, Eliza J.R. Peterson, Mario L. Arrieta-Ortiz, Min Pan, Alessandro Di Maio, Nitin S. Baliga, Apoorva Bhatt
Software Mentions: 2
Published: over 4 years ago

10.1289/ehp.11229

Murine Lung Responses to Ambient Particulate Matter: Genomic Analysis and Influence on Airway Hyperresponsiveness
Cited by: 55
Author(s): Ting Wang, Liliana Moreno‐Vinasco, Yong Huang, Gabriel Lang, Jered Linares, Sascha N. Goonewardena, Alayna Grabavoy, Jonathan M. Samet, Alison S. Geyh, Patrick N. Breysse, Yves A. Lussier, Viswanathan Natarajan, Joe G.N. Garcia
Software Mentions: 2
Published: over 17 years ago

10.1111/1462-2920.14590

Riding the wave of genomics to investigate aquatic coliphage diversity and activity
Cited by: 25
Author(s): Slawomir Michniewski, Tamsin Redgwell, Aurelija Grigonyte, Branko Rihtman, Maria del Mar Aguiló-Ferretjans, Joseph Alexander Christie-Oleza, Eleanor Jameson, David J. Scanlan, Andrew Millard
Software Mentions: 2
Published: over 7 years ago

10.1016/j.celrep.2018.04.044

mTOR Senses Environmental Cues to Shape the Fibroblast-like Synoviocyte Response to Inflammation
Cited by: 46
Author(s): Thomas Karonitsch, Richard K. Kandasamy, Felix Kartnig, Barbara Herdy, K Dalwigk, Birgit Niederreiter, Johannes Holinka, Florian Sevelda, Reinhard Windhager, Martin Bilban, Thomas Weichhart, Marcus D. Säemann, Thomas Pap, Günter Steiner, Josef S Smolen, Hans P. Kiener, Giulio Superti‐Furga
Software Mentions: 2
Published: about 8 years ago

10.3390/ani11061693

Evaluation of Tannin Extracts, Leonardite and Tributyrin Supplementation on Diarrhoea Incidence and Gut Microbiota of Weaned Piglets
Cited by: 14
Author(s): Matteo Dell’Anno, Serena Reggi, V. Caprarulo, Monika Hejna, C.A. Sgoifo Rossi, Maria Luisa Callegari, Alfonso Baldi, Luciana Rossi
Software Mentions: 2
Published: about 5 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566