cran: SAM | Projects | Ecosyste.ms: Papers

10.1186/ar2300

The influence of the NOD Nss1/Idd5 loci on sialadenitis and gene expression in salivary glands of congenic mice
Cited by: 13
Author(s): Trond Ove R. Hjelmervik, Anna-Karin Lindqvist, Kjell Petersen, Martina Johannesson, Anne-Kristin Stavrum, Ann-Katrin Johansson, Roland Jönsson, Rikard Holmdahl, Anne Isine Bolstad
Software Mentions: 1
Published: over 19 years ago

10.1186/ar4637

Identification of stage-specific genes associated with lupus nephritis and response to remission induction in NZB/W and NZM2410 mice
Cited by: 0
Author(s): Ramalingam Bethunaickan, Céline C. Berthier, Weijia Zhang, Ridvan Eksi, Hongdong Li, Yuanfang Guan, Matthias Kretzler, Anne Davidson
Software Mentions: 1
Published: over 12 years ago

10.1186/s13075-016-1050-x

Whole-genome transcription and DNA methylation analysis of peripheral blood mononuclear cells identified aberrant gene regulation pathways in systemic lupus erythematosus
Cited by: 95
Author(s): Honglin Zhu, Wentao Mi, Hui Luo, Tao Chen, Shengxi Liu, Indu Raman, Xiaoxia Zuo, Quan Zhen Li
Software Mentions: 1
Published: about 10 years ago

10.1186/s13075-015-0695-1

Molecular characterization of systemic sclerosis esophageal pathology identifies inflammatory and proliferative signatures
Cited by: 47
Author(s): Jaclyn N. Taroni, Viktor Martyanov, Chiang Ching Huang, James Mahoney, Ikuo Hirano, Brandon B. Shetuni, Guang Yang, Darren M. Brenner, Barbara Jung, Tammara A. Wood, Swati Bhattacharyya, Orit Almagor, Jung Hwa Lee, Arlene Sirajuddin, John Varga, Rowland W. Chang, Michael L. Whitfield, Monique Hinchcliff
Software Mentions: 1
Published: about 11 years ago

10.1186/ar4362

Transcriptional landscapes of emerging autoimmunity: transient aberrations in the targeted tissue’s extracellular milieu precede immune responses in Sjögren’s syndrome
Cited by: 25
Author(s): Nicolas Delaleu, Cuong Q. Nguyen, Kidane Tekle, Roland Jönsson, Ammon B. Peck
Software Mentions: 1
Published: over 13 years ago

10.1186/ar1985

Identification of arthritis-related gene clusters by microarray analysis of two independent mouse models for rheumatoid arthritis
Cited by: 52
Author(s): Noriyuki Fujikado, Shinobu Saijo, Yoichiro Iwakura
Software Mentions: 1
Published: over 20 years ago

10.1186/s13075-016-0991-4

Comparative analysis of gene expression profiles in normal hip human cartilage and cartilage from patients with necrosis of the femoral head
Cited by: 20
Author(s): Ruiyu Liu, Qi Liu, Kunzheng Wang, Xiaoqian Dang, Feng Zhang
Software Mentions: 1
Published: about 10 years ago

10.1186/s13075-017-1360-7

Limited cutaneous systemic sclerosis skin demonstrates distinct molecular subsets separated by a cardiovascular development gene expression signature
Cited by: 13
Author(s): Emma Derrett-Smith, Viktor Martyanov, Cecilia Beatrice Chighizola, Pia Moinzadeh, Corrado Campochiaro, Korsa Khan, Tammara A. Wood, Pier Luigi Meroni, David Abraham, Voon H Ong, Robert Lafyatis, Michael L. Whitfield, Christopher P. Denton
Software Mentions: 1
Published: about 9 years ago

10.1186/ar4609

Inflammatory expression profiles in monocyte-to-macrophage differentiation in patients with systemic lupus erythematosus and relationship with atherosclerosis
Cited by: 27
Author(s): Benjamin Korman, Chiang-Ching Huang, Carly Skamra, Peggy Wu, Renee E. Koessler, David Yao, Qi Huang, William Pearce, Kim Sutton-Tyrrell, George T. Kondos, Daniel Edmundowicz, Richard M. Pope, Rosalind Ramsey‐Goldman
Software Mentions: 1
Published: over 12 years ago

10.1186/ar1990

Gene profiling in white blood cells predicts infliximab responsiveness in rheumatoid arthritis
Cited by: 132
Author(s): Thierry Lequerré, Anne-Christine Gauthier-Jauneau, Carine Bansard, Céline Derambure, Martine Hiron, Olivier Vittecoq, Maryvonne Daveau, O. Mejjad, A. Daragon, François Tron, Xavier Le Loët, Jean‐Philippe Salier
Software Mentions: 1
Published: over 20 years ago

10.1186/ar1751

Cited by: 57
Author(s): Takahito Tsubaki, Norimasa Arita, Takuma Kawakami, Takayuki Shiratsuchi, Haruyasu Yamamoto, Nobuo Takubo, Kazuhito Yamada, Satoshi Nakata, Sachiko Yamamoto, Masato Nose
Software Mentions: 1
Published: over 21 years ago

10.1186/ar3555

Plasma proteins present in osteoarthritic synovial fluid can stimulate cytokine production via Toll-like receptor 4
Cited by: 254
Author(s): Dong Hyun Sohn, Jeremy Sokolove, Orr Sharpe, Jennifer C. Erhart, Piyanka Chandra, Lauren J. Lahey, Tamsin M. Lindström, Inyong Hwang, Katherine A. Boyer, Thomas P. Andriacchi, William H. Robinson
Software Mentions: 1
Published: over 14 years ago

10.1186/ar2706

Blood autoantibody and cytokine profiles predict response to anti-tumor necrosis factor therapy in rheumatoid arthritis
Cited by: 104
Author(s): Wolfgang Hueber, Beren Tomooka, Franak Batliwalla, Wentian Li, Paul A. Monach, Robert Tibshirani, Ronald F. van Vollenhoven, Jon Lampa, Kazuyoshi Saito, Yoshiya Tanaka, Mark C. Genovese, Lars Klareskog, Peter K. Gregersen, William H. Robinson
Software Mentions: 1
Published: over 17 years ago

10.1186/s13075-017-1252-x

Multiplex serum protein analysis reveals potential mechanisms and markers of response to hyperimmune caprine serum in systemic sclerosis
Cited by: 6
Author(s): Niamh Quillinan, Kristina E. N. Clark, Bryan Youl, Jeffrey Vernes, D. McIntosh, Syed Atiqul Haq, Christopher P. Denton
Software Mentions: 1
Published: over 9 years ago

10.1186/s13075-015-0839-3

A subset of CD163+ macrophages displays mixed polarizations in discoid lupus skin
Cited by: 36
Author(s): Benjamin F. Chong, Lin Chiang Tseng, Gregory A. Hosler, Noelle Teske, Song Zhang, David R. Karp, Nancy J. Olsen, Chandra Mohan
Software Mentions: 1
Published: over 10 years ago

10.1186/ar1501

Cited by: 137
Author(s): Dominique Baeten, Elli Kruithof, Leen De Rycke, Anemieke M Boots, Herman Mielants, Eric Veys, Filip De Keyser
Software Mentions: 1
Published: over 21 years ago

10.1186/ar2771

Type I interferon receptor controls B-cell expression of nucleic acid-sensing Toll-like receptors and autoantibody production in a murine model of lupus
Cited by: 66
Author(s): Donna L Thibault, Kareem Graham, Lowen Y. Lee, Imelda Balboni, Paul J. Hertzog, Paul J. Utz
Software Mentions: 1
Published: over 17 years ago

10.1186/s13075-016-1113-z

A functional variant of TLR10 modifies the activity of NFkB and may help predict a worse prognosis in patients with rheumatoid arthritis
Cited by: 34
Author(s): Silvia Torices, Antonio Julià, Pedro Muñoz, Ignacio Varela, Alejandro Balsa, Sara Marsal, Antonio Fernández‐Nebro, Francisco J. Blanco, Marcos López‐Hoyos, Víctor M. Martínez‐Taboada, José L. Fernández-Luna
Software Mentions: 1
Published: almost 10 years ago

10.1186/ar3707

Specific post-translational histone modifications of neutrophil extracellular traps as immunogens and potential targets of lupus autoantibodies
Cited by: 148
Author(s): Chih Long Liu, Stephanie Tangsombatvisit, Jacob M. Rosenberg, Gil Mandelbaum, Emily C Gillespie, Or Gozani, Ash A. Alizadeh, Paul J. Utz
Software Mentions: 1
Published: over 14 years ago

10.1089/ast.2017.1717

The Search for Hesperian Organic Matter on Mars: Pyrolysis Studies of Sediments Rich in Sulfur and Iron
Cited by: 16
Author(s): J. M. T. Lewis, Jens Najorka, Jonathan S. Watson, M. A. Sephton
Software Mentions: 1
Published: over 8 years ago

10.1089/ast.2018.1819

Recovery of Fatty Acids from Mineralogic Mars Analogs by TMAH Thermochemolysis for the Sample Analysis at Mars Wet Chemistry Experiment on the Curiosity Rover
Cited by: 30
Author(s): Amy J. Williams, J. L. Eigenbrode, Melissa Floyd, Mary Beth Wilhelm, Shane S. O’Reilly, S. S. Johnson, Kathleen L. Craft, C. A. Knudson, S. Andrejkovičová, J. M. T. Lewis, Arnaud Buch, Daniel P. Glavin, Caroline Freissinet, R. Williams, Cyril Szopa, M. Millán, Roger E. Summons, A. C. McAdam, Kathleen C. Benison, Rafael Navarro‐González, C. A. Malespin, P. R. Mahaffy
Software Mentions: 1
Published: over 7 years ago

10.5194/amt-11-4129-2018

CALIPSO lidar level 3 aerosol profile product: version 3 algorithm design
Cited by: 98
Author(s): Jason L. Tackett, David M. Winker, Brian Getzewich, Mark Vaughan, Stuart A. Young, Jayanta Kar
Software Mentions: 1
Published: about 8 years ago

10.3758/s13414-020-02105-z

Influence of arousal on intentional binding: Impaired action binding, intact outcome binding
Cited by: 8
Author(s): Anna Render, Petra Jansen
Software Mentions: 1
Published: almost 6 years ago

10.1192/pb.bp.114.050005

Mobile telephone apps in mental health practice: uses, opportunities and challenges
Cited by: 32
Author(s): Justin Marley, Saeed Farooq
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2105-15-S7-S5

Inference of radio-responsive gene regulatory networks using the graphical lasso algorithm
Cited by: 18
Author(s): Jung Hun Oh, Joseph O. Deasy
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-7-S4-S8

The impact of sample imbalance on identifying differentially expressed genes
Cited by: 22
Author(s): Kun Yang, Jianzhong Li, Hong Gao
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2105-12-304

Applications of the pipeline environment for visual informatics and genomics computations
Cited by: 31
Author(s): Ivo D. Dinov, Federica Torri, Fabìo Macciardi, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan, Paul Eggert, Jonathan Pierce, Alex Genco, James A. Knowles, Andrew P. Clark, John D. Van Horn, Joseph Ames, Carl Kesselman, Arthur W. Toga
Software Mentions: 1
Published: about 15 years ago

10.1186/s12859-017-1829-z

Detecting large deletions at base pair level by combining split read and paired read data
Cited by: 2
Author(s): Matthew J. Hayes, Jeremy S. Pearson
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2105-6-172

The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
Cited by: 87
Author(s): Jan Kosiński, Marcin Feder, Janusz M. Bujnicki
Software Mentions: 1
Published: about 21 years ago

10.1186/1471-2105-8-242

Improving gene set analysis of microarray data by SAM-GS
Cited by: 240
Author(s): Irina Dinu, John D. Potter, Thomas Mueller, Qi Liu, Adeniyi J. Adewale, Gian S. Jhangri, G. Einecke, Konrad S. Famulski, Philip F. Halloran, Yutaka Yasui
Software Mentions: 1
Published: about 19 years ago

10.1186/1471-2105-9-357

Impact of residue accessible surface area on the prediction of protein secondary structures
Cited by: 42
Author(s): Amir Momen-Roknabadi, Mehdi Sadeghi, Hamid Pezeshk, Sayed-Amir Marashi
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2105-7-333

A methodology for global validation of microarray experiments
Cited by: 69
Author(s): Mathieu Miron, Owen Z. Woody, Alexandre Marcil, Carl Murie, Robert Sladek, Robert Nadon
Software Mentions: 1
Published: about 20 years ago

10.1186/1471-2105-14-S14-S10

Towards human-computer synergetic analysis of large-scale biological data
Cited by: 6
Author(s): Rahul Singh, Hui Yang, Ben Dalziel, Daniel Asarnow, William Murad, David Foote, Matthew Gormley, Jonathon H. Stillman, Susan J. Fisher
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2105-10-131

SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip
Cited by: 7
Author(s): Hironori Fujisawa, Youko Horiuchi, Yoshiaki Harushima, Toyoyuki Takada, Shinto Eguchi, Takako Mochizuki, Takayuki Sakaguchi, Toshihiko Shiroishi, Nori Kurata
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2105-9-231

Automating dChip: toward reproducible sharing of microarray data analysis
Cited by: 61
Author(s): Cheng Li
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2105-6-67

Cited by: 28
Author(s): Li Fu, Casey S Fu-Liu
Software Mentions: 1
Published: over 21 years ago

10.1186/1471-2105-9-187

Significance analysis of microarray for relative quantitation of LC/MS data in proteomics
Cited by: 56
Author(s): Bryan A. P. Roxas, Qingbo Li
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2105-15-S11-S10

SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data
Cited by: 7
Author(s): Yan Peng, Andrew S. Maxwell, Natalie D. Barker, Jennifer G. Laird, Alan J. Kennedy, Nan Wang, Chaoyang Zhang, Ping Gong
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2105-7-399

Cancer diagnosis marker extraction for soft tissue sarcomas based on gene expression profiling data by using projective adaptive resonance theory (PART) filtering method
Cited by: 28
Author(s): Hiro Takahashi, Toru Nemoto, Teruhiko Yoshida, Hiroyuki Honda, Tadashi Hasegawa
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2105-7-297

Impact of RNA structure on the prediction of donor and acceptor splice sites
Cited by: 19
Author(s): Sayed-Amir Marashi, Changiz Eslahchi, Hamid Pezeshk, Mehdi Sadeghi
Software Mentions: 1
Published: about 20 years ago

10.1186/1471-2105-6-99

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER
Cited by: 53
Author(s): Markus Wistrand, Erik L. L. Sonnhammer
Software Mentions: 1
Published: over 21 years ago

10.1186/1471-2105-14-S5-S3

Joint genotype inference with germline and somatic mutations
Cited by: 4
Author(s): Eric Bareke, Virginie Saillour, Jean-François Spinella, Ramón Vidal, Jasmine Healy, Daniel Sinnett, Miklós Csürös
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-6-86

Cited by: 24
Author(s): Prinal Trivedi, Jode W. Edwards, Jelai Wang, Gary L. Gadbury, Vinodh Srinivasasainagendra, Stanislav O. Zakharkin, Kyoungmi Kim, Tapan Mehta, Jacob P. L. Brand, Amit Patki, Grier P. Page, David B. Allison
Software Mentions: 1
Published: over 21 years ago

10.1186/1471-2105-7-181

Detection of divergent genes in microbial aCGH experiments
Cited by: 8
Author(s): Lars Snipen, Dirk Repsilber, Ludvig Nyquist, Andreas Ziegler, Ågot Aakra, Are H. Aastveit
Software Mentions: 1
Published: over 20 years ago

10.1186/s12859-015-0594-0

Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data
Cited by: 16
Author(s): Susan Higashi, Cyril Fournier, Christian Gautier, Christine Gaspin, Marie‐France Sagot
Software Mentions: 1
Published: about 11 years ago

10.1186/s12859-020-03918-3

S-conLSH: alignment-free gapped mapping of noisy long reads
Cited by: 8
Author(s): Angana Chakraborty, Burkhard Morgenstern, Sanghamitra Bandyopadhyay
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-10-240

Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology
Cited by: 17
Author(s): Tao Xu, Jianlei Gu, Yan Zhou, Linfang Du
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2105-7-19

OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments
Cited by: 18
Author(s): Morgan N. Price, Adam P. Arkin, Eric J. Alm
Software Mentions: 1
Published: over 20 years ago

10.1186/1471-2105-15-S7-S1

ADaM: augmenting existing approximate fast matching algorithms with efficient and exact range queries
Cited by: 2
Author(s): Nathan Clement, Lee Parnell Thompson, Daniel P. Miranker
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-7-49

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

10.1186/1471-2105-10-5

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

10.1186/1471-2105-16-S18-S5

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

10.1186/1471-2105-7-99

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

10.1186/1471-2105-15-S9-S12

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

10.1186/1471-2105-11-400

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

10.1186/1471-2105-13-244

The LO-BaFL method and ALS microarray expression analysis
Cited by: 9
Author(s): Cristina Baciu, Kevin J. Thompson, Jean-Luc Mougeot, Benjamin Rix Brooks, Juliane Weller
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2105-9-S9-S10

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
Cited by: 222
Author(s): Leming Shi, Wendell Jones, Roderick V. Jensen, Stephen Harris, Roger Perkins, Federico Goodsaid, Lei Guo, Lisa J. Croner, Cecilie Boysen, Hong Fang, Feng Qian, Shashi Amur, Wenjun Bao, Cátálin Bárbácioru, Vincent Bertholet, Xiaoxi Cao, Tzu Ming Chu, Patrick J. Collins, Xiao Hui Fan, Felix W. Frueh, James C. Fuscoe, Xu Guo, Jing Han, Damir Herman, Huixiao Hong, Ernest S. Kawasaki, Quan Zhen Li, Yuling Luo, Yunqing Ma, Nan Mei, Ron L. Peterson, Raj K. Puri, Richard Shippy, Zhenqiang Su, Yongming Sun, Hongmei Sun, Brett T. Thorn, Yaron Turpaz, Charles Wang, Sue Jane Wang, Janet A. Warrington, James C. Willey, Jie Wu, Qian Xie, Liang Zhang, Lu Zhang, Sheng Zhong, Russell D. Wolfinger, Weida Tong
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2105-9-49

A dynamic Bayesian network approach to protein secondary structure prediction
Cited by: 62
Author(s): Xin‐Qiu Yao, Huaiqiu Zhu, Zhen‐Su She
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2105-9-142

Ranking analysis of F-statistics for microarray data
Cited by: 10
Author(s): Yuan De Tan, Myriam Fornage, Hongyan Xu
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2105-13-S7-S9

Comparison of data-merging methods with SVM attribute selection and classification in breast cancer gene expression
Cited by: 38
Author(s): Vitoantonio Bevilacqua, Paolo Pannarale, Mirko Abbrescia, Claudia Cava, Angelo Paradiso, Stefania Tommasi
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2105-5-185

Cited by: 33
Author(s): Virginie Aris, Michael J. Cody, Jeff Cheng, James Dermody, Patricia Soteropoulos, Michael Recce, Peter Tolias
Software Mentions: 1
Published: over 22 years ago

10.1186/s12859-018-2207-1

NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
Cited by: 28
Author(s): Fang Li, Jiang Hu, Depeng Wang, Kai Wang
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-019-2690-z

Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking
Cited by: 12
Author(s): David Gilbert, Monika Heiner, Leila Ghanbar, Jacek Chodak
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-5-201

Cited by: 12
Author(s): Kayvan Najarian, Maryam Zaheri, Ali Ajdari Rad, Siamak Najarian, Javad Dargahi
Software Mentions: 1
Published: over 22 years ago

10.1186/1471-2105-15-89

TSSAR: TSS annotation regime for dRNA-seq data
Cited by: 52
Author(s): Fabian Amman, Michael T. Wolfinger, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler, Sven Findeiß
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-13-65

The MULTICOM toolbox for protein structure prediction
Cited by: 27
Author(s): Jianlin Cheng, Jilong Li, Zheng Wang, Jesse Eickholt, Xin Deng
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-11-26

Detecting disease associated modules and prioritizing active genes based on high throughput data
Cited by: 70
Author(s): Yuqing Qiu, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-13-238

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
Cited by: 1,003
Author(s): Mark Chaisson, Glenn Tesler
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12859-015-0523-2

Secondary structural entropy in RNA switch (Riboswitch) identification
Cited by: 15
Author(s): Amirhossein Manzourolajdad, Jonathan Arnold
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-7-105

The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies
Cited by: 26
Author(s): Roel G.W. Verhaak, Frank J. T. Staal, Peter J.M. Valk, Bob Löwenberg, Marcel J. T. Reinders, Dick de Ridder
Software Mentions: 1
Published: over 20 years ago

10.1186/1471-2105-8-359

Differential analysis for high density tiling microarray data
Cited by: 7
Author(s): Srinka Ghosh, Heather A. Hirsch, Edward A. Sekinger, Philipp Kapranov, Kevin Struhl, T Gingeras
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2105-14-123

An efficient post-hoc integration method improving peak alignment of metabolomics data from GCxGC/TOF-MS
Cited by: 10
Author(s): Jaesik Jeong, Xiang Zhang, Xue Shi, Seongho Kim, Changyu Shen
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-7-369

Robust computational reconstitution – a new method for the comparative analysis of gene expression in tissues and isolated cell fractions
Cited by: 13
Author(s): Martin Hoffmann, Dirk Pohlers, Dirk Koczan, Hans‐Jürgen Thiesen, Stefan Wölfl, Raimund W. Kinne
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2105-5-148

Cited by: 27
Author(s): Dietmar E. Martin, Philippe Demougin, Michael N. Hall, Michel Bellis
Software Mentions: 1
Published: over 22 years ago

10.1186/1471-2105-8-422

SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets
Cited by: 14
Author(s): Carmen Lai, Hugo M. Horlings, Marc J. van de Vijver, Eric H. van Beers, Petra M. Nederlof, Lodewyk Wessels, Marcel J. T. Reinders
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2105-8-74

Gene selection with multiple ordering criteria
Cited by: 34
Author(s): James J. Chen, Chen‐An Tsai, ShengLi Tzeng, Chun-Houh Chen
Software Mentions: 1
Published: over 19 years ago

10.1186/s12859-015-0512-5

Identification of active miRNA and transcription factor regulatory pathways in human obesity-related inflammation
Cited by: 22
Author(s): Ximei Zhang, Lin Guo, Mei-Hua Chi, Hongmei Sun, Xiaowen Chen
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-8-230

A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance
Cited by: 70
Author(s): Shunpu Zhang
Software Mentions: 1
Published: about 19 years ago

10.1186/1471-2105-14-S15-S15

Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat
Cited by: 14
Author(s): Vincent Ranwez, Yan Holtz, Gautier Sarah, Morgane Ardisson, Sylvain Santoni, Sylvain Glémin, Muriel Tavaud-Pirra, Jacques David
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12859-019-3078-9

A disease-related gene mining method based on weakly supervised learning model
Cited by: 1
Author(s): Han Zhang, Xueting Huo, Xia Guo, Xin Su, Xiongwen Quan, Jin Chen
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-8-149

Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli
Cited by: 12
Author(s): Gunnar Schramm, Marc Zapatka, Roland Eils, Rainer König
Software Mentions: 1
Published: about 19 years ago

10.1186/1471-2105-7-30

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data
Cited by: 192
Author(s): Ming Yi, Jay D. Horton, Jonathan C. Cohen, Helen H. Hobbs, Robert M. Stephens
Software Mentions: 1
Published: over 20 years ago

10.1186/1471-2105-8-14

Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation
Cited by: 47
Author(s): Rob Jelier, Guido Jenster, Lambert C. J. Dorssers, Bas J. Wouters, Peter J.M. Hendriksen, Barend Mons, Ruud Delwel, Jan A. Kors
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2105-9-114

Effects of dependence in high-dimensional multiple testing problems
Cited by: 197
Author(s): KI Kyung In Kim, Mark A. van de Wiel
Software Mentions: 1
Published: over 18 years ago

10.1186/s12859-018-2253-8

HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads
Cited by: 8
Author(s): Stefano Beretta, Murray Patterson, Tobias Marschall, Marcel Martin, Simone Zaccaria, Gianluca Della Vedova, Paola Bonizzoni
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-020-03584-5

Hap10: reconstructing accurate and long polyploid haplotypes using linked reads
Cited by: 8
Author(s): Sina Majidian, Mohammad Hossein Kahaei, Dick de Ridder
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2105-11-299

poolMC: Smart pooling of mRNA samples in microarray experiments
Cited by: 35
Author(s): Raghunandan M. Kainkaryam, Angela Bruex, Anna C. Gilbert, John Schiefelbein, Peter J. Woolf
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2105-7-414

Semi-supervised discovery of differential genes
Cited by: 2
Author(s): Shigeyuki Oba, Shin lshii
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2105-12-90

Using context to improve protein domain identification
Cited by: 32
Author(s): Alejandro Ochoa, Manuel Llinás, Mona Singh
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-017-1470-x

BATVI: Fast, sensitive and accurate detection of virus integrations
Cited by: 17
Author(s): Chandana Tennakoon, Wing-Kin Sung
Software Mentions: 1
Published: over 9 years ago

10.1186/s12859-021-04088-6

Fast and SNP-aware short read alignment with SALT
Cited by: 0
Author(s): Wei Quan, Bo Liu, Yadong Wang
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2105-12-305

IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data
Cited by: 27
Author(s): Hyunsoo Kim, Yingtao Bi, Sharmistha Pal, Ravi Gupta, Ramana V. Davuluri
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2105-10-43

An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters
Cited by: 17
Author(s): Qingbo Li, Bryan A. P. Roxas
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-12-S13-S15

Finding consistent disease subnetworks across microarray datasets
Cited by: 39
Author(s): Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-13-135

β-empirical Bayes inference and model diagnosis of microarray data
Cited by: 7
Author(s): Mohammad Manir Hossain Mollah, Md. Nurul Haque Mollah, Hirohisa Kishino
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2105-14-6

More powerful significant testing for time course gene expression data using functional principal component analysis approaches
Cited by: 40
Author(s): Shuang Wu, Hulin Wu
Software Mentions: 1
Published: over 13 years ago

10.1186/s12859-021-04184-7

SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks
Cited by: 1
Author(s): Shaya Akbarinejad, Mostafa Hadadian Nejad Yousefi, Maziar Goudarzi
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2105-7-328

Computational expression deconvolution in a complex mammalian organ
Cited by: 76
Author(s): Min Wang, Stephen R. Master, Lewis A. Chodosh
Software Mentions: 1
Published: about 20 years ago

10.1186/s12859-017-1515-1

Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO
Cited by: 35
Author(s): Yuan Zuo, Yi Cui, Guoqiang Yu, Ruijiang Li, Habtom W. Ressom
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-8-364

A Latent Variable Approach for Meta-Analysis of Gene Expression Data from Multiple Microarray Experiments
Cited by: 58
Author(s): Hyungwon Choi, Ronglai Shen, Arul M. Chinnaiyan, Debashis Ghosh
Software Mentions: 1
Published: almost 19 years ago

Projects: cran: SAM

Science Score: 85/100

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Papers Mentioning SAM 4,566