cran: SAM | Projects | Ecosyste.ms: Papers

10.1186/1471-2164-11-388

Expression of a retinoic acid signature in circulating CD34 cells from coronary artery disease patients
Cited by: 8
Author(s): Tineke C. T. M. van der Pouw Kraan, Stephan H. Schirmer, Joost O. Fledderus, Perry D. Moerland, Josefien M. Baggen, Thomas A. Leyen, A.M. van der Laan, Jan J. Piek, Niels van Royen, Anton J.G. Horrevoets
Software Mentions: 2
Published: over 16 years ago

10.1534/g3.115.017921

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

10.1186/1471-2407-9-104

Prediction of breast cancer by profiling of urinary RNA metabolites using Support Vector Machine-based feature selection
Cited by: 65
Author(s): Carsten Henneges, Dino Bullinger, Richard Fux, Natascha Friese, Harald Seeger, Hans Neubauer, Stefan Laufer, Christoph H. Gleiter, Matthias Schwab, Andreas Zell, Bernd Kammerer
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pgen.1004684

Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability
Cited by: 65
Author(s): Ayesha Hasan, Cristina Cotobal, Caia D. S. Duncan, Juan Mata
Software Mentions: 2
Published: over 11 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/s12885-017-3109-8

Tumour-associated glial host cells display a stem-like phenotype with a distinct gene expression profile and promote growth of GBM xenografts
Cited by: 12
Author(s): Lina Leiss, Ercan Mutlu, Anne Margrete Øyan, Tao Yan, Oleg Tsinkalovsky, Linda Sleire, Kjell Petersen, Mohummad Aminur Rahman, Mireille Kayitesi Johannessen, Siddharta S. Mitra, Hege Karine Jacobsen, Krishna M. Talasila, Hrvoje Miletić, Inge Jonassen, Xingang Li, Nicolas H.C. Brons, Karl‐Henning Kalland, Jian Wang, Per Øyvind Enger
Software Mentions: 2
Published: over 9 years ago

10.1186/s12859-018-2241-z

BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data
Cited by: 5
Author(s): Kristiina Ausmees, Aji John, Salman Toor, Andreas Hellander, Carl Nettelblad
Software Mentions: 2
Published: about 8 years ago

10.1186/s12885-015-1895-4

Argonaute 2 and nasopharyngeal carcinoma: a genetic association study and functional analysis
Cited by: 14
Author(s): Peiyao Li, Jinfeng Meng, Yun Zhai, Hongxing Zhang, Lan Yu, Zhifu Wang, Xiao-Ai Zhang, Pengbo Cao, Xi Chen, Yaling Han, Yang Zhang, Huipeng Chen, Yan Ling, Yuxia Li, Ying Cui, Jin Xin Bei, Yi Xin Zeng, Fuchu He, Gangqiao Zhou
Software Mentions: 2
Published: over 10 years ago

10.1016/j.tplants.2014.02.004

Modelling hormonal response and development
Cited by: 87
Author(s): Ute Voß, Anthony Bishopp, Etienne Farcot, Malcolm J. Bennett
Software Mentions: 2
Published: about 12 years ago

10.1186/s12915-020-00928-8

The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content
Cited by: 5
Author(s): Aristeidis G. Telonis, Isidore Rigoutsos
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-15-540

Building the sugarcane genome for biotechnology and identifying evolutionary trends
Cited by: 97
Author(s): Nathalia de Setta, Cláudia Barros Monteiro-Vitorello, Cushla J. Metcalfe, Guilherme M. Q. Cruz, Luiz-Eduardo Del-Bem, Renato Vicentini, Fábio Tebaldi Silveira Nogueira, Roberto Augusto de Carvalho Campos, Sideny Lima Nunes, Paula Cristina Gasperazzo Turrini, Andréia Prata Vieira, Edgar Andrés Ochoa Cruz, Tatiana Caroline Silveira Corrêa, Carlos Takeshi Hotta, Alessandro de Mello Varani, Sonia Vautrin, Adilson Silva da Trindade, Mariane de Mendonça Vilela, Carolina Gimiliani Lembke, Paloma Mieko Sato, Rodrigo Fandiño de Andrade, Milton Yutaka Nishiyama, Cláudio Benício Cardoso-Silva, Kátia Castanho Scortecci, Antônio Augusto Franco Garcia, Monalisa Sampaio Carneiro, Changsoo Kim, Andrew H. Paterson, Hélène Bergès, Angélique D’Hont, Anete Pereira de Souza, Gláucia Mendes Souza, Michel Vincentz, João Paulo Kitajima, Marie‐Anne Van Sluys
Software Mentions: 2
Published: about 12 years ago

10.1534/g3.116.036673

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

10.1186/1471-2164-14-355

Phase-defined complete sequencing of the HLA genes by next-generation sequencing
Cited by: 106
Author(s): Kazuyoshi Hosomichi, Timothy A. Jinam, Shigeki Mitsunaga, Hirofumi Nakaoka, Ituro Inoue
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2164-14-653

HANDS: a tool for genome-wide discovery of subgenome- specific base-identity in polyploids
Cited by: 9
Author(s): Aziz Mithani, Eric J. Belfield, C. Titus Brown, Caifu Jiang, Lindsey Leach, Nicholas P. Harberd
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

10.1534/g3.118.200134

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

10.1371/journal.pone.0040399

Dynamic Changes in Ezh2 Gene Occupancy Underlie Its Involvement in Neural Stem Cell Self-Renewal and Differentiation towards Oligodendrocytes
Cited by: 56
Author(s): Falak Sher, Erik Boddeke, Marta Olah, Sjef Copray
Software Mentions: 2
Published: about 14 years ago

10.1534/g3.118.200417

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

10.1534/g3.118.200481

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

10.1534/g3.118.200171

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

10.1186/s12859-018-2432-7

Assessing the impact of exact reads on reducing the error rate of read mapping
Cited by: 2
Author(s): Farzaneh Salari, Fatemeh Zare-Mirakabad, Mehdi Sadeghi, Hassan Rokni‐Zadeh
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0093751

Studying the System-Level Involvement of MicroRNAs in Parkinson's Disease
Cited by: 18
Author(s): Paulami Chatterjee, Malay Bhattacharyya, Sanghamitra Bandyopadhyay, Dilip Roy
Software Mentions: 2
Published: over 12 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

10.1002/eji.200838232

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

10.1534/g3.120.401402

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

10.1534/g3.120.401460

Characterization and Fine Mapping of a Yellow-Virescent Gene Regulating Chlorophyll Biosynthesis and Early Stage Chloroplast Development in Brassica napus
Cited by: 16
Author(s): Chuanji Zhao, Lijiang Liu, Luqman Bin Safdar, Meili Xie, Xiaohui Cheng, Yueying Liu, Yu‐Tao Xiang, Chaobo Tong, Jinxing Tu, Junyan Huang, Liu S
Software Mentions: 2
Published: almost 6 years ago

10.1093/g3journal/jkaa053

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

10.1093/g3journal/jkab076

Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen
Cited by: 5
Author(s): Andreína I. Castillo, Rodrigo P. P. Almeida
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0132296

Lung Transcriptomics during Protective Ventilatory Support in Sepsis-Induced Acute Lung Injury
Cited by: 20
Author(s): Marialbert Acosta‐Herrera, Fabián Lorenzo-Díaz, Maria Pino‐Yanes, Almudena Corrales, Francisco Valladares, Tilman E. Klassert, Basilio Valladares, Hortense Slevogt, Shwu‐Fan Ma, Jesús Villar, Carlos Flores
Software Mentions: 2
Published: about 11 years ago

10.1186/s40001-014-0052-x

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

10.1002/1878-0261.12326

Rapid proteomic analysis for solid tumors reveals <scp>LSD</scp> 1 as a drug target in an end‐stage cancer patient
Cited by: 21
Author(s): Sophia Doll, Maximilian C. Kriegmair, Alberto Santos, Michael Wierer, Fabian Coscia, Helen Michele Neil, Štefan Porubský, Philipp Geyer, Andreas Mund, Philipp Nuhn, Matthias Mann
Software Mentions: 2
Published: about 8 years ago

10.3390/genes5020366

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

10.3389/fcell.2020.00242

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

10.1186/s12885-019-5328-7

Identification of non-invasive biomarkers for chronic atrophic gastritis from serum exosomal microRNAs
Cited by: 27
Author(s): Hong Liu, Peiwu Li, Weiqin Yang, Hong Mi, Jinglin Pan, Yuancheng Huang, Zheng-kun Hou, Qiuke Hou, Qi Luo, Fengbin Liu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1006162

Fragment Length of Circulating Tumor DNA
Cited by: 472
Author(s): Hunter R. Underhill, Jacob O. Kitzman, Sabine Hellwig, Noah C. Welker, Riza M. Daza, David Baker, Keith M. Gligorich, Robert Rostomily, Mary P. Bronner, Jay Shendure
Software Mentions: 2
Published: about 10 years ago

10.1128/mBio.00202-18

Community Development betweenPorphyromonas gingivalisandCandida albicansMediated by InlJ and Als3
Cited by: 65
Author(s): Maryta Sztukowska, Lindsay C. Dutton, Christopher Delaney, Mark Ramsdale, Gordon Ramage, Howard F. Jenkinson, Angela H. Nobbs, Richard J. Lamont
Software Mentions: 2
Published: about 8 years ago

10.1128/mBio.00966-18

cAMP Receptor Protein Controls Vibrio cholerae Gene Expression in Response to Host Colonization
Cited by: 41
Author(s): Jainaba Manneh-Roussel, James R. J. Haycocks, Andrés Magán, Nicolás Pérez-Soto, Kerstin Voelz, Andrew Camilli, Anne Marie Krachler, David C. Grainger
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0059190

Compression of FASTQ and SAM Format Sequencing Data
Cited by: 175
Author(s): James K. Bonfield, Matthew V. Mahoney
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2105-15-S8-S3

Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features
Cited by: 27
Author(s): Ashraf Yaseen, Yaohang Li
Software Mentions: 2
Published: about 12 years ago

10.3390/genes9060313

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

10.3390/medicina55090531

The Extent of Extemporaneous Preparation and Regulatory Framework of Extemporaneous Compounding in Latvia
Cited by: 3
Author(s): Olga Kiseļova, Baiba Mauriņa, Venta Šidlovska, Jānis Zvejnieks
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes9090452

Recent Selection on a Class I ADH Locus Distinguishes Southwest Asian Populations Including Ashkenazi Jews
Cited by: 9
Author(s): Shuangshuang Gu, Hui Li, Andrew J. Pakstis, William C. Speed, David Genevieve, Judith R. Kidd, Kenneth K. Kídd
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-021-07554-w

Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Cited by: 10
Author(s): Audald Lloret-Villas, Meenu Bhati, Naveen Kumar Kadri, R. Fries, Hubert Pausch
Software Mentions: 2
Published: about 5 years ago

10.3390/genes10030219

DNA Methylation Patterns in the Round Goby Hypothalamus Support an On-The-Spot Decision Scenario for Territorial Behavior
Cited by: 10
Author(s): Vincent Somerville, Michaela Schwaiger, Philipp Hirsch, Jean‐Claude Walser, Karen Bussmann, Alexandra Weyrich, Patricia Burkhardt‐Holm, Irene Adrian‐Kalchhauser
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-8-383

Genes involved in TGFβ1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map
Cited by: 19
Author(s): Stefano Campanaro, Simone Picelli, Rossella Torregrossa, Laura Colluto, Monica Ceol, Dorella Del Prete, Angela D’Angelo, Giorgio Valle, Franca Anglani
Software Mentions: 2
Published: almost 19 years ago

10.1186/s13058-019-1195-z

Oral metronomic vinorelbine combined with endocrine therapy in hormone receptor-positive HER2-negative breast cancer: SOLTI-1501 VENTANA window of opportunity trial
Cited by: 19
Author(s): Bárbara Adamo, Meritxell Bellet, Laia Paré, Tomás Pascual, María Vidal, José Alejandro Pérez Fidalgo, S. Blanch, Noelia Martínez, Laura Murillo, Patricia Gómez-Pardo, Ana López-González, Kepa Amillano, Jordi Canes, Patricia Galván, Blanca González-Farré, Xavier González, Patricia Villagrasa, Eva Ciruelos, Aleix Prat
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes10090650

Affinity Purification of NF1 Protein–Protein Interactors Identifies Keratins and Neurofibromin Itself as Binding Partners
Cited by: 11
Author(s): Rachel M. Carnes, Robert A. Kesterson, Bruce R. Korf, James A. Mobley, Deeann Wallis
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0005242

Short-Term Calorie Restriction in Male Mice Feminizes Gene Expression and Alters Key Regulators of Conserved Aging Regulatory Pathways
Cited by: 82
Author(s): Preston W. Estep, Jason Warner, Martha L. Bulyk
Software Mentions: 2
Published: over 17 years ago

10.1128/mBio.00764-19

Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to Cryptococcus Pathogens
Cited by: 32
Author(s): Andrew Ryan Passer, Marco A. Coelho, R. Blake Billmyre, Minou Nowrousian, Moritz Mittelbach, Andrey Yurkov, Anna Floyd Averette, Christina A. Cuomo, Sheng Sun, Joseph Heitman
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0091894

A Systematic In Silico Mining of the Mechanistic Implications and Therapeutic Potentials of Estrogen Receptor (ER)-α in Breast Cancer
Cited by: 5
Author(s): Xin Li, Rong Sun, Wanpeng Chen, Bangmin Lu, Xiaoyu Li, Zijie Wang, Ji Bao
Software Mentions: 2
Published: over 12 years ago

10.1007/978-3-030-49392-9_15

Results from a Replicated Experiment on the Affective Reactions of Novice Developers When Applying Test-Driven Development
Cited by: 0
Author(s): Simone Romano, Giuseppe Scanniello, María Teresa Baldassarre, Davide Fucci, Danilo Caivano
Software Mentions: 2
Published: over 6 years ago

10.3390/genes11050534

Investigating Human Mitochondrial Genomes in Single Cells
Cited by: 8
Author(s): Maria Angela Diroma, Angelo Sante Varvara, Marcella Attimonelli, Graziano Pesole, Ernesto Picardi
Software Mentions: 2
Published: about 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

10.1371/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

10.1186/1471-2164-15-765

Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature
Cited by: 80
Author(s): Alba Nicoletta Mininni, Massimo Milan, Serena Ferraresso, T. Petochi, Patrizia Di Marco, G. Marino, Silvia Livi, Chiara Romualdi, Luca Bargelloni, Tomaso Patarnello
Software Mentions: 2
Published: almost 12 years ago

10.1186/1476-4598-12-13

Transcription signatures encoded by ultraconserved genomic regions in human prostate cancer
Cited by: 58
Author(s): Robert S. Hudson, Ming Yi, Natalia Volfovsky, Robyn L. Prueitt, Dominic Esposito, Stefano Volinia, Chang Gong Liu, Aaron J. Schetter, Katrien Van Roosbroeck, Robert M. Stephens, George A. Calin, Carlo M. Croce, Stefan Ambs
Software Mentions: 2
Published: over 13 years ago

10.1186/s13058-021-01457-0

Sensitivity to targeted therapy differs between HER2-amplified breast cancer cells harboring kinase and helical domain mutations in PIK3CA
Cited by: 5
Author(s): Joseph P. Garay, Rebecca Smith, Kaylyn L. Devlin, Daniel P. Hollern, Tiera Liby, Moqing Liu, Shanta Boddapati, Spencer S. Watson, Amanda Esch, Ting Zheng, Wallace Thompson, Darcie Babcock, Sunjong Kwon, Koei Chin, Laura M. Heiser, Joe W. Gray, James E. Korkola
Software Mentions: 2
Published: almost 5 years ago

10.1128/mBio.00633-21

Genome Scale Analysis Reveals IscR Directly and Indirectly Regulates Virulence Factor Genes in Pathogenic Yersinia
Cited by: 4
Author(s): David Balderas, Erin L. Mettert, Hanh Lam, Rajdeep Banerjee, Tomas Gverzdys, Pablo Álvarez, Geetha Saarunya, N. Kyle Tanner, Adam Zoubedi, Yahan Wei, Patricia J. Kiley, Victoria Auerbuch
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-9-478

Global analysis of gene expression changes during retinoic acid-induced growth arrest and differentiation of melanoma: comparison to differentially expressed genes in melanocytes vs melanoma
Cited by: 19
Author(s): Mary H. Estler, Goran Bošković, James Denvir, Sarah Miles, Donald A. Primerano, Richard M. Niles
Software Mentions: 2
Published: almost 18 years ago

10.3390/genes12010046

DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification
Cited by: 8
Author(s): Αθανάσιος Αλεξίου, Dimitrios Zisis, Ioannis Kavakiotis, Marios Miliotis, Antonis Koussounadis, Dimitra Karagkouni, Artemis G. Hatzigeorgiou
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12020167

Leishmania Sexual Reproductive Strategies as Resolved through Computational Methods Designed for Aneuploid Genomes
Cited by: 10
Author(s): Jahangheer Shaik, Deborah E. Dobson, David L. Sacks, Stephen M. Beverley
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2091-11-38

Sex-different hepatic glycogen content and glucose output in rats
Cited by: 38
Author(s): Catharina Gustavsson, Kamal Yassin, Erik Wahlström, Louisa Cheung, Johan Lindberg, Kerstin Brismar, Claes‐Göran Östenson, Gunnar Norstedt, Petra Tollet-Egnell
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2164-15-801

Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach
Cited by: 31
Author(s): Matteo Dell’Acqua, Andrea Zuccolo, Metin Tuna, L. Gianfranceschi, Mario Enrico Pè
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0041001

Transcriptome Profiling of the Cancer, Adjacent Non-Tumor and Distant Normal Tissues from a Colorectal Cancer Patient by Deep Sequencing
Cited by: 65
Author(s): Yanan Wu, Xuetao Wang, WU Fang-bo, Ruolei Huang, Fangqin Xue, Guantao Liang, Min Tao, Peng Cai, Yi Huang
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2105-7-353

A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates
Cited by: 12
Author(s): Anne-Mette K. Hein, Sylvia Richardson
Software Mentions: 2
Published: about 20 years ago

10.1186/1471-2164-9-546

Transcriptional response of rat frontal cortex following acute In Vivo exposure to the pyrethroid insecticides permethrin and deltamethrin
Cited by: 18
Author(s): Joshua Harrill, Zhen Li, Fred A. Wright, Nicholas M. Radio, William R. Mundy, Rogelio Tornero‐Velez, Kevin M. Crofton
Software Mentions: 2
Published: over 17 years ago

10.1186/s12859-015-0626-9

BitMapper: an efficient all-mapper based on bit-vector computing
Cited by: 31
Author(s): Haoyu Cheng, Huaipan Jiang, Jiaoyun Yang, Yun Xu, Yi Shang
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0065571

Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia
Cited by: 36
Author(s): Qiaojun Wen, Linda Y. Liu, Ting Yang, Cantas Alev, Shao-Yi Wu, David K. Stevenson, Guojun Sheng, Atul J. Butte, Xuefeng B. Ling
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pgen.1007494

Evolutionary plasticity in the innate immune function of Akirin
Cited by: 30
Author(s): Jolanta Polanowska, Jia‐Xuan Chen, Julien Soulé, Shizue Omi, Jérôme Belougne, Clara Taffoni, Nathalie Pujol, Matthias Selbach, Olivier Zugasti, Jonathan J. Ewbank
Software Mentions: 2
Published: about 8 years ago

10.1128/mSystems.00023-16

Thermus and the Pink Discoloration Defect in Cheese
Cited by: 67
Author(s): Lisa Quigley, Daniel J. O’Sullivan, David F.M. Daly, Órla O’Sullivan, Zuzana Burdíková, Rostislav Váňa, Tom Beresford, R. Paul Ross, Gerald F. Fitzgerald, P.L.H. McSweeney, Linda Giblin, Jeremiah J. Sheehan, Paul D. Cotter
Software Mentions: 2
Published: about 10 years ago

10.1590/1678-4685-GMB-2017-0031

Ecological drivers of plant genetic diversity at the southern edge of geographical distributions: Forestal vines in a temperate region
Cited by: 7
Author(s): Michel J. F. Barros, José Alexandre Felizola Diniz‐Filho, Loreta B. Freitas
Software Mentions: 2
Published: over 8 years ago

10.1186/1479-5876-4-29

Gene expression in acute Stanford type A dissection: a comparative microarray study
Cited by: 44
Author(s): Barbara Theresia Weis-Müller, Olga Modlich, Irina Drobinskaya, Derya Unay, Rita Huber, Hans Bojar, Jochen D. Schipke, P. Feindt, E. Gams, Wolfram Müller, Timm O. Goecke, W. Sandmann
Software Mentions: 2
Published: about 20 years ago

10.1128/mSystems.00156-18

Neisseria gonorrhoeae Exposed to Sublethal Levels of Hydrogen Peroxide Mounts a Complex Transcriptional Response
Cited by: 14
Author(s): Sarah J. Quillin, Adam J. Hockenberry, Michael C. Jewett, H. Steven Seifert
Software Mentions: 2
Published: over 7 years ago

10.1155/2018/3797214

CRISPR/Cas9 System: A Bacterial Tailor for Genomic Engineering
Cited by: 15
Author(s): Bilal Ahmad Lone, Shibendra Kumar Lal Karna, Fawad Ahmad, Nerina Shahi, Yuba Raj Pokharel
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12943-018-0890-1

Proteogenomic characterization and comprehensive integrative genomic analysis of human colorectal cancer liver metastasis
Cited by: 56
Author(s): Yu‐Shui Ma, Tao Huang, Xiaoming Zhong, Hongwei Zhang, Xianling Cong, Hong Xu, Gai‐Xia Lu, Fei Yu, Sheng Xue, Zhongwei Lv, Da Fu
Software Mentions: 2
Published: almost 8 years ago

10.1128/mSystems.00920-20

phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes
Cited by: 156
Author(s): Harald R. Gruber‐Vodicka, Brandon K. B. Seah, Elmar Pruesse
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2407-6-92

Genomic alterations identified by array comparative genomic hybridization as prognostic markers in tamoxifen-treated estrogen receptor-positive breast cancer
Cited by: 67
Author(s): Wonshik Han, Mi Seon Han, Jason Kang, Ji-Yeon Bae, Ji Hyun Lee, Young Ju Bae, Jeong Eon Lee, Hwa Yong Shin, Ki‐Tae Hwang, Sungeun Hwang, Sung-Won Kim, Dong‐Young Noh
Software Mentions: 2
Published: over 20 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/s12859-016-0942-8

Intra- and interspecies gene expression models for predicting drug response in canine osteosarcoma
Cited by: 30
Author(s): Jared S. Fowles, Kristen C. Brown, Ann Hess, Dawn L. Duval, Daniel L. Gustafson
Software Mentions: 2
Published: over 10 years ago

10.1016/j.gdata.2014.10.008

Base-resolution DNA methylation landscape of zebrafish brain and liver
Cited by: 21
Author(s): Aniruddha Chatterjee, Peter A. Stockwell, Julia A. Horsfield, Ian M. Morison, Shinichi Nakagawa
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-016-0881-4

PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events
Cited by: 40
Author(s): Osagie Izuogu, Abd A. Alhasan, Hani M. Al-Afghani, Mauro Santibanez‐Koref, David J. Elliott, Michael S. Jackson
Software Mentions: 2
Published: over 10 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.pntd.0005216

Yersinia enterocolitica, a Neglected Cause of Human Enteric Infections in Côte d’Ivoire
Cited by: 28
Author(s): Saraka Daniel, Cyril Savin, Stéphane Kan Kouassi, Bakary Cissé, Eugène Koffi, Nicolas Cabanel, Sylvie Brémont, H. Faye-Ketté, Mireille Dosso, Élisabeth Carniel
Software Mentions: 2
Published: over 9 years ago

10.1186/s12935-018-0603-2

Expression profile analysis of antisense long non-coding RNA identifies WDFY3-AS2 as a prognostic biomarker in diffuse glioma
Cited by: 30
Author(s): Fan Wu, Zheng Zhao, Rui‐Chao Chai, Yuqing Liu, Kuanyu Wang, Zhiliang Wang, Guanzhang Li, Ruoyu Huang, Haiyan Jiang, Kenan Zhang
Software Mentions: 2
Published: about 8 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

10.1371/journal.pntd.0005398

A multistrain approach to studying the mechanisms underlying compatibility in the interaction between Biomphalaria glabrata and Schistosoma mansoni
Cited by: 34
Author(s): Richard Galinier, Emmanuel Roger, Yves Moné, David Timothy Duval, Anaïs Portet, Silvain Pinaud, Cristian Chaparro, Christoph Grunau, Clémence Genthon, Emeric Dubois, Anne Rognon, Nathalie Arancibia, Bernard Dejean, André Thèron, Benjamin Gourbal, Guillaume Mitta
Software Mentions: 2
Published: over 9 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

10.1186/gb-2006-7-9-r83

Cited by: 53
Author(s): Nandini Krishnamurthy, D. Brown, Daniel Kirshner, Kimmen Sjölander
Software Mentions: 2
Published: over 20 years ago

10.1186/1471-2164-15-1084

RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature
Cited by: 72
Author(s): Derrick Coble, Damarius S. Fleming, Michael E. Persia, C. M. Ashwell, Max F. Rothschild, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 2
Published: over 12 years ago

10.1155/2020/5859023

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

10.1186/bcr1608

Gene expression signatures of morphologically normal breast tissue identify basal-like tumors
Cited by: 121
Author(s): Greg Finak, Svetlana Sadekova, François Pépin, Michael Hallett, Sarkis Meterissian, Fawaz Halwani, Karim Khetani, Margarita Souleimanova, Brent Zabolotny, Atilla Ömeroğlu, Morag Park
Software Mentions: 2
Published: almost 20 years ago

10.1186/s12864-017-3980-3

Mining sequence variations in representative polyploid sugarcane germplasm accessions
Cited by: 37
Author(s): Xiping Yang, Song Jiang, Qi You, Dev Paudel, Jisen Zhang, Jianping Wang
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0165543

Identification of Genes Discriminating Multiple Sclerosis Patients from Controls by Adapting a Pathway Analysis Method
Cited by: 4
Author(s): Lei Zhang, Linlin Wang, Pu Tian, Suyan Tian
Software Mentions: 2
Published: over 9 years ago

10.1007/s00439-016-1658-6

Novel bioinformatic developments for exome sequencing
Cited by: 36
Author(s): Stefan H. Lelieveld, Joris A. Veltman, Christian Gilissen
Software Mentions: 2
Published: over 10 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/gb-2007-8-5-r69

Towards the uniform distribution of null P values on Affymetrix microarrays
Cited by: 29
Author(s): Anthony A. Fodor, Timothy L. Tickle, Christine Richardson
Software Mentions: 2
Published: over 19 years ago

10.1186/1471-2105-10-S8-S5

An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D
Cited by: 6
Author(s): José M. G. Izarzugaza, Anja Barešić, Lisa E. M. McMillan, Corin Yeats, Andrew B. Clegg, Christine A. Orengo, Andrew C.R. Martin, Alfonso Valencia
Software Mentions: 2
Published: almost 17 years ago

10.1186/1748-7188-7-17

Analysis of Metabolic Subnetworks by Flux Cone Projection
Cited by: 31
Author(s): Sayed-Amir Marashi, László Dávid, Alexander Bockmayr
Software Mentions: 2
Published: about 14 years ago

10.1186/gb-2008-9-2-r38

Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia
Cited by: 27
Author(s): Li Wei Chang, Jacqueline E. Payton, Wenlin Yuan, Timothy J. Ley, Rakesh Nagarajan, Gary D. Stormo
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pntd.0004930

Sex-Biased Transcriptome of Schistosoma mansoni: Host-Parasite Interaction, Genetic Determinants and Epigenetic Regulators Are Associated with Sexual Differentiation
Cited by: 53
Author(s): Marion Picard, Jérôme Boissier, David Roquis, Christoph Grunau, Jean‐François Allienne, David Timothy Duval, Ève Toulza, Nathalie Arancibia, Conor R. Caffrey, Ting Long, Sabine Nidelet, Marine Rohmer, Céline Cosseau
Software Mentions: 2
Published: almost 10 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566