cran: SAM | Projects | Ecosyste.ms: Papers

10.1038/srep43109

miR-125b-5p enhances chemotherapy sensitivity to cisplatin by down-regulating Bcl2 in gallbladder cancer
Cited by: 62
Author(s): Dong Yang, Ming Zhan, Tao Chen, Wei Chen, Yunhe Zhang, Sunwang Xu, Jinchun Yan, Qihong Huang, Jian Wang
Software Mentions: 2
Published: over 9 years ago

10.1038/srep44389

A novel strategy for clustering major depression individuals using whole-genome sequencing variant data
Cited by: 16
Author(s): Chenglong Yu, Bernhard T. Baune, Júlio Licinio, Ma Li Wong
Software Mentions: 2
Published: over 9 years ago

10.1038/srep09506

The effect of music performance on the transcriptome of professional musicians
Cited by: 36
Author(s): Chakravarthi Kanduri, Tuire Kuusi, Minna Ahvenainen, Anju K. Philips, Harri Lähdesmäki, Irma Järvelä
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0100068

BRCA1 Haploinsufficiency Leads to Altered Expression of Genes Involved in Cellular Proliferation and Development
Cited by: 16
Author(s): Harriet Feilotter, Claire S. Michel, Paolo Uy, Lauren Bathurst, Scott Davey
Software Mentions: 2
Published: about 12 years ago

10.1038/s41598-017-00788-3

Multimodal Regulation Orchestrates Normal and Complex Disease States in the Retina
Cited by: 13
Author(s): Ana María Olivares, Austin S. Jelcick, James B. Reinecke, Barrett Leehy, Ali Haider, Margaux A. Morrison, Lin Cheng, D. F. Chen, Margaret M. DeAngelis, Neena B. Haider
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0238231

Treatment outcome of Severe Acute Malnutrition and associated factors among under-five children in outpatient therapeutics unit in Gubalafto Wereda, North Wollo Zone, Ethiopia, 2019
Cited by: 14
Author(s): Biruk Beletew Abate, Befkad Deresse Tilahun, Ayelign Mengesha Kassie, Mesfin Wudu Kassaw
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0008003

Novel Rank-Based Statistical Methods Reveal MicroRNAs with Differential Expression in Multiple Cancer Types
Cited by: 153
Author(s): Roy Navon, Hui Wang, Israel Steinfeld, Anya Tsalenko, Amir Ben-Dor, Zohar Yakhini
Software Mentions: 2
Published: over 16 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/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

10.1371/journal.pone.0083674

Behaviorally Activated mRNA Expression Profiles Produce Signatures of Learning and Enhanced Inhibition in Aged Rats with Preserved Memory
Cited by: 31
Author(s): Rebecca P. Haberman, Carlo Colantuoni, Ming Teng Koh, Michela Gallagher
Software Mentions: 2
Published: over 12 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

10.1038/s41598-017-09285-z

Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat
Cited by: 11
Author(s): Xuguang Qiao, Rui Su, Yan Wang, Ruijun Wang, Ting Yang, Xiaokai Li, Wei Chen, Shiyang He, Yu Jiang, Qiwu Xu, Wenting Wan, Yaolei Zhang, Wenguang Zhang, Chen Jiang, Bin Liu, Xin Liu, Yixing Fan, Duoyuan Chen, Jiang Huai-zhi, Dongming Fang, Zhihong Liu, Xiaowen Wang, Yanjun Zhang, Danqing Mao, Zhiying Wang, Ran Di, Qianjun Zhao, Tao Zhong, Huanming Yang, Jian Wang, Wen Wang, Yang Dong, Xiaoli Chen, Xun Xu, Jinquan Li
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-017-08492-y

Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts
Cited by: 55
Author(s): Natallia Shved, Gregor Warsow, Felix Eichinger, David Hoogewijs, Simone Brandt, Peter J. Wild, Matthias Kretzler, Clemens D. Cohen, Maja T. Lindenmeyer
Software Mentions: 2
Published: almost 9 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: over 5 years ago

10.1038/s41598-017-09089-1

Accelerating next generation sequencing data analysis with system level optimizations
Cited by: 14
Author(s): Nagarajan Kathiresan, Ramzi Temanni, Hakeem Almabrazi, Najeeb Syed, Puthen V. Jithesh, Rashid Al‐Ali
Software Mentions: 2
Published: almost 9 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

10.1038/s41598-017-09247-5

Prevalence of Rare Genetic Variations and Their Implications in NGS-data Interpretation
Cited by: 17
Author(s): Yangrae Cho, Chul‐Ho Lee, Eun-Goo Jeong, Minho Kim, Jong Hui Hong, Yun Woong Ko, Bomnun Lee, Gilly Yun, Byong Joon Kim, Jongcheol Jung, Jongsun Jung, Jin Sung Lee
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-017-10493-w

Functional proteomics outlines the complexity of breast cancer molecular subtypes
Cited by: 48
Author(s): Angelo Gámez‐Pozo, Lucía Trilla-Fuertes, Julia Berges-Soria, Nathalie Selevsek, Rocío López-Vacas, Mariana Díaz-Almirón, Paolo Nanni, Jorge M. Arevalillo, Hilario Navarro, Jonas Grossmann, Francisco Gayá Moreno, Rubén Gómez Rioja, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Paloma Maı́n, Jaime Feliú, Purificación Martínez del Prado, Pilar Zamora, Eva Ciruelos, Enrique Espinosa, Juan Ángel Fresno Vara
Software Mentions: 2
Published: almost 9 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

10.1186/1471-2180-12-22

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

10.1038/s41598-017-15516-0

Identification of selection signals by large-scale whole-genome resequencing of cashmere goats
Cited by: 35
Author(s): Xiaokai Li, Rui Su, Wenting Wan, Wenguang Zhang, Jiang Huai-zhi, Xuguang Qiao, Yixing Fan, Yanjun Zhang, Ruijun Wang, Zhihong Liu, Zhiying Wang, Bin Liu, Yue Ma, Hongping Zhang, Qianjun Zhao, Tao Zhong, Ran Di, Yu Jiang, Wei Chen, Wen Wang, Yang Dong, Jinquan Li
Software Mentions: 2
Published: over 8 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

10.1038/s41598-017-16700-y

A microsatellite repeat in PCA3 long non-coding RNA is associated with prostate cancer risk and aggressiveness
Cited by: 10
Author(s): John Lai, Leire Moya, Jiyuan An, Andrea Hoffman, Srilakshmi Srinivasan, Janaththani Panchadsaram, Carina Walpole, Joanna Perry-Keene, Suzanne K. Chambers, Melanie Lehman, Colleen C. Nelson, Judith A. Clements, Jyotsna Batra
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0044800

Mining Gene Expression Signature for the Detection of Pre-Malignant Melanocytes and Early Melanomas with Risk for Metastasis
Cited by: 21
Author(s): Cláudia Souza, Patrícia Xander, Ana Carolina Monteiro, Amanda Gonçalves dos Santos Silva, Débora Castanheira Pereira da Silva, Sabine Mai, Viviane Bernardo, José Daniel Lopes, Miriam Galvonas Jasiulionis
Software Mentions: 2
Published: almost 14 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

10.1186/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

10.1038/s41598-018-20727-0

Differential long non-coding RNA expression profiles in human oocytes and cumulus cells
Cited by: 51
Author(s): Julien Bouckenheimer, Patricia Fauque, Charles-Henri Lecellier, Céline Bruno, Thérèse Commes, Jean-Marc Lemaı̂tre, John De Vos, Saïd Assou
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-8-452

Gene expression analysis reveals early changes in several molecular pathways in cerebral malaria-susceptible mice versus cerebral malaria-resistant mice
Cited by: 55
Author(s): Nicolas Nf Delahaye, Nicolas Coltel, Denis Puthier, Mathieu Barbier, P. Benech, Florence Joly, Fuad Fa Iraqi, Georges E. Grau, Catherine Nguyen, Pascal Rihet
Software Mentions: 2
Published: over 18 years ago

10.1038/s41598-018-21608-2

Flexible migratory choices of Cory’s shearwaters are not driven by shifts in prevailing air currents
Cited by: 10
Author(s): Gaia Dell’Ariccia, Simon Benhamou, Maria P. Dias, José Pedro Granadeiro, Joël Sudre, Paulo Catry, Francesco Bonadonna
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0090346

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
Cited by: 1,282
Author(s): Jeffrey C. Glaubitz, Terry M. Casstevens, Fei Lü, James Harriman, Robert J. Elshire, Qibin Sun, Edward S. Buckler
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0084439

Effective Identification of Gram-Negative Bacterial Type III Secreted Effectors Using Position-Specific Residue Conservation Profiles
Cited by: 25
Author(s): Xiaojiao Yang, Yanzhi Guo, Jiesi Luo, Xuemei Pu, Menglong Li
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0196251

Convolutional neural network-based classification system design with compressed wireless sensor network images
Cited by: 20
Author(s): Jungmo Ahn, Jae Yeon Park, Donghwan Park, Jeongyeup Paek, Jeong Gil Ko
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-23337-y

Comparative whole-genome sequence analysis of Mycobacterium tuberculosis isolated from tuberculous meningitis and pulmonary tuberculosis patients
Cited by: 21
Author(s): Kiatichai Faksri, Eryu Xia, Rick Twee‐Hee Ong, Jun Tan, Ditthawat Nonghanphithak, Nampueng Makhao, Nongnard Thamnongdee, Arirat Thanormchat, Arisa Phurattanakornkul, Somcharn Rattanarangsee, Chate Ratanajaraya, Prapat Suriyaphol, Therdsak Prammananan, Yik-Ying Teo, Angkana Chaiprasert
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-018-4475-6

Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome
Cited by: 6
Author(s): Fedor Naumenko, Irina Abnizova, Nathan Beka, Mikhail A. Genaev, Yuriy L. Orlov
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-23168-x

Identification of p38 MAPK as a novel therapeutic target for Friedreich’s ataxia
Cited by: 9
Author(s): M. Grazia Cotticelli, Shujuan J. Xia, Avinash Kaur, Daniel W. Lin, Yongping Wang, Eric Ruff, John W. Tobias, Robert B. Wilson
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0157524

Whole Genome Re-Sequencing and Characterization of Powdery Mildew Disease-Associated Allelic Variation in Melon
Cited by: 29
Author(s): Sathishkumar Natarajan, Hoy‐Taek Kim, Senthil Kumar Thamilarasan, Karpagam Veerappan, Jong-In Park, Ill–Sup Nou
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0062415

A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)
Cited by: 49
Author(s): Christopher M. Seabury, Scot E. Dowd, Paul Seabury, Terje Raudsepp, Donald J. Brightsmith, Poul Liboriussen, Yvette A. Halley, Colleen A. Fisher, Elaine Owens, Ganesh Viswanathan, Ian R. Tizard
Software Mentions: 2
Published: about 13 years ago

10.1038/s41598-018-29190-3

Assembly and Analysis of Unmapped Genome Sequence Reads Reveal Novel Sequence and Variation in Dogs
Cited by: 4
Author(s): Lindsay A. Holden, Meharji Arumilli, Marjo K. Hytönen, Sruthi Hundi, Jarkko Salojärvi, Kim H. Brown, Hannes Lohi
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2105-14-310

A method to identify differential expression profiles of time-course gene data with Fourier transformation
Cited by: 12
Author(s): Jaehee Kim, R. Todd Ogden, Haseong Kim
Software Mentions: 2
Published: almost 13 years ago

10.1038/s41598-018-29240-w

Urine-derived cells: a promising diagnostic tool in Fabry disease patients
Cited by: 22
Author(s): Gisela G. Slaats, Fabian Braun, Martin Hoehne, Laura E. Frech, Linda Blomberg, Thomas Benzing, Bernhard Schermer, Markus M. Rinschen, Christine Kurschat
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2164-12-384

Temperature stress differentially modulates transcription in meiotic anthers of heat-tolerant and heat-sensitive tomato plants
Cited by: 96
Author(s): Craita E. Bita, Sara Zenoni, Wim H. Vriezen, Celestina Mariani, Mario Pezzotti, Tom Geräts
Software Mentions: 2
Published: almost 15 years ago

10.1038/s41598-018-33752-w

The pathogenic mechanisms of Tilletia horrida as revealed by comparative and functional genomics
Cited by: 13
Author(s): Ai‐Jun Wang, Linxiu Pang, Na Wang, Peng Ai, Desuo Yin, Shuangcheng Li, Qi Deng, Jun Zhu, Yueyang Liang, Jianqing Zhu, Ping Li, Anqi Zheng
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-018-34812-x

A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence
Cited by: 35
Author(s): Patrick Lypaczewski, Johanna Hoshizaki, Wen-Wei Zhang, Laura-Isobel McCall, John Torcivia-Rodriguez, Vahan Simonyan, Amanpreet Kaur, Ken Dewar, Greg Matlashewski
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

10.1186/s12859-020-3428-7

LCQS: an efficient lossless compression tool of quality scores with random access functionality
Cited by: 2
Author(s): Jiabing Fu, Bixin Ke, Sujun Dong
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-39808-9

High density linkage map construction and QTL mapping for runner production in allo-octoploid strawberry Fragaria × ananassa based on ddRAD-seq derived SNPs
Cited by: 17
Author(s): Mohammad Rashed Hossain, Sathishkumar Natarajan, Hoy‐Taek Kim, Denison Michael Immanuel Jesse, Lee Cheol-Gyu, Jong-In Park, Ill–Sup Nou
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0147369

Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform
Cited by: 21
Author(s): Tariq Pervaiz, Haifeng Jia, Muhammad Salman Haider, Cheng Zhang, Mengjie Cui, Mengqi Wang, Liwen Cui, Xicheng Wang, Jinggui Fang
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-019-40739-8

Featherweight long read alignment using partitioned reference indexes
Cited by: 13
Author(s): Hasindu Gamaarachchi, Sri Parameswaran, Martin A. Smith
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-015-0705-y

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data
Cited by: 7
Author(s): Gregory K. Farrant, Mark Hoebeke, Frédéric Partensky, Gwendoline Andres, Matthieu Le Corre, Laurence Garczarek
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2105-10-198

A Bayesian approach to efficient differential allocation for resampling-based significance testing
Cited by: 6
Author(s): Shane T. Jensen, Sameer Soi, Li-San Wang
Software Mentions: 2
Published: about 17 years ago

10.1038/s41598-019-41672-6

Utilization of NGS technologies to investigate transcriptomic and epigenomic mechanisms in trastuzumab resistance
Cited by: 7
Author(s): Miguel Nava, Pranabananda Dutta, Robin Farias‐Eisner, Jaydutt V. Vadgama, Yanyuan Wu
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-7-106

A simple method for assessing sample sizes in microarray experiments
Cited by: 94
Author(s): Robert Tibshirani
Software Mentions: 2
Published: over 20 years ago

10.1371/journal.pone.0254796

Removal of peptidoglycan and inhibition of active cellular processes leads to daptomycin tolerance in Enterococcus faecalis
Cited by: 7
Author(s): Rachel D. Johnston, Brittni M. Woodall, Johnathan Harrison, Shawn R. Campagna, Elizabeth Fozo
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-47218-0

E2F1 Drives Breast Cancer Metastasis by Regulating the Target Gene FGF13 and Altering Cell Migration
Cited by: 48
Author(s): Daniel P. Hollern, Matthew Swiatnicki, Jonathan Rennhack, Sean A. Misek, Brooke C. Matson, Andrew McAuliff, Kathleen A. Gallo, Kathleen M. Caron, Eran R. Andrechek
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-47318-x

Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice
Cited by: 3
Author(s): Lin Cheng, Kyu‐Won Kim, Yong‐Jin Park
Software Mentions: 2
Published: about 7 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

10.1371/journal.pone.0174446

Evaluating alignment and variant-calling software for mutation identification in C. elegans by whole-genome sequencing
Cited by: 18
Author(s): Harold E. Smith, Sijung Yun
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-019-50897-4

Enhanced glacial discharge from the eastern Antarctic Peninsula since the 1700s associated with a positive Southern Annular Mode
Cited by: 24
Author(s): William A. Dickens, Gerhard Kuhn, Melanie J. Leng, Alastair G C Graham, Julian A. Dowdeswell, Michael P. Meredith, C. D. Hillenbrand, Dominic A. Hodgson, Roberts Sj, Hilary J. Sloane, James A Smith
Software Mentions: 2
Published: almost 7 years ago

10.1007/s10456-016-9527-4

Identification of HIF-2α-regulated genes that play a role in human microvascular endothelial sprouting during prolonged hypoxia in vitro
Cited by: 40
Author(s): Tessa D. Nauta, Marloes van den Broek, S. Gibbs, Tineke C. T. M. van der Pouw‐Kraan, Cees B.M. Oudejans, Victor W.M. van Hinsbergh, Pieter Koolwijk
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-13-187

Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit
Cited by: 32
Author(s): Viviana Lima-Silva, Abel Rosado, Vítor Amorim‐Silva, Antonio Muñoz‐Mérida, Clara Pons, Aureliano Bombarely, Oswaldo Trelles, Rafael Fernández-Muñoz, Antonio Granell, Victoriano Valpuesta, Miguel A. Botella
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2105-16-S18-S11

Light-RCV: a lightweight read coverage viewer for next generation sequencing data
Cited by: 1
Author(s): Chih Ching Chang, Wen Bin Lee, An Chen-Deng, Tsunglin Liu, Joseph T. Tseng, Darby Tien Hao Chang
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0003686

Dysregulation of Mitochondrial Dynamics and the Muscle Transcriptome in ICU Patients Suffering from Sepsis Induced Multiple Organ Failure
Cited by: 138
Author(s): Katarina Fredriksson, Inga Tjäder, Pernille Keller, Nataša Petrovič, B. Ahlman, Camilla Schéele, Jan Wernerman, James A. Timmons, Olav Rooyackers
Software Mentions: 2
Published: over 17 years ago

10.1186/s12859-019-2996-x

Magic-BLAST, an accurate RNA-seq aligner for long and short reads
Cited by: 178
Author(s): Grzegorz M. Boratyn, Jean Thierry‐Mieg, Danielle Thierry-Mieg, Ben Busby, Thomas Madden
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-020-59207-9

Relationships Between Environmental Conditions And Fish Assemblages In Tropical Savanna Headwater Streams
Cited by: 11
Author(s): Thiago Bernardi Vieira, Francisco Leonardo Tejerina‐Garro
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-59375-8

Full annual monitoring of Subantarctic Emiliania huxleyi populations reveals highly calcified morphotypes in high-CO2 winter conditions
Cited by: 17
Author(s): Andrés S. Rigual-Hernández, Thomas W. Trull, José-Abel Flores, Scott D. Nodder, Ruth Eriksen, Diana M. Davies, Gustaaf M. Hallegraeff, Francisco J. Sierro, Shramik Patil, Aleix Cortina, Anne-Marie Ballegeer, Lisa C. Northcote, F. Abrantes, Marta M. Rufino
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-7-538

Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments
Cited by: 226
Author(s): Maureen A. Sartor, Craig R. Tomlinson, Scott C. Wesselkamper, Siva Sivaganesan, George D. Leikauf, Mario Medvedovic
Software Mentions: 2
Published: over 19 years ago

10.1371/journal.pone.0081004

Development of NMDAR Antagonists with Reduced Neurotoxic Side Effects: a Study on GK11
Cited by: 8
Author(s): Delphine Vandame, Lauriane Ulmann, Marisa Teigell, Monica Prieto-Cappellini, Jacques Vignon, Alain Privat, Regino Perez‐Polo, Olivera Nešić, Hélène Hirbec
Software Mentions: 2
Published: over 12 years ago

10.1038/s41598-020-61942-y

Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome
Cited by: 13
Author(s): Leila Ghanbari Maman, Fahimeh Palizban, Fereshteh Fallah Atanaki, Naser Elmi, Shohreh Ariaeenejad, Mohammad Reza Ghaffari, Kaveh Kavousi
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-62467-0

The trends in land surface heat fluxes over global monsoon domains and their responses to monsoon and precipitation
Cited by: 11
Author(s): Jian Zeng, Qiang Zhang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-62975-z

Metabolomic alternations of follicular fluid of obese women undergoing in-vitro fertilization treatment
Cited by: 14
Author(s): Jing-Yan Song, Shufen Xiang, Conghui Pang, Jiayin Guo, Zhen‐Gao Sun
Software Mentions: 2
Published: over 6 years ago

10.3390/s20164551

CNN and LSTM-Based Emotion Charting Using Physiological Signals
Cited by: 50
Author(s): Muhammad Najam Dar, M. Usman Akram, Sajid Gul Khawaja, Amit N. Pujari
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-8-431

Comparative evaluation of gene-set analysis methods
Cited by: 94
Author(s): Qi Liu, Irina Dinu, Adeniyi J. Adewale, John D. Potter, Yutaka Yasui
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pone.0084060

Whi3, an S. cerevisiae RNA-Binding Protein, Is a Component of Stress Granules That Regulates Levels of Its Target mRNAs
Cited by: 16
Author(s): Kristen J. Holmes, Daniel M. Klass, Evan L. Guiney, Martha S. Cyert
Software Mentions: 2
Published: over 12 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

10.1186/1471-2210-8-16

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: almost 18 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

10.1186/1471-2164-11-47

Expression profiling of prospero in the Drosophila larval chemosensory organ: Between growth and outgrowth
Cited by: 10
Author(s): Laure Guenin, Mahatsangy Raharijaona, Rémi Houlgatte, Fawzia Baba‐Aïssa
Software Mentions: 2
Published: over 16 years ago

10.3390/s21041138

Open-Design for a Smart Cover of a Night-Time Telescope for Day-Time Use
Cited by: 1
Author(s): R. Cedazo, Alberto Brunete, Hugo R. Albarracin, Esteban González
Software Mentions: 2
Published: over 5 years ago

10.3390/s21051792

Learning Subject-Generalized Topographical EEG Embeddings Using Deep Variational Autoencoders and Domain-Adversarial Regularization
Cited by: 7
Author(s): Juan Lorenzo Hagad, Tsukasa Kimura, Kenichi Fukui, Masayuki Numao
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0182756

Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation
Cited by: 20
Author(s): Andrés Chana-Muñoz, Agnieszka Jendroszek, Malene Sønnichsen, Rune Kristiansen, Jan K. Jensen, Peter A. Andreasen, Christian Berthou, Frank Panitz
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-016-2778-z

Multiple adaptive routes of Salmonella enterica Typhimurium to biocide and antibiotic exposure
Cited by: 36
Author(s): Tânia Curião, Emmanuela Marchi, Denis Grandgirard, Ricardo León‐Sampedro, Carlo Viti, Stephen L. Leib, Fernando Baquero, Marco R. Oggioni, José Luis Martínez, Teresa M. Coque
Software Mentions: 2
Published: about 10 years ago

10.3390/s21165279

Rapid Foreign Object Detection System on Seaweed Using VNIR Hyperspectral Imaging
Cited by: 6
Author(s): Donghoon Kwak, Guk-Jin Son, Mi‐Kyung Park, Young-Duk Kim
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0121154

Method Designed to Respect Molecular Heterogeneity Can Profoundly Correct Present Data Interpretations for Genome-Wide Expression Analysis
Cited by: 2
Author(s): Chih‐Hao Chen, Chueh Lin Hsu, Shih-Hao Huang, Shih Yuan Chen, Yi Lin Hung, Hsiao Rong Chen, Yu Chung Wu, Li Su, H. C. Lee
Software Mentions: 2
Published: over 11 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

10.1186/1758-907X-2-2

Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments
Cited by: 83
Author(s): Kevin McCormick, Matthew R. Willmann, Blake C. Meyers
Software Mentions: 2
Published: over 15 years ago

10.1186/1751-0473-7-6

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments
Cited by: 63
Author(s): Ricardo H. Ramírez-González, Raoul Jean Pierre Bonnal, Mario Cáccamo, Dan MacLean
Software Mentions: 2
Published: about 14 years ago

10.1186/s13029-016-0056-8

A new tool for prioritization of sequence variants from whole exome sequencing data
Cited by: 9
Author(s): Brigitte Glanzmann, Hendri Herbst, Craig Kinnear, Marlo Möller, Junaid Gamieldien, Soraya Bardien
Software Mentions: 2
Published: about 10 years ago

10.1186/s13029-016-0058-6

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing
Cited by: 4
Author(s): Takuji Takeuchi, Atsuo Yamada, Takashi Aoki, Kunihiro Nishimura
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12870-021-02970-2

BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon
Cited by: 7
Author(s): Kaori Sakai, Sylvie Citerne, Sébastien Antelme, Philippe Le Bris, Sylviane Daniel, Axelle Bouder, Angélina D’Orlando, Amy Cartwright, Frédérique Tellier, Stéphanie Pateyron, Étienne Delannoy, Debbie Laudencia‐Chingcuanco, Grégory Mouille, Jean-Christophe Palauqui, John P. Vogel, Richard Sibout
Software Mentions: 2
Published: over 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/s40064-016-3728-6

Characterization of saliva microbiota’s functional feature based on metagenomic sequencing
Cited by: 13
Author(s): Fang Yang, Kang Ning, Xiaowei Zeng, Qian Zhou, Xiaoquan Su, Xiao Yuan
Software Mentions: 2
Published: over 9 years ago

10.1186/scrt535

Loss of non-coding RNA expression from the DLK1-DIO3 imprinted locus correlates with reduced neural differentiation potential in human embryonic stem cell lines
Cited by: 106
Author(s): Chu Fan Mo, Fang Wu, Kang-Yu Tai, Wei Chun Chang, Kai Wei Chang, Hung‐Chi Kuo, Hong Nerng Ho, H.-F. Chen, Shau-Ping Lin
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0137404

The Olfactory Transcriptome and Progression of Sexual Maturation in Homing Chum Salmon Oncorhynchus keta
Cited by: 16
Author(s): Arjan P. Palstra, Kosuke Fukaya, Hiroaki Chiba, Ron P. Dirks, Josep V. Planas, Hiroshi Ueda
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13287-018-1050-7

Key genes and integrated modules in hematopoietic differentiation of human embryonic stem cells: a comprehensive bioinformatic analysis
Cited by: 11
Author(s): Pengfei Li, Mengyao Wu, Qiwang Lin, Shu Wang, Tong Chen, Hua Jiang
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-14-337

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data
Cited by: 7
Author(s): Changjin Hong, Nathan Clement, Spencer C. Clement, Saher Sue Hammoud, Douglas T. Carrell, Bradley R. Cairns, Quinn Snell, Mark J. Clement, W. Evan Johnson
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-15-1115

Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo
Cited by: 47
Author(s): Kenji Nakahigashi, Yuki Takai, Yuh Shiwa, Masahiko Wada, Masayuki Honma, Hideki Yoshikawa, Masaru Tomita, Akio Kanai, Hirotada Mori
Software Mentions: 2
Published: over 12 years ago

10.1186/s13287-020-01962-7

Co-encapsulation of HNF4α overexpressing UMSCs and human primary hepatocytes ameliorates mouse acute liver failure
Cited by: 14
Author(s): Defu Kong, Huiming Xu, Mo Chen, Yingchun Yu, Yongbing Qian, Tian Qin, Ying Tong, Qiang Xia, Hualian Hang
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0016807

Microgenomic Analysis in Skeletal Muscle: Expression Signatures of Individual Fast and Slow Myofibers
Cited by: 89
Author(s): Francesco Chemello, Camilla Bean, Pasqua Cancellara, Paolo Laveder, Carlo Reggiani, Gerolamo Lanfranchi
Software Mentions: 2
Published: over 15 years ago

10.1186/s13011-021-00404-8

The Alcohol Use Disorders Identification Test (AUDIT) in the Russian language - a systematic review of validation efforts and application challenges
Cited by: 4
Author(s): Maria Neufeld, Anna Bunova, Carina Ferreira‐Borges, Evgeny А. Bryun, E.V. Fadeeva, Artyom Gil, Б. Э. Горный, Daria Khaltourina, Evgenia Koshkina, А. В. Надеждин, Elena Tetenova, Melita Vujnović, Artyom Gil, Elena Yurasova, Jürgen Rehm
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0004702

Transcript-Specific Expression Profiles Derived from Sequence-Based Analysis of Standard Microarrays
Cited by: 22
Author(s): Anton G. Moll, Maja T. Lindenmeyer, Matthias Kretzler, Peter J. Nelson, Ralf Zimmer, Clemens D. Cohen
Software Mentions: 2
Published: over 17 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566