cran: SAM | Projects | Ecosyste.ms: Papers

10.1107/S1600576716019750

New synchrotron powder diffraction facility for long-duration experiments
Cited by: 35
Author(s): Claire Murray, Joseph L. Potter, Sarah Day, Annabelle R. Baker, Stephen P. Thompson, Jon Kelly, Christopher G. Morris, Sihai Yang, Chiu C. Tang
Software Mentions: 2
Published: over 9 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

10.1093/g3journal/jkaa053

Multivariate linear mixed model enhanced the power of identifying genome-wide association to poplar tree heights in a randomized complete block design
Cited by: 13
Author(s): Yuhua Chen, Hualong Wu, Wenguo Yang, Wei Zhao, Chunfa Tong
Software Mentions: 2
Published: over 5 years ago

10.3390/genes5020366

Characterization of the Genomic Architecture and Mutational Spectrum of a Small Cell Prostate Carcinoma
Cited by: 9
Author(s): Alan F. Scott, David Mohr, Hua Ling, Robert B. Scharpf, Peng Zhang, Gregory S. Liptak
Software Mentions: 2
Published: about 12 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

10.1186/1471-2105-14-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: about 13 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

10.1534/g3.120.401402

Training Population Optimization for Genomic Selection in <i>Miscanthus</i>
Cited by: 21
Author(s): Marcus O. Olatoye, Lindsay V. Clark, Nicholas R. LaBonte, Hongxu Dong, Maria Stefanie Dwiyanti, Kossonou Guillaume Anzoua, Joe E. Brummer, Bimal Kumar Ghimire, Elena Dzyubenko, N. I. Dzyubenko, Л. В. Багмет, Andrey Sabitov, Pavel Chebukin, Katarzyna Głowacka, Kweon Heo, Xiaoli Jin, Hironori Nagano, Junhua Peng, Chang Yeon Yu, Ji Hye Yoo, Hua Zhao, Stephen P. Long, Toshihiko Yamada, Erik J. Sacks, Alexander E. Lipka
Software Mentions: 2
Published: almost 6 years ago

10.1534/g3.116.036673

Genome Report: Identification and Validation of Antigenic Proteins from Pajaroellobacter abortibovis Using De Novo Genome Sequence Assembly and Reverse Vaccinology
Cited by: 8
Author(s): Bryan T. Welly, Michael R. Miller, Jeffrey L Stott, M Blanchard, Alma Islas–Trejo, Sean O’Rourke, Amy Young, Juan F. Medrano, Alison L. Van Eenennaam
Software Mentions: 2
Published: over 9 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

10.1534/g3.118.200134

Programmable Single and Multiplex Base-Editing in <i>Bombyx mori</i> Using RNA-Guided Cytidine Deaminases
Cited by: 14
Author(s): Yufeng Li, Sanyuan Ma, Le Sun, Tong Zhang, Jiasong Chang, Wei Lu, Xiaoxu Chen, Yue Liu, Xiaogang Wang, Run Shi, Ping Zhao, Qingyou Xia
Software Mentions: 2
Published: about 8 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

10.3390/genes9060313

CoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads
Cited by: 2
Author(s): Dongmei Ai, Hongfei Pan, Ruocheng Huang, Xia Li
Software Mentions: 2
Published: almost 8 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

10.1186/1471-2164-13-62

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

10.1186/s40360-020-00402-9

Prospects of Indole derivatives as methyl transfer inhibitors: antimicrobial resistance managers
Cited by: 4
Author(s): Suprim Tha, Sapana Shakya, Rajani Malla, Pramod Aryal
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2210-8-16

Pharmacokinetics and transcriptional effects of the anti-salmon lice drug emamectin benzoate in Atlantic salmon (Salmo salar L.)
Cited by: 23
Author(s): Pål A. Olsvik, Kai Kristoffer Lie, Eva Mykkeltvedt, Ole Bent Samuelsen, Kjell Petersen, Anne-Kristin Stavrum, Bjørn Tore Lunestad
Software Mentions: 2
Published: over 17 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/fpsyg.2015.01232

Microtiming in Swing and Funk affects the body movement behavior of music expert listeners
Cited by: 34
Author(s): Lorenz Kilchenmann, Olivier Senn
Software Mentions: 2
Published: almost 11 years ago

10.3389/fpsyg.2021.626118

Interindividual Variation Refuses to Go Away: A Bayesian Computer Model of Language Change in Communicative Networks
Cited by: 3
Author(s): Mathilde Josserand, Marc Allassonnière-Tang, François Pellegrino, Dan Dediu
Software Mentions: 2
Published: almost 5 years ago

10.3389/fpsyg.2018.00657

Physiological Response to Facial Expressions in Peripersonal Space Determines Interpersonal Distance in a Social Interaction Context
Cited by: 55
Author(s): Alice Cartaud, Gennaro Ruggiero, Laurent Ott, Tina Iachini, C. Yann
Software Mentions: 2
Published: about 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/fpsyt.2021.633102

Spouse-Appraised Memory Functioning Predicts Memory Decline Better Than Subjective Memory Complaints in Community Dwelling Older Adults at Genetic Risk for Alzheimer's Disease
Cited by: 3
Author(s): Youssef Bellaali, John L. Woodard, Bernard Hanseeuw, Adrian Ivanoiu
Software Mentions: 2
Published: over 5 years ago

10.3389/fpsyg.2017.01709

Rhythmic Density Affects Listeners' Emotional Response to Microtiming
Cited by: 9
Author(s): Olivier Senn, Claudia Bullerjahn, Lorenz Kilchenmann, Richard von Georgi
Software Mentions: 2
Published: over 8 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: over 10 years ago

10.3390/genes9090452

Recent Selection on a Class I ADH Locus Distinguishes Southwest Asian Populations Including Ashkenazi Jews
Cited by: 9
Author(s): Shuangshuang Gu, Hui Li, Andrew J. Pakstis, William C. Speed, David Genevieve, Judith R. Kidd, Kenneth K. Kídd
Software Mentions: 2
Published: over 7 years ago

10.1074/jbc.M114.561845

Involvement of MicroRNAs in the Regulation of Muscle Wasting during Catabolic Conditions
Cited by: 120
Author(s): Ricardo Soares, Stefano Cagnin, Francesco Chemello, Matteo Silvestrin, Antonio Musarò, Cristiano De Pittà, Gerolamo Lanfranchi, Marco Sandri
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/fpls.2020.603380

Role of Chromatin Architecture in Plant Stress Responses: An Update
Cited by: 46
Author(s): Sneha Lata Bhadouriya, Santosh Mehrotra, Mahesh Kumar Basantani, Gary J. Loake, Rajesh Mehrotra
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2017.02136

Ten Years of Landscape Genomics: Challenges and Opportunities
Cited by: 54
Author(s): Yong Li, Xuexia Zhang, Run-Li Mao, Jie Yang, Cai-Yun Miao, Zhuo Li, Ying‐Xiong Qiu
Software Mentions: 2
Published: over 8 years ago

10.3389/fpls.2020.570915

Expression of LhFT1, the Flowering Inducer of Asiatic Hybrid Lily, in the Bulb Scales
Cited by: 5
Author(s): Kana Kurokawa, Junya Kobayashi, Keiichirou Nemoto, Akira Nozawa, Tatsuya Sawasaki, Takashi Nakatsuka, Masumi Yamagishi
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2020.610307

Boron: More Than an Essential Element for Land Plants?
Cited by: 30
Author(s): Greice Leal Pereira, João Antônio Siqueira, Willian Batista‐Silva, Flávio Barcellos Cardoso, Adriano Nunes‐Nesi, Wagner L. Araújo
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2018.00976

FNBtools: A Software to Identify Homozygous Lesions in Deletion Mutant Populations
Cited by: 8
Author(s): Liang Sun, Yinbing Ge, Andrew Charles Bancroft, Xiaofei Cheng, Jiangqi Wen
Software Mentions: 2
Published: almost 8 years ago

10.3389/fpls.2016.00567

Trait Specific Expression Profiling of Salt Stress Responsive Genes in Diverse Rice Genotypes as Determined by Modified Significance Analysis of Microarrays
Cited by: 20
Author(s): Mohammad Rashed Hossain, George W. Bassel, Jeremy Pritchard, Garima P Sharma, B. V. Ford‐Lloyd
Software Mentions: 2
Published: about 10 years ago

10.3389/fpls.2020.00813

Single Nucleotide Polymorphism Charting of P. patens Reveals Accumulation of Somatic Mutations During in vitro Culture on the Scale of Natural Variation by Selfing
Cited by: 16
Author(s): Fabian B. Haas, Noe Fernandez‐Pozo, Rabea Meyberg, Pierre‐François Perroud, Marco Göttig, Nora Stingl, Denis Saint-Marcoux, Jane A. Langdale, Stefan A. Rensing
Software Mentions: 2
Published: almost 6 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/fpls.2014.00633

Effects of proteome rebalancing and sulfur nutrition on the accumulation of methionine rich Î´-zein in transgenic soybeans
Cited by: 27
Author(s): Won‐Seok Kim, Joseph M. Jez, Hari B. Krishnan
Software Mentions: 2
Published: over 11 years ago

10.3389/fpls.2016.00794

Nod Factor Effects on Root Hair-Specific Transcriptome of Medicago truncatula: Focus on Plasma Membrane Transport Systems and Reactive Oxygen Species Networks
Cited by: 47
Author(s): Isabelle Damiani, Alice Drain, Marjorie Guichard, Sandrine Balzergue, Alexandre Boscari, Jean-Christophe Boyer, Véronique Brunaud, Sylvain Cottaz, Corinne Rancurel, Martine Da Rocha, Cécile Fizames, Sébastien Fort, Isabelle Gaillard, Vincent Maillol, Etienne G. J. Danchin, Hatem Rouached, E. Samain, Yanhua Su, Julien Thouin, Bruno Touraine, Alain Puppo, Jean‐Marie Frachisse, Nicolas Pauly, Hervé Sentenac
Software Mentions: 2
Published: almost 10 years ago

10.3389/fpls.2018.00881

Assessing European Wheat Sensitivities to Parastagonospora nodorum Necrotrophic Effectors and Fine-Mapping the Snn3-B1 Locus Conferring Sensitivity to the Effector SnTox3
Cited by: 39
Author(s): Rowena Downie, Laura Bouvet, Eiko Furuki, N. Gosman, Keith A. Gardner, Ian Mackay, Camila Campos Mantello, Greg Mellers, H. Phan, Gemma A. Rose, Kar‐Chun Tan, Richard P. Oliver, James Cockram
Software Mentions: 2
Published: almost 8 years ago

10.3389/fped.2021.652011

Identification of a Rare Exon 19 Skipping Mutation in ALMS1 Gene in Alström Syndrome Patients From Two Unrelated Saudi Families
Cited by: 8
Author(s): Omar I. Saadah, Babajan Banaganapalli, Naglaa M. Kamal, Ahmed N. Sahly, Hadeel A. Alsufyani, Arif Mohammed, Aftab Ahmad, Khalidah Khalid Nasser, Jumana Y. Al‐Aama, Noor Ahmad Shaik
Software Mentions: 2
Published: about 5 years ago

10.3389/fphys.2020.610049

Physiological Effects of Water Flow Induced Swimming Exercise in Seabream Sparus aurata
Cited by: 16
Author(s): Arjan P. Palstra, Ana Roque, L. Kruijt, Pauline Jéhannet, Jaume Pérez‐Sánchez, Ron P. Dirks
Software Mentions: 2
Published: over 5 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/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: almost 11 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

10.3389/fphys.2018.00625

Immunomodulatory Effects of Dietary Seaweeds in LPS Challenged Atlantic Salmon Salmo salar as Determined by Deep RNA Sequencing of the Head Kidney Transcriptome
Cited by: 19
Author(s): Arjan P. Palstra, J. Kals, A. Blanco Garcia, Ron P. Dirks, M. Poelman
Software Mentions: 2
Published: about 8 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: about 6 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: over 5 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.2020.603093

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

10.1186/1471-2105-11-483

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: over 15 years ago

10.3389/fpls.2014.00533

A chromatin modifying enzyme, SDG8, is involved in morphological, gene expression, and epigenetic responses to mechanical stimulation
Cited by: 43
Author(s): Christopher I. Cazzonelli, Nazia Nisar, Andrea C. Roberts, Kevin Murray, Justin O. Borevitz, Barry J. Pogson
Software Mentions: 2
Published: over 11 years ago

10.3389/fpls.2021.580846

QTL-Seq and Transcriptome Analysis Disclose Major QTL and Candidate Genes Controlling Leaf Size in Sesame (Sesamum indicum L.)
Cited by: 12
Author(s): Sheng Chen, Shengnan Song, Rong Zhou, Donghua Li, Yuan Gao, Xianghua Cui, Xin Tang, Yanxin Zhang, Jinxing Tu, Xiurong Zhang, Linhai Wang
Software Mentions: 2
Published: over 5 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.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

10.1186/1471-2148-14-19

Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes
Cited by: 85
Author(s): Han Ming Gan, Mark B. Schultz, Christopher M. Austin
Software Mentions: 2
Published: over 12 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.2019.00296

Mining Magnaporthe oryzae sRNAs With Potential Transboundary Regulation of Rice Genes Associated With Growth and Defense Through Expression Profile Analysis of the Pathogen-Infected Rice
Cited by: 7
Author(s): Hao Zhang, Sifei Liu, Haowu Chang, Mengping Zhan, Qing‐Ming Qin, Borui Zhang, Zhi Li, Yuanning Liu
Software Mentions: 2
Published: about 7 years ago

10.1186/s12862-018-1127-z

Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
Cited by: 26
Author(s): Jonna Sofia Eriksson, Filipe de Sousa, Yann Bertrand, Alexandre Antonelli, Bengt Oxelman, Bernard E. Pfeil
Software Mentions: 2
Published: over 8 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/fncom.2016.00077

ARTIE: An Integrated Environment for the Development of Affective Robot Tutors
Cited by: 7
Author(s): Luis-Eduardo Imbernón Cuadrado, Ángeles Manjarrés Riesco, Félix de la Paz López
Software Mentions: 2
Published: almost 10 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: almost 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/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/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

10.1002/acn3.51119

Using urine to diagnose large‐scale mtDNA deletions in adult patients
Cited by: 10
Author(s): Kristin Nielsen Varhaug, Gonzalo S. Nido, I.F.M. de Coo, Pirjo Isohanni, Anu Suomalainen, Charalampos Tzoulis, Per M. Knappskog, Laurence A. Bindoff
Software Mentions: 2
Published: almost 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

10.3389/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: almost 6 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.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: about 6 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: almost 6 years ago

10.1186/s12920-020-00733-w

A machine learning framework for genotyping the structural variations with copy number variant
Cited by: 1
Author(s): Zheng Tian, Xiaoyan Zhu, Xuanping Zhang, Zhongmeng Zhao, Xin Yi, Jiayin Wang, Hongle Li
Software Mentions: 2
Published: almost 6 years ago

10.18632/aging.202888

Genetic landscape of breast cancer and mutation tracking with circulating tumor DNA in Chinese women
Cited by: 6
Author(s): Yinghao Wang, Lizhi Lin, Linhong Li, Jialiang Wen, Yili Chi, Rutian Hao, Xuanxuan Dai, Yizuo Chen, Du-Ping Huang, Yi-Li Zhou, Jie You, Zhiqiang Ye, Hao Chen, Liping Jin, Danxiang Chen, Fan Yang, Erjie Xia, Xueyan Ma, Fengyu Guo, Yunguang Tong, Min Zheng, Ouchen Wang
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

10.12688/f1000research.21142.2

Falco: high-speed FastQC emulation for quality control of sequencing data
Cited by: 104
Author(s): Guilherme de Sena Brandine, Andrew D. Smith
Software Mentions: 2
Published: over 5 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: over 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/fpsyt.2021.554621

Protein Biomarkers of Autism Spectrum Disorder Identified by Computational and Experimental Methods
Cited by: 9
Author(s): Fang Yao, Kaoyuan Zhang, Chengyun Feng, Yan Gao, Liming Shen, Xukun Liu, Jiazuan Ni
Software Mentions: 2
Published: over 5 years ago

10.1074/jbc.M115.698589

The Tomato Nucleotide-binding Leucine-rich Repeat Immune Receptor I-2 Couples DNA-binding to Nucleotide-binding Domain Nucleotide Exchange
Cited by: 18
Author(s): Stepan Fenyk, Christopher H. Dixon, William Gittens, Philip D. Townsend, Gary J. Sharples, Lars‐Olof Pålsson, Frank L. W. Takken, Martin J. Cann
Software Mentions: 2
Published: over 10 years ago

10.1186/s12920-019-0477-8

Transcriptomic and ChIP-sequence interrogation of EGFR signaling in HER2+ breast cancer cells reveals a dynamic chromatin landscape and S100 genes as targets
Cited by: 8
Author(s): Miguel Nava, Pranabananda Dutta, Nathan R. Zemke, Robin Farias‐Eisner, Jaydutt V. Vadgama, Yanyuan Wu
Software Mentions: 2
Published: over 7 years ago

10.1186/1755-8794-7-12

Exploring the molecular causes of hepatitis B virus vaccination response: an approach with epigenomic and transcriptomic data
Cited by: 20
Author(s): LU Yi-chen, Yi C, Weili Yan, Christine Nardini
Software Mentions: 2
Published: about 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: about 16 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

10.1002/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: about 8 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/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

10.1186/1471-213X-13-29

Stage-specific transcription during development of Aedes aegypti
Cited by: 19
Author(s): Brent W. Harker, Susanta K. Behura, Becky deBruyn, Diane D. Lovin, Akio Mori, Jeanne Romero‐Severson, David W. Severson
Software Mentions: 2
Published: almost 13 years ago

10.1155/2020/5859023

Quyushengxin Formula Causes Differences in Bacterial and Phage Composition in Ulcerative Colitis Patients
Cited by: 7
Author(s): Haojie Yang, Dan Gan, Ying Li, Xiaosu Wang, Lan Jin, Kaijian Qin, Can Cui, Jiong Wu, Zhenyi Wang
Software Mentions: 2
Published: about 6 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: about 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: about 11 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: about 7 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

10.12688/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

10.1186/1755-8794-5-22

Relation between smoking history and gene expression profiles in lung adenocarcinomas
Cited by: 36
Author(s): Johan Staaf, Göran Jönsson, Mats Jönsson, Anna Karlsson, Sten Isaksson, Annette Salomonsson, Helen Pettersson, Maria Soller, Sven-Börje Ewers, Leif Johansson, Per Jönsson, Maria Planck
Software Mentions: 2
Published: almost 14 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566