cran: SAM | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1000160

The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function
Cited by: 90
Author(s): Marco Punta, Yishai Ofran
Software Mentions: 2
Published: almost 18 years ago

10.1186/1471-2105-7-152

Domain-based small molecule binding site annotation
Cited by: 27
Author(s): Kevin A. Snyder, Hume A. Feldman, Michel Dumontier, John J. Salama, Christopher W. V. Hogue
Software Mentions: 2
Published: over 20 years ago

10.1186/s12958-015-0088-y

The rat placental renin-angiotensin system - a gestational gene expression study
Cited by: 14
Author(s): Kanchan Vaswani, Hsiu‐Wen Chan, Pali Verma, Marloes Dekker Nitert, Hassendrini N. Peiris, Ryan J Wood-Bradley, James A. Armitage, Gregory E. Rice, Murray D. Mitchell
Software Mentions: 2
Published: about 11 years ago

10.1186/1465-9921-14-80

Microarray profiling reveals suppressed interferon stimulated gene program in fibroblasts from scleroderma-associated interstitial lung disease
Cited by: 81
Author(s): Gisela Lindahl, Carmel Stock, Shiwen Xu, Patricio Clark Di Leoni, Piersante Sestini, Sarah Howat, George Bou‐Gharios, Andrew G. Nicholson, Christopher P. Denton, Jan C. Grutters, Toby M. Maher, Adrian Wells, David Abraham, Elisabetta A. Renzoni
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pcbi.1002256

Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers
Cited by: 9
Author(s): Andrew Tae-Jun Kwon, Alice Chou, David J. Arenillas, Wyeth W. Wasserman
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pcbi.1008809

Latching dynamics as a basis for short-term recall
Cited by: 7
Author(s): Kwang Il Ryom, Vezha Boboeva, Oleksandra Soldatkina, Alessandro Treves
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1000574

Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis
Cited by: 47
Author(s): Wolfram Stacklies, Fei Xia, Frauke Gräter
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pcbi.1000718

Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance
Cited by: 11
Author(s): Bernie J. Daigle, Alicia Deng, Tracey McLaughlin, Samuel W. Cushman, Margaret C. Cam, Gerald M. Reaven, Philip S. Tsao, Russ B. Altman
Software Mentions: 2
Published: over 16 years ago

10.1038/srep09506

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

10.1371/journal.pgen.1000081

Genomic Profiling Identifies GATA6 as a Candidate Oncogene Amplified in Pancreatobiliary Cancer
Cited by: 94
Author(s): Kevin Kwei, Murali D. Bashyam, Jennifer L. Kao, Raman Ratheesh, E. Chandrakanth Reddy, Young H. Kim, Kelli Montgomery, Craig P. Giacomini, Yoon La Choi, Sreejata Chatterjee, Collins Karikari, Keyan Salari, Pei Wang, Tina Hernandez‐Boussard, G Swarnalata, Matt van de Rijn, Anirban Maitra, Jonathan R. Pollack
Software Mentions: 2
Published: over 18 years ago

10.1038/s41598-017-00788-3

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

10.1371/journal.pgen.1005483

Retinoic Acid Signaling Regulates Differential Expression of the Tandemly-Duplicated Long Wavelength-Sensitive Cone Opsin Genes in Zebrafish
Cited by: 49
Author(s): Diana Mitchell, Craig B. Stevens, Ruth A. Frey, Samuel S. Hunter, Ryuichi Ashino, Shoji Kawamura, Deborah L. Stenkamp
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1008871

Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans
Cited by: 14
Author(s): Shelby Priest, Marco A. Coelho, Verónica Mixão, Shelly Applen Clancey, Yitong Xu, Sheng Sun, Toni Gabaldón, Joseph Heitman
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1007092

Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway
Cited by: 12
Author(s): Sara J. Hanson, Kevin Byrne, Kenneth H. Wolfe
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pgen.1000163

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq
Cited by: 518
Author(s): Alexandra Sittka, Sacha Lucchini, Kai Papenfort, Cynthia M. Sharma, Katarzyna Rolle, Tim T. Binnewies, Jay C. D. Hinton, Jörg Vogel
Software Mentions: 2
Published: about 18 years ago

10.1186/s12864-015-1227-8

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential
Cited by: 33
Author(s): Joshua D. Welch, Jeanette Baran-Gale, Charles M. Perou, Praveen Sethupathy, Jan F. Prins
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1004766

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences
Cited by: 155
Author(s): Val F. Lanza, María de Toro, M. Pilar Garcillán-Barcia, Azucena Mora, Jorge Blanco, Teresa M. Coque
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-017-09285-z

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

10.1038/s41598-017-08492-y

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

10.1038/s41598-017-09089-1

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

10.1371/journal.pgen.1007812

Stress-responsive and metabolic gene regulation are altered in low S-adenosylmethionine
Cited by: 19
Author(s): Wei Ding, Daniel P. Higgins, Dilip Kumar Yadav, Adwait Anand Godbole, Read Pukkila-Worley, Alec J. Walker
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-017-09247-5

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

10.1038/s41598-017-10493-w

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

10.1186/s12913-016-1871-y

A systematic review of the quality of studies on dementia prevalence in Italy
Cited by: 7
Author(s): G. Bruti, Elisabetta Cavallucci, Michele Mancini, Alessandro Bitossi, Marzia Baldereschi, Sandro Sorbi
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12913-016-1741-7

A systematic review of the quality of studies on dementia prevalence in Italy
Cited by: 5
Author(s): G. Bruti, Elisabetta Cavallucci, Michele Mancini, Alessandro Bitossi, Marzia Baldereschi, Sandro Sorbi
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12915-020-0763-0

Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner
Cited by: 28
Author(s): Tess Cherlin, Rogan Magee, Jing Yi, Venetia Pliatsika, Phillipe Loher, Isidore Rigoutsos
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-017-15516-0

Identification of selection signals by large-scale whole-genome resequencing of cashmere goats
Cited by: 35
Author(s): Xiaokai Li, Rui Su, Wenting Wan, Wenguang Zhang, Jiang Huai-zhi, Xuguang Qiao, Yixing Fan, Yanjun Zhang, Ruijun Wang, Zhihong Liu, Zhiying Wang, Bin Liu, Yue Ma, Hongping Zhang, Qianjun Zhao, Tao Zhong, Ran Di, Yu Jiang, Wei Chen, Wen Wang, Yang Dong, Jinquan Li
Software Mentions: 2
Published: almost 9 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

10.1038/s41598-017-16700-y

A microsatellite repeat in PCA3 long non-coding RNA is associated with prostate cancer risk and aggressiveness
Cited by: 10
Author(s): John Lai, Leire Moya, Jiyuan An, Andrea Hoffman, Srilakshmi Srinivasan, Janaththani Panchadsaram, Carina Walpole, Joanna Perry-Keene, Suzanne K. Chambers, Melanie Lehman, Colleen C. Nelson, Judith A. Clements, Jyotsna Batra
Software Mentions: 2
Published: almost 9 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: over 11 years ago

10.1038/s41598-018-20727-0

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

10.1038/s41598-018-21608-2

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

10.1186/1471-2334-14-314

Inflammatory and myeloid-associated gene expression before and one day after infant vaccination with MVA85A correlates with induction of a T cell response
Cited by: 19
Author(s): Magali Matsumiya, Stephanie A. Harris, Iman Satti, Lisa Stockdale, Rachel Tanner, Matthew K. O’Shea, Michèle Tameris, Hassan Mahomed, Mark Hatherill, Thomas J. Scriba, Willem A. Hanekom, Helen McShane, Helen A. Fletcher
Software Mentions: 2
Published: over 12 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: over 15 years ago

10.1038/s41598-018-23337-y

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

10.1038/s41598-018-23168-x

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

10.1186/1471-2407-10-490

Transcriptional profiling of ErbB signalling in mammary luminal epithelial cells - interplay of ErbB and IGF1 signalling through IGFBP3 regulation
Cited by: 17
Author(s): Jenny Worthington, Mariana Fianco Bertani, Hong‐Lin Chan, Bertran Gerrits, John F. Timms
Software Mentions: 2
Published: about 16 years ago

10.1186/s12879-019-4123-z

DisV-HPV16, versatile and powerful software to detect HPV in RNA sequencing data
Cited by: 1
Author(s): Bingqing Yan, Xinyi Liu, Siwei Zhang, Siyang Yu, Fangjia Tong, Huanhuan Xie, Lixia Song, Yan Zhang, Lanlan Wei
Software Mentions: 2
Published: over 7 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: almost 12 years ago

10.1186/1741-7015-9-130

A diagnostic algorithm combining clinical and molecular data distinguishes Kawasaki disease from other febrile illnesses
Cited by: 41
Author(s): Xuefeng B. Ling, Kenneth Lau, John T. Kanegaye, Pan Zheng, Syd S. Peng, Jun Ji, Gigi Liu, Yuichiro Sato, Tom Yu, John C. Whitin, James Schilling, Jane C. Burns, Harvey J. Cohen
Software Mentions: 2
Published: almost 15 years ago

10.1038/s41598-018-29190-3

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

10.1186/1471-2407-10-196

Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma
Cited by: 88
Author(s): Min‐Han Tan, Chin Fong Wong, Hwei Ling Tan, Ximing J. Yang, Jonathon A. Ditlev, Daisuke Matsuda, Sok Kean Khoo, Jun Sugimura, Tomoaki Fujioka, Kyle A. Furge, Eric J. Kort, Sophie Giraud, Sophie Ferlicot, Philippe Vielh, Delphine Amsellem-Ouazana, B Debré, T. Flam, Nicolas Thiounn, Marc Zerbib, Benoît Galand, S. Droupy, Vincent Molinié, Annick Vieillefond, Puay Hoon Tan, Stéphane Richard, Bin Tean Teh
Software Mentions: 2
Published: over 16 years ago

10.1038/s41598-018-29240-w

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

10.1186/1471-2105-10-47

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

10.1371/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: almost 16 years ago

10.1038/s41598-018-33752-w

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

10.1038/s41598-018-34812-x

A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence
Cited by: 35
Author(s): Patrick Lypaczewski, Johanna Hoshizaki, Wen-Wei Zhang, Laura-Isobel McCall, John Torcivia-Rodriguez, Vahan Simonyan, Amanpreet Kaur, Ken Dewar, Greg Matlashewski
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2350-15-80

Meta-analysis of differentially expressed genes in osteosarcoma based on gene expression data
Cited by: 51
Author(s): Zuozhang Yang, Yongbin Chen, Yu Fu, Yihao Yang, Zhang Ya, Yanjin Chen, Dongqi Li
Software Mentions: 2
Published: about 12 years ago

10.1186/1471-2350-15-29

Expression analysis of genes and pathways associated with liver metastases of the uveal melanoma
Cited by: 30
Author(s): Yuanyuan Zhang, Yong Yang, Lei Chen, Jianhong Zhang
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2350-9-17

Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission
Cited by: 56
Author(s): Ariel Arthur, Patricia J. Armati, Chris R. Bye, Robert Heard, Graeme J. Stewart, John D. Pollard, David R. Booth
Software Mentions: 2
Published: over 18 years ago

10.1038/s41598-019-39808-9

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

10.1371/journal.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

10.1038/s41598-019-40739-8

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

10.1186/s12881-020-01095-x

Whole-exome sequencing identifies a novel mutation in spermine synthase gene (SMS) associated with Snyder-Robinson Syndrome
Cited by: 2
Author(s): Talal Jamil Qazi, Qiao Wu, Ailikemu Aierken, Daru Lu, Ihtisham Bukhari, Hafiz Muhammad Jafar Hussain, Jingming Yang, Asif Mir, Hong Qing
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-019-41672-6

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

10.1186/s12920-016-0218-1

A 19-Gene expression signature as a predictor of survival in colorectal cancer
Cited by: 60
Author(s): Nurul Ainin Abdul Aziz, Norfilza Mohd Mokhtar, Roslan Harun, Manir Hossain Mollah, Isa Mohamed Rose, Ismail Sagap, Azmi Mohd Tamil, Wan Zurinah Wan Ngah, A. Rahman A. Jamal
Software Mentions: 2
Published: about 10 years ago

10.1038/s41598-019-47218-0

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

10.1038/s41598-019-47318-x

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

10.1371/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

10.1186/1755-8794-2-65

Gene expression profiling in sinonasal adenocarcinoma
Cited by: 32
Author(s): Dominique Tripodi, Sylvia Quéméner, Karine Renaudin, Christophe Ferron, O. Malard, Isabelle Guisle‐Marsollier, Véronique Sebille, Christian Verger, C. Géraut, Catherine Gratas
Software Mentions: 2
Published: almost 17 years ago

10.1186/1755-8794-4-35

Exon array analysis reveals neuroblastoma tumors have distinct alternative splicing patterns according to stage and MYCN amplification status
Cited by: 37
Author(s): Xiang Guo, Qingrong Chen, Young K. Song, Jun S. Wei, Javed Khan
Software Mentions: 2
Published: over 15 years ago

10.1038/s41598-019-50897-4

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

10.1186/1471-2407-11-332

Serum estradiol levels associated with specific gene expression patterns in normal breast tissue and in breast carcinomas
Cited by: 35
Author(s): Vilde Drageset Haakensen, Trine Bjøro, Torben Lüders, Margit Riis, Ida K. Bukholm, Vessela N. Kristensen, Melissa A. Troester, Marit M. Homen, Giske Ursin, Anne Lise Børresen-Dale, Åslaug Helland
Software Mentions: 2
Published: about 15 years ago

10.1186/1755-8794-5-33

The effects of MicroRNA transfections on global patterns of gene expression in ovarian cancer cells are functionally coordinated
Cited by: 29
Author(s): Shubin Shahab, Lilya V. Matyunina, Christopher G. Hill, Limin Wang, Roman Mezencev, L. DeEtte Walker, John F. McDonald
Software Mentions: 2
Published: about 14 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

10.1186/1755-8794-1-51

Expression-based Pathway Signature Analysis (EPSA): Mining publicly available microarray data for insight into human disease
Cited by: 15
Author(s): Jessica D. Tenenbaum, Michael G. Walker, Paul J. Utz, Atul J. Butte
Software Mentions: 2
Published: almost 18 years ago

10.1107/S1744309109050416

Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction
Cited by: 7
Author(s): Gye Won Han, Constantina Bakolitsa, Mitchell D. Miller, Abhinav Kumar, Dennis Carlton, Rafaël Najmanovich, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Connie Chen, Hsiu Ju Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Dustin C. Ernst, Julie Feuerhelm, Joanna C Grant, Anna Grzechnik, Lukasz Jaroszewski, Kevin K. Jin, Hope A. Johnson, Heath E. Klock, Mark W. Knuth, Piotr Koźbiał, Sanjeev Krishna, David Marciano, Daniel McMullan, Andrew Morse, Edward Nigoghossian, Linda Okach, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry J Tien, Christine B Trame, H. van den Bedem, Dana Weekes, Qingping Xu, Keith O. Hodgson, John Wooley, Marc‐André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson
Software Mentions: 2
Published: over 16 years ago

10.1038/s41598-020-59207-9

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

10.1038/s41598-020-59375-8

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

10.1186/s12885-016-2109-4

Regulation of the tumour suppressor PDCD4 by miR-499 and miR-21 in oropharyngeal cancers
Cited by: 49
Author(s): Xiaoying Zhang, Harriet E. Gee, Barbara Rose, Cheok Soon Lee, Jonathan Clark, Michael Elliott, Jennifer R. Gamble, Murray J. Cairns, Adrian L. Harris, Samantha Khoury, Nham Tran
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-020-61942-y

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

10.1038/s41598-020-62467-0

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

10.1038/s41598-020-62975-z

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

10.1371/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

10.1038/s41598-020-64370-0

Genetic basis for virulence differences of various Cryptosporidium parvum carcinogenic isolates
Cited by: 7
Author(s): Christophe Audebert, Franck Bonardi, Ségolène Caboche, Karine Guyot, Hélène Touzet, Sophie Merlin, Nausicâa Gantois, Colette Creusy, Dionigia Meloni, Anthony Mouray, Éric Viscogliosi, Gabriela Certad, Sadia Benamrouz-Vanneste, Magali Chabé
Software Mentions: 2
Published: over 6 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: over 8 years ago

10.1038/s41598-020-66331-z

Shedding light on dark genes: enhanced targeted resequencing by optimizing the combination of enrichment technology and DNA fragment length
Cited by: 5
Author(s): Barbara Iadarola, Luciano Xumerle, Denise Lavezzari, Marta Paterno, Luca Marcolungo, Cristina Beltrami, Elisabetta Fortunati, Davide Mei, Annalisa Vetro, Renzo Guerrini, Elena Parrini, Marzia Rossato, Massimo Delledonne
Software Mentions: 2
Published: over 6 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: about 11 years ago

10.1186/s12885-019-5786-y

miR-520d-5p can reduce the mutations in hepatoma cancer cells and iPSCs-derivatives
Cited by: 5
Author(s): Naruhisa Miura, Y. Ishihara, Yugo Miura, Mai Kimoto, Keigo Miura
Software Mentions: 2
Published: over 7 years ago

10.1186/s12920-017-0255-4

CLImAT-HET: detecting subclonal copy number alterations and loss of heterozygosity in heterogeneous tumor samples from whole-genome sequencing data
Cited by: 15
Author(s): Zhenhua Yu, Ao Li, Minghui Wang
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-020-68141-9

Proteomic and transcriptomic profiling identifies mediators of anchorage-independent growth and roles of inhibitor of differentiation proteins in invasive lobular carcinoma
Cited by: 16
Author(s): Nilgun Tasdemir, Kai Ding, Laura Savariau, Kevin M. Levine, Tian Du, Ashuvinee Elangovan, Emily A. Bossart, Adrian V. Lee, Nancy E. Davidson
Software Mentions: 2
Published: about 6 years ago

10.1186/1755-8794-5-22

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

10.1038/s41598-020-69351-x

A negative covariation between toxoplasmosis and CoVID-19 with alternative interpretations
Cited by: 20
Author(s): Łukasz Jankowiak, Lajos Rózsa, Piotr Tryjanowski, Anders Pape Møller
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-69152-2

Transcriptional portrait of M. bovis BCG during biofilm production shows genes differentially expressed during intercellular aggregation and substrate attachment
Cited by: 10
Author(s): Mario Alberto Flores-Valdéz, Michel de Jesús Aceves-Sánchez, Eliza J.R. Peterson, Nitin S. Baliga, Jorge Madrigal, Miguel A. De la Cruz, Miguel A. Ares, Sarah E M Born, Martin I. Voskuil, Nayeli Areli Pérez-Padilla, Mirna Burciaga-Flores, Tanya A. Camacho-Villegas, María Guadalupe Espinoza-Jorge
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-69861-8

Modelling transport of inhibiting and activating signals and their combined effects on floral induction: application to apple tree
Cited by: 1
Author(s): Farés Belhassine, Damien Fumey, Jérôme Chopard, Christophe Pradal, Sébastien Martinez, Evelyne Costes, Benoît Pallas
Software Mentions: 2
Published: about 6 years ago

10.1186/s12885-017-3226-4

Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer
Cited by: 27
Author(s): Tyler McInnes, Donghui Zou, Dasari S. Rao, Francesca Maree Munro, Vicky Phillips, John L. McCall, Michael A. Black, Anthony E. Reeve, Parry Guilford
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-020-72103-6

Long-term changes in habitat and trophic level of Southern Ocean squid in relation to environmental conditions
Cited by: 8
Author(s): José Abreu, Richard A. Phillips, Filipe R. Ceia, Louise Ireland, Vítor H. Paiva, José C. Xavier
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-71997-6

Identification of miRNA signatures for kidney renal clear cell carcinoma using the tensor-decomposition method
Cited by: 13
Author(s): Ka-Lok Ng, Y-h. Taguchi
Software Mentions: 2
Published: about 6 years ago

10.1186/s12920-015-0088-y

Gene expression network analysis reveals new transcriptional regulators as novel factors in human ischemic cardiomyopathy
Cited by: 19
Author(s): Isabel Herrer, Esther Roselló‐Lletí, Ana Ortega, Estefanía Tarazón, Maria Micaela Molina‐Navarro, Juan Carlos Triviño, Luis Martínez‐Dolz, Luís Almenar, Francisca Lago, Ignacio Sánchez‐Lázaro, José Ramón González-Juanatey, Antonio Salvador, Manuel Portolés, Miguel Rivera
Software Mentions: 2
Published: over 11 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

10.1038/s41598-020-76302-z

Inhabited subsurface wet smectites in the hyperarid core of the Atacama Desert as an analog for the search for life on Mars
Cited by: 21
Author(s): Armando Azua‐Bustos, Alberto González Fairén, Carlos González-Silva, Daniel Carrizo, Miguel Ángel Fernández-Martínez, Cristián Arenas-Fajardo, M. Fernández-Sampedro, Carolina Gil-Lozano, Laura Sánchez-García, Carmen Ascaso, Jacek Wierzchoś, E. B. Rampe
Software Mentions: 2
Published: almost 6 years ago

10.1186/1755-8794-1-10

Identification of differentially expressed genes in fibroblasts derived from patients with Dupuytren's Contracture
Cited by: 56
Author(s): Latha Satish, William A. LaFramboise, David B. O’Gorman, Sharon L. Johnson, Benjamin Janto, Bing Siang Gan, Mark E. Baratz, Fang Hu, J. Christopher Post, Garth D. Ehrlich, Sandeep Kathju
Software Mentions: 2
Published: over 18 years ago

10.1038/s41598-020-77110-1

Strategies to produce T-DNA free CRISPRed fruit trees via Agrobacterium tumefaciens stable gene transfer
Cited by: 35
Author(s): Lorenza Dalla Costa, Stefano Piazza, Valerio Pompili, Umberto Salvagnin, Alessandro Cestaro, Loredana Moffa, Lorenzo Vittani, C. Moser, Mickaël Malnoy
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-77403-5

Antarctic ice mass variations from 1979 to 2017 driven by anomalous precipitation accumulation
Cited by: 6
Author(s): Byeong‐Hoon Kim, Ki‐Weon Seo, Jooyoung Eom, Jianli Chen, Clark R. Wilson
Software Mentions: 2
Published: almost 6 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: over 11 years ago

10.1038/s41598-021-81932-y

Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep
Cited by: 13
Author(s): Yingyue Zhang, Xianglan Xue, Yue Liu, Adam Abied, Yangyang Ding, Shengguo Zhao, Wenqiang Wang, Liqing Ma, Ji-Jun Guo, Weijun Guan, Pu Yun, Joram M. Mwacharo, Jianlin Han, Yue Ma, Qianjun Zhao
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-83015-4

Transcriptome analysis of the procession from chronic pancreatitis to pancreatic cancer and metastatic pancreatic cancer
Cited by: 4
Author(s): Jihao Tu, Zhehao Huang, Yin Wang, Meijing Wang, Zukun Yin, Xianglin Mei, Meiying Li, Lisha Li
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2407-6-54

Cross-platform expression profiling demonstrates that SV40 small tumor antigen activates Notch, Hedgehog, and Wnt signaling in human cells
Cited by: 17
Author(s): Mohamed Ali-Seyed, Noelani Laycock, Suresh Karanam, Wenming Xiao, Eric T. Blair, Carlos S. Moreno
Software Mentions: 2
Published: over 20 years ago

Projects: cran: SAM

Science Score: 85/100

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Papers Mentioning SAM 4,566