cran: SAM | Projects | Ecosyste.ms: Papers

10.1186/s12937-018-0384-4

Severely malnourished children with a low weight-for-height have a higher mortality than those with a low mid-upper-arm-circumference: I. Empirical data demonstrates Simpson’s paradox
Cited by: 23
Author(s): Emmanuel Grellety, Michael Golden
Software Mentions: 2
Published: almost 8 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

10.1371/journal.pone.0168585

The Effect of Random Error on Diagnostic Accuracy Illustrated with the Anthropometric Diagnosis of Malnutrition
Cited by: 31
Author(s): Emmanuel Grellety, Michael Golden
Software Mentions: 2
Published: over 9 years ago

10.3390/nu10091255

Lactobacillus acidophilus DDS-1 Modulates the Gut Microbiota and Improves Metabolic Profiles in Aging Mice
Cited by: 57
Author(s): Ravichandra Vemuri, Rajaraman Eri, Rohit Gundamaraju, Shakuntla Gondalia, Avinash V. Karpe, David J. Beale, Christopher Martoni, Rajaraman Eri
Software Mentions: 2
Published: almost 8 years ago

10.3390/nu9040390

Novel Genetic Variants Associated with Child Refractory Esophageal Stricture with Food Allergy by Exome Sequencing
Cited by: 1
Author(s): Min Yang, Min Xiong, Huan Chen, Lanlan Geng, Peiyu Chen, Jing Xie, Shui Qing Ye, Ding‐You Li, Sitang Gong
Software Mentions: 2
Published: over 9 years ago

10.3390/nu13062120

Untargeted Plasma Metabolomics Unravels a Metabolic Signature for Tissue Sensitivity to Glucocorticoids in Healthy Subjects: Its Implications in Dietary Planning for a Healthy Lifestyle
Cited by: 4
Author(s): Nicolas C. Nicolaides, Maria-Konstantina Ioannidi, Eleni Koniari, Ifigeneia Papageorgiou, Αnastasia Bartzeliotou, Amalia Sertedaki, Maria I. Klapa, Evangelia Charmandari
Software Mentions: 2
Published: about 5 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

10.3389/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

10.1186/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

10.1186/1471-2105-12-453

iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences
Cited by: 119
Author(s): Yi Zheng, Liangjun Zhao, Junping Gao, Zhangjun Fei
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2105-5-157

Cited by: 33
Author(s): Andrew F. Neuwald, Jun S. Liu
Software Mentions: 2
Published: over 22 years ago

10.1186/1471-2105-12-494

Identifying elemental genomic track types and representing them uniformly
Cited by: 24
Author(s): Sveinung Gundersen, Matúš Kalaš, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Kjetil Sandve
Software Mentions: 2
Published: over 14 years ago

10.1128/AEM.01808-20

Mapping the Efficacy and Mode of Action of Ethylzingerone [4-(3-Ethoxy-4-Hydroxyphenyl) Butan-2-One] as an Active Agent against Burkholderia Bacteria
Cited by: 1
Author(s): Laura Rushton, Ahmad Khodr, Florence Ménard-Szczebara, Jean‐Yves Maillard, Sylvie Cupferman, Eshwar Mahenthiralingam
Software Mentions: 2
Published: almost 6 years ago

10.3390/biology10090841

Spatiotemporal Regulation and Functional Analysis of Circular RNAs in Skeletal Muscle and Subcutaneous Fat during Pig Growth
Cited by: 9
Author(s): Biao Li, Jinzeng Yang, Jun He, Yan Gong, Yu Xiao, Qinghua Zeng, Kang Xu, Yehui Duan, Jun He, Haiming Ma
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2105-10-61

A comparison on effects of normalisations in the detection of differentially expressed genes
Cited by: 16
Author(s): Monica Chiogna, M. Sofia Massa, Davide Risso, Chiara Romualdi
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pgen.1002972

Tethering of the Conserved piggyBac Transposase Fusion Protein CSB-PGBD3 to Chromosomal AP-1 Proteins Regulates Expression of Nearby Genes in Humans
Cited by: 30
Author(s): Lucas T. Gray, Kimberly K. Fong, Thomas Pavelitz, Alan M. Weiner
Software Mentions: 2
Published: almost 14 years ago

10.1242/bio.011585

The canonical eIF4E isoform ofC. elegansregulates growth, embryogenesis, and germline sex-determination
Cited by: 8
Author(s): Richard S. Mangio, SarahBeth Votra, David Pruyne
Software Mentions: 2
Published: about 11 years ago

10.1186/1745-6150-4-12

Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans
Cited by: 2
Author(s): Karim Mezhoud, Haïtham Sghaier, Insaf Barkallah
Software Mentions: 2
Published: over 17 years ago

10.1186/1745-6150-1-18

Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples
Cited by: 21
Author(s): Jaroslav Novák, Mia Miller, Douglas A. Bell
Software Mentions: 2
Published: about 20 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

10.1186/1471-2105-14-310

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

10.1093/bioinformatics/btv524

RNF: a general framework to evaluate NGS read mappers
Cited by: 8
Author(s): Karel Břinda, Valentina Boeva, Grégory Kucherov
Software Mentions: 2
Published: almost 11 years ago

10.1093/bioinformatics/bts408

Accurate estimation of short read mapping quality for next-generation genome sequencing
Cited by: 30
Author(s): Matthew Ruffalo, Mehmet Koyutürk, Soumya Ray, Thomas LaFramboise
Software Mentions: 2
Published: almost 14 years ago

10.1093/bioinformatics/btaa051

BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis
Cited by: 6
Author(s): Gianvito Urgese, Emanuele Parisi, Orazio Maria Scicolone, Santa Di Cataldo, Elisa Ficarra
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-10-295

Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus
Cited by: 20
Author(s): Christian Obermeier, Bashir Hosseini, W. Friedt, Rod J. Snowdon
Software Mentions: 2
Published: over 17 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

10.1186/1471-2105-11-176

Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays
Cited by: 17
Author(s): Gregor Štiglic, Mateja Bajgot, Peter Kokol
Software Mentions: 2
Published: over 16 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

10.1371/journal.pntd.0003951

Lutzomyia longipalpis Presence and Abundance Distribution at Different Micro-spatial Scales in an Urban Scenario
Cited by: 22
Author(s): María Soledad Santini, María Eugenia Utgés, Pablo Berrozpe, Mariana Manteca Acosta, Natalia Casas, Paola Heuer, Oscar Daniel Salomón
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pntd.0006452

Metabolite profiling for biomarkers in Schistosoma haematobium infection and associated bladder pathologies
Cited by: 17
Author(s): Adewale Adebayo, Swapnil Mundhe, Henrietta Oluwatoyin Awobode, Olugbenga Samson Onile, Atinuke M Agunloye, Raphael D. Isokpehi, Yogesh S. Shouche, Santhakumari Bayatigeri, Chiaka I. Anumudu
Software Mentions: 2
Published: about 8 years ago

10.1093/bioinformatics/btw526

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V’DJer
Cited by: 57
Author(s): Lisle E. Mose, Sara R. Selitsky, Lisa M. Bixby, David Marron, Michael D. Iglesia, Jonathan S. Serody, Charles M. Perou, Benjamin G. Vincent, Joel S. Parker
Software Mentions: 2
Published: almost 10 years ago

10.1093/bioinformatics/btt422

DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments
Cited by: 1
Author(s): Chiao‐Feng Lin, Otto Valladares, Daniel Micah Childress, Egor Klevak, Evan Geller, Yi‐Ting Hwang, Ellen Tsai, Gerard D. Schellenberg, Li-San Wang
Software Mentions: 2
Published: almost 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

10.1186/1471-2105-8-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

10.1093/bioinformatics/btz041

SVIM: structural variant identification using mapped long reads
Cited by: 148
Author(s): David Heller, Martin Vingron
Software Mentions: 2
Published: over 7 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: about 10 years ago

10.1093/bioinformatics/btaa760

OGRE: Overlap Graph-based metagenomic Read clustEring
Cited by: 5
Author(s): Marleen Balvert, Xiao Luo, Ernestina Hauptfeld, Alexander Schönhuth, Bas E. Dutilh
Software Mentions: 2
Published: almost 6 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: about 8 years ago

10.1371/journal.pntd.0001966

Temporal Dynamics of the Transcriptional Response to Dengue Virus Infection in Nicaraguan Children
Cited by: 51
Author(s): Stephen J. Popper, Aubree Gordon, Minghsun Liu, Ángel Balmaseda, Eva Harris, David A. Relman
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0128059

Chronic Hyperglycemia Induces Trans-Differentiation of Human Pancreatic Stellate Cells and Enhances the Malignant Molecular Communication with Human Pancreatic Cancer Cells
Cited by: 20
Author(s): Katalin Kiss, Kornélia Baghy, Sándor Spisák, Szilárd Szanyi, Zsolt Tulassay, Attila Zalatnai, Matthias Löhr, Ralf Jesenofsky, Ilona Kovalszky, Gábor Firneisz
Software Mentions: 2
Published: about 11 years ago

10.1186/1756-0381-3-4

SICTIN: Rapid footprinting of massively parallel sequencing data
Cited by: 11
Author(s): Stefan Enroth, Robin Andersson, Claes Wadelius, Jan Komorowski
Software Mentions: 2
Published: almost 16 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

10.1186/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

10.1371/journal.pone.0123925

Computational Ranking of Yerba Mate Small Molecules Based on Their Predicted Contribution to Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus
Cited by: 9
Author(s): Caroline S. Rempe, Kellie P. Burris, Hyun-Joo Woo, Benjamin Goodrich, Denise Koessler Gosnell, Timothy J. Tschaplinski, C. Neal Stewart
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2105-12-210

A novel and well-defined benchmarking method for second generation read mapping
Cited by: 73
Author(s): Manuel Holtgrewe, Anne-Katrin Emde, David Weese, Knut Reinert
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pgen.1001231

Identification of Y-Box Binding Protein 1 As a Core Regulator of MEK/ERK Pathway-Dependent Gene Signatures in Colorectal Cancer Cells
Cited by: 79
Author(s): Karsten Jürchott, Ralf‐Jürgen Kuban, Till Krech, Nils Blüthgen, Ulrike Stein, Wolfgang Walther, Christian Friese, Szymon M. Kiełbasa, Ute Ungethüm, Per Lund, Thomas Knösel, Wolfgang Kemmner, Markus Morkel, Johannes Fritzmann, Peter M. Schlag, Walter Birchmeier, Tammo Krueger, Silke Sperling, Christine Sers, Hans-Dieter Royer, Hanspeter Herzel, Reinhold Schäfer
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0079523

Comprehensive RNA-Seq Expression Analysis of Sensory Ganglia with a Focus on Ion Channels and GPCRs in Trigeminal Ganglia
Cited by: 106
Author(s): Stavros Manteniotis, Ramona Lehmann, Caroline Flegel, Felix C. E. Vogel, Adrian Hofreuter, Benjamin S. P. Schreiner, Janine Altmüller, Christian Becker, Nicole Schöbel, Hanns Hatt, Günter Gisselmann
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-10-47

A general modular framework for gene set enrichment analysis
Cited by: 322
Author(s): Marit Ackermann, Korbinian Strimmer
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2164-7-33

Tests for differential gene expression using weights in oligonucleotide microarray experiments
Cited by: 9
Author(s): Pingzhao Hu, Joseph Beyene, Celia M.T. Greenwood
Software Mentions: 2
Published: over 20 years ago

10.1186/1471-2156-10-48

Single-feature polymorphism discovery by computing probe affinity shape powers
Cited by: 11
Author(s): Wayne Xu, Seungho Cho, Sungjin Yang, Yung–Tsi Bolon, Hatice Bilgiç, Haiyan Jia, Yongqiang Xiong, Gary J. Muehlbauer
Software Mentions: 2
Published: almost 17 years ago

10.1186/1752-0509-4-136

Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks
Cited by: 77
Author(s): Monika Ray, Weixiong Zhang
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2156-15-4

On the relationship between an Asian haplotype on chromosome 6 that reduces androstenone levels in boars and the differential expression of SULT2A1 in the testis
Cited by: 7
Author(s): A.M. Hidalgo, J.W.M. Bastiaansen, B. Harlizius, Hendrik‐Jan Megens, Ole Madsen, R.P.M.A. Crooijmans, Martien A. M. Groenen
Software Mentions: 2
Published: over 12 years ago

10.1186/s12918-018-0656-9

Analysis of significant protein abundance from multiple reaction-monitoring data
Cited by: 0
Author(s): Jongsu Jun, Jungsoo Gim, Yongkang Kim, Hyunsoo Kim, Su Jong Yu, Injun Yeo, Jiyoung Park, Jeong‐Ju Yoo, Young Youn Cho, Dong Hoon Lee, Eun Ju Cho, Jeong Hoon Lee, Yoon Jun Kim, Seungyeoun Lee, Jung Hwan Yoon, Youngsoo Kim, Taesung Park
Software Mentions: 2
Published: over 7 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

10.1186/1752-0509-4-S2-S5

Shrunken methodology to genome-wide SNPs selection and construction of SNPs networks
Cited by: 7
Author(s): Yang Liu, Michael K. Ng
Software Mentions: 2
Published: almost 16 years ago

10.1186/1752-0509-7-S6-S12

Missing value imputation for microarray data: a comprehensive comparison study and a web tool
Cited by: 34
Author(s): Chia Chun Chiu, Shih Yao Chan, Chung Ching Wang, Wei Wu
Software Mentions: 2
Published: over 12 years ago

10.1186/1752-0509-7-14

Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties
Cited by: 51
Author(s): Yuanhua Liu, Valentina Devescovi, Suning Chen, Christine Nardini
Software Mentions: 2
Published: over 13 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

10.1186/s12918-018-0653-z

Reframing gene essentiality in terms of adaptive flexibility
Cited by: 11
Author(s): Gabriela I. Guzmán, Connor A. Olson, Ying Hefner, Patrick V. Phaneuf, Edward Catoiu, Lais B. Crepaldi, Lucas Goldschmidt Micas, Bernhard Ø. Palsson, Adam M. Feist
Software Mentions: 2
Published: over 7 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

10.1186/1752-0509-4-134

Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche
Cited by: 58
Author(s): Eugenio Azpeitia, Mariana Benítez, Iliusi Vega, Cuauhtémoc Calderón Villarreal, Elena Alvarez–Buylla
Software Mentions: 2
Published: almost 16 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

10.1186/s12864-016-3030-6

Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler
Cited by: 125
Author(s): Samuel S. Shepard, Sarah Meno, Justin Bahl, Malania M. Wilson, John Barnes, Elizabeth B. Neuhaus
Software Mentions: 2
Published: almost 10 years ago

10.1186/1752-0509-5-46

Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells
Cited by: 8
Author(s): Francisco Azuaje, Haiying Wang, Huiru Zheng, Frédérique Léonard, Magali Rolland-Turner, Lu Zhang, Yvan Devaux, Daniel R. Wagner
Software Mentions: 2
Published: over 15 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

10.1186/1471-2148-14-19

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

10.1186/1471-2105-13-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

10.1186/1472-6807-6-9

Fold-recognition and comparative modeling of human α2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni
Cited by: 8
Author(s): Sujatha, Petety V. Balaji
Software Mentions: 2
Published: over 20 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/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

10.1186/1472-6807-6-24

Cited by: 26
Author(s): Rudra P. Saha, Pinak Chakrabarti
Software Mentions: 2
Published: over 20 years ago

10.1186/1756-0500-7-157

In silico prediction of protein-protein interactions in human macrophages
Cited by: 4
Author(s): Oussema Souiai, Fatma Z. Guerfali, Slimane Ben Miled, Catherine Brun, Alia Benkahla
Software Mentions: 2
Published: over 12 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

10.1002/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: about 6 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/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

10.1186/s13104-016-1847-3

SeqTools: visual tools for manual analysis of sequence alignments
Cited by: 22
Author(s): Gemma Barson, Ed Griffiths
Software Mentions: 2
Published: over 10 years ago

10.1186/1756-0500-6-365

Variable selection methods for developing a biomarker panel for prediction of dengue hemorrhagic fever
Cited by: 17
Author(s): Huangxian Ju, Allan R. Brasier
Software Mentions: 2
Published: almost 13 years ago

10.18632/oncotarget.12624

LncRNA profile study reveals four-lncRNA signature associated with the prognosis of patients with anaplastic gliomas
Cited by: 57
Author(s): Wen Wang, Fan Yang, Lu Zhang, Jing Chen, Zheng Zhao, Haoyuan Wang, Fan Wu, Tingyu Liang, Xiaoyan Yan, Jiye Li, Qing Lan, Jiangfei Wang, Jizong Zhao
Software Mentions: 2
Published: almost 10 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

10.18632/oncotarget.13718

DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival
Cited by: 15
Author(s): Thomas Fleischer, Jovana Klajic, Miriam Ragle Aure, Riku Louhimo, Arne V. Pladsen, Lars Ottestad, Nizar Touleimat, Marko Laakso, Ann Rita Halvorsen, Grethe I.G. Alnæs, Margit Riis, Åslaug Helland, Sampsa Hautaniemi, Per Eystein Lønning, Bjørn Naume, Anne‐Lise Børresen‐Dale, Jörg Tost, Vessela N. Kristensen
Software Mentions: 2
Published: over 9 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

10.18632/oncotarget.11931

A highly invasive subpopulation of MDA-MB-231 breast cancer cells shows accelerated growth, differential chemoresistance, features of apocrine tumors and reduced tumorigenicityin vivo
Cited by: 26
Author(s): Adriana Amaro, Giovanna Ángelini, Valentina Mirisola, Alba Esposito, Daniele Reverberi, Serena Matis, Massimo Maffei, Walter Giaretti, Maurizio Viale, Rosaria Gangemi, Laura Emionite, Simonetta Astigiano, Michele Cilli, Beatrice E. Bachmeier, Peter H. Killian, Adriana Albini, Ulrich Pfeffer
Software Mentions: 2
Published: almost 10 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

10.18632/oncotarget.11996

Differential expression analysis for individual cancer samples based on robust within-sample relative gene expression orderings across multiple profiling platforms
Cited by: 41
Author(s): Qingzhou Guan, Rou Chen, Haidan Yan, Hao Cai, You Guo, Mengyao Li, Xiangyu Li, Man‐Li Tong, Lu Ao, Hongdong Li, Hong Guan, Zheng Guo
Software Mentions: 2
Published: almost 10 years ago

10.18632/oncotarget.10586

Bioinformatics facilitating the use of microarrays to delineate potential miRNA biomarkers in aristolochic acid nephropathy
Cited by: 3
Author(s): Yana Lv, Yumei Que, Qiao Su, Qiang Li, Xi Chen, Haitao Lü
Software Mentions: 2
Published: about 10 years ago

10.18632/oncotarget.11570

Comparative profiling between primary colorectal carcinomas and metastases identifies heterogeneity on drug resistance
Cited by: 10
Author(s): Feng Luo, Jinbang Li, Shuai Wu, Xuefang Wu, Meixiang Chen, Xueyun Zhong, Kunping Liu
Software Mentions: 2
Published: almost 10 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/s13104-015-1382-7

cFinder: definition and quantification of multiple haplotypes in a mixed sample
Cited by: 6
Author(s): Norbert Niklas, Julia Hafenscher, Agnes Barna, Karin Wiesinger, Johannes Pröll, Stephan Dreiseitl, Sandra Preuner-Stix, Peter Valent, Thomas Lion, Christian Gabriel
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13048-015-0176-9

Gene expression profiling of ovarian carcinomas and prognostic analysis of outcome
Cited by: 10
Author(s): Shengyun Cai, Tian Yang, Yu Chen, Jingwen Wang, L i Li, Man Xu
Software Mentions: 2
Published: almost 11 years ago

10.18632/oncotarget.11726

A three-gene signature for prognosis in patients with MGMT promoter-methylated glioblastoma
Cited by: 37
Author(s): Wen Wang, Lu Zhang, Zheng Wang, Fan Yang, Haoyuan Wang, Tingyu Liang, Fan Wu, Qing Lan, Jiangfei Wang, Jizong Zhao
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12984-017-0312-4

Adaptive hybrid robotic system for rehabilitation of reaching movement after a brain injury: a usability study
Cited by: 18
Author(s): Francisco Resquín, José González-Vargas, Jaime Ibáñez, F. Brunetti, I. Dimbwadyo, Laura Carrasco, Silas Franco dos Reis Alves, Carlos González-Alted, A. Gomez-Blanco, José L. Pons
Software Mentions: 2
Published: almost 9 years ago

10.2196/jmir.4233

Preventing Alcohol Abuse Through Social Networking Sites: A First Assessment of a Two-Year Ecological Approach
Cited by: 12
Author(s): Valentin Flaudias, Ingrid de Chazeron, Oulmann Zerhouni, Jordane Boudesseul, Laurent Bègue, Renaud Bouthier, Christel Lévrier, Pierre Michel Llorca, Georges Brousse
Software Mentions: 2
Published: over 10 years ago

10.1186/s12974-020-01992-1

NFATc2-dependent epigenetic upregulation of CXCL14 is involved in the development of neuropathic pain induced by paclitaxel
Cited by: 13
Author(s): Meng Li, Subo Zhang, Yuxuan Luo, Yanling Yang, Xiangzhong Zhang, Bo Li, Yan Meng, Yuan-Jie Chen, Ruixian Guo, Yang Xiong, Wenjun Xin, Dai Li
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms22020512

Chromatin Manipulation and Editing: Challenges, New Technologies and Their Use in Plants
Cited by: 8
Author(s): Kateryna Fal, Denisa Tomkova, Gilles Vachon, Marie‐Edith Chabouté, Alexandre Berr, Cristel C. Carles
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22041703

Transcriptome-Wide Analysis of Stationary Phase Small ncRNAs in E. coli
Cited by: 13
Author(s): Nicole Raad, Hannes Luidalepp, Michel Fasnacht, Norbert Polacek
Software Mentions: 2
Published: over 5 years ago

10.1186/s12974-017-0937-z

Bioinformatics analysis of glial inflammatory responses to air pollution
Cited by: 0
Author(s): Chenyu Li, Wei Jiang, Nina Tang, Yan Xu
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.12038

COL3A1 and SNAP91: novel glioblastoma markers with diagnostic and prognostic value
Cited by: 52
Author(s): Yuanfeng Gao, Xiao‐Yuan Mao, Tao Zhu, Chen-Xue Mao, Zhixiong Liu, Zhibin Wang, Ling Li, Xi Li, Ji‐Ye Yin, Wei Zhang, Hong‐Hao Zhou, Zhao‐Qian Liu
Software Mentions: 2
Published: almost 10 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566