cran: SAM | Projects | Ecosyste.ms: Papers

10.3390/life11080862

Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon
Cited by: 6
Author(s): Zulema Udaondo, Kanchana Sittikankaew, Tanaporn Uengwetwanit, Thidathip Wongsurawat, Chutima Sonthirod, Piroon Jenjaroenpun, Wirulda Pootakham, Nitsara Karoonuthaisiri, Intawat Nookaew
Software Mentions: 4
Published: about 5 years ago

10.1002/path.4886

Molecular classification of urothelial carcinoma: global mRNA classification versus tumour-cell phenotype classification
Cited by: 245
Author(s): Gottfrid Sjödahl, Pontus Eriksson, Fredrik Liedberg, Mattias Höglund
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.51109

Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
Cited by: 47
Author(s): Sarah E Dremel, Neal A. DeLuca
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0056657

Significance and Suppression of Redundant IL17 Responses in Acute Allograft Rejection by Bioinformatics Based Drug Repositioning of Fenofibrate
Cited by: 15
Author(s): Silke Roedder, Naoyuki Kimura, Homare Okamura, Szu‐Chuan Hsieh, Yongquan Gong, Minnie M. Sarwal
Software Mentions: 4
Published: over 13 years ago

10.1186/s13058-019-1159-3

On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer
Cited by: 32
Author(s): Richard J. Bownes, Arran Turnbull, Carlos Martínez-Pérez, David Cameron, Andrew H. Sims, Olga Oikonomidou
Software Mentions: 4
Published: about 7 years ago

10.1002/emmm.201201823

Functional genomics identifies five distinct molecular subtypes with clinical relevance and pathways for growth control in epithelial ovarian cancer
Cited by: 172
Author(s): Tuan Zea Tan, Qing Hao Miow, Ruby Yun‐Ju Huang, Ming Keong Wong, Jieru Ye, Jieying Amelia Lau, Meng Wu, Luqman Hakim Bin Abdul Hadi, Richie Soong, Mahesh Choolani, Ben Davidson, Jahn M. Nesland, Ling Zhi Wang, Noriomi Matsumura, Masaki Mandai, Ikuo Konishi, Boon Cher Goh, Jeffrey T. Chang, Jean Paul Thiery, Seiichi Mori
Software Mentions: 4
Published: over 13 years ago

10.1186/s12967-020-02372-2

Whole blood transcriptomic investigation identifies long non-coding RNAs as regulators in sepsis
Cited by: 38
Author(s): Lixin Cheng, Chuanchuan Nan, Lin Kang, Ning Zhang, Sheng Liu, Huaisheng Chen, Chengying Hong, Youlian Chen, Zhen Liang, Xueyan Liu
Software Mentions: 4
Published: over 6 years ago

10.1038/s42003-020-01463-6

Transfer learning efficiently maps bone marrow cell types from mouse to human using single-cell RNA sequencing
Cited by: 15
Author(s): Patrick S. Stumpf, Xin Du, Haruka Imanishi, Yuya Kunisaki, Yuichiro Semba, Timothy J. Noble, R Smith, Matthew Rose-Zerili, Jonathan West, Richard O.C. Oreffo, Katayoun Farrahi, Mahesan Niranjan, Koichi Akashi, Fumio Arai, Ben D. MacArthur
Software Mentions: 4
Published: almost 6 years ago

10.3390/nu9040407

Prenatal Exposure to a Maternal High-Fat Diet Affects Histone Modification of Cardiometabolic Genes in Newborn Rats
Cited by: 24
Author(s): Bijaya Upadhyaya, Tricia D. Larsen, Shivon Barwari, Eli J. Louwagie, Michelle Baack, Moul Dey
Software Mentions: 4
Published: over 9 years ago

10.3389/fpls.2021.664250

New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana
Cited by: 1
Author(s): Kim Hixson, Joaquim V. Marques, Jason P. Wendler, Jason McDermott, Karl K. Weitz, Therese RW Clauss, Matthew E. Monroe, Ronald J. Moore, Joseph N. Brown, Mary Lipton, Callum J. Bell, Ljiljana Paša‐Tolić, Laurence Davin, Norman Lewis
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2016.01651

Modeling the Morphometric Evolution of the Maize Shoot Apical Meristem
Cited by: 10
Author(s): Samuel Leiboff, Christopher K. DeAllie, Michael J. Scanlon
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0033575

Genetic Dissection of Acute Ethanol Responsive Gene Networks in Prefrontal Cortex: Functional and Mechanistic Implications
Cited by: 78
Author(s): Aaron R. Wolen, Charles Phillips, Michael A. Langston, Alex H. Putman, Paul J. Vorster, Nathan A. Bruce, Timothy P. York, Robert W. Williams, Michael F. Miles
Software Mentions: 4
Published: over 14 years ago

10.1002/ece3.5604

Contribution of rare and common species to subterranean species richness patterns
Cited by: 28
Author(s): Petra Bregović, Cene Fišer, Maja Zagmajster
Software Mentions: 4
Published: almost 7 years ago

10.1002/ece3.1695

Genome‐wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore
Cited by: 19
Author(s): Astrid Vik Strønen, Bogumiła Jędrzejewska, Cino Pertoldi, Ditte Demontis, Ettore Randi, Magdalena Niedziałkowska, Tomasz Borowik, Vadim E. Sidorovich, Josip Kusak, Ilpo Kojola, Alexandros A. Karamanlidis, Jurijs Ozoliņš, Vitalii Dumenko, Sylwia D. Czarnomska
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0240474

Were domestic camelids present on the prehispanic South American agricultural frontier? An ancient DNA study
Cited by: 7
Author(s): Cinthia Carolina Abbona, Gustavo Adolfo, Jeff Johnson, Tracy Kim, Adolfo Gil, Steve Wolverton
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12944-018-0915-1

Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue
Cited by: 19
Author(s): Guoze Wang, Kun Du, Shiyan Hu, Shiyi Chen, Xianbo Jia, Mingcheng Cai, Yu Shi, Jie Wang, Songjia Lai
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0001344

Adipose Gene Expression Prior to Weight Loss Can Differentiate and Weakly Predict Dietary Responders
Cited by: 48
Author(s): David M. Mutch, Ramzi Temanni, Corneliu Hénégar, Florence Combes, Véronique Pelloux, Claus Holst, Thorkild I A Sørensen, Arne Astrup, J. Alfredo Martínez, Wim H. M. Saris, Nathalie Viguerie, Dominique Langin, Jean-Daniel Zucker, Karine Clément
Software Mentions: 4
Published: over 18 years ago

10.26508/lsa.201800283

Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements
Cited by: 13
Author(s): Verena Thormann, Laura V. Glaser, Maika C. Rothkegel, Marina Borschiwer, Melissa Bothe, Alisa Fuchs, Sebastiaan H. Meijsing
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0031490

The Gene Expression Analysis of Blood Reveals S100A11 and AQP9 as Potential Biomarkers of Infective Endocarditis
Cited by: 44
Author(s): Franck Thuny, Julien Textoris, Amira Ben Amara, Adil El Filali, Christian Capo, Gilbert Habib, Didier Raoult, Jean‐Louis Mège
Software Mentions: 3
Published: over 14 years ago

10.1186/1746-1596-9-142

NF-κB signaling and vesicle transport are correlated with the reactivation of the memory trace of morphine dependence
Cited by: 9
Author(s): Junyi Ye, Zhaoyang Yang, Candong Li, Meimei Cai, Daizhan Zhou, Qin Zhang, Wei Y, Ting Wang, Yun Liu
Software Mentions: 3
Published: about 12 years ago

10.1186/bcr3672

A genomic analysis of mouse models of breast cancer reveals molecular features ofmouse models and relationships to human breast cancer
Cited by: 71
Author(s): Daniel P. Hollern, Eran R. Andrechek
Software Mentions: 3
Published: over 12 years ago

10.1186/s40168-017-0341-z

Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats
Cited by: 39
Author(s): Hong Shen, Zhongyan Lu, Zhihui Xu, Zhan Chen, Zongzhuan Shen
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0139889

Gene-Set Local Hierarchical Clustering (GSLHC)—A Gene Set-Based Approach for Characterizing Bioactive Compounds in Terms of Biological Functional Groups
Cited by: 8
Author(s): Feng-Hsiang Chung, Jinhan Zhu, Tzu-Ting Hsu, Chueh-Lin Hsu, Hsueh-Chuan Liu, Hoong-Chien Lee
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0236197

Family-based exome sequencing combined with linkage analyses identifies rare susceptibility variants of MUC4 for gastric cancer
Cited by: 3
Author(s): Young-Wook Choi, Jung Hun Ohn, Nayoung Kim, Wonji Kim, Kyungtaek Park, Sungho Won, Lee Sael, Cheol Min Shin, Sun Min Lee, Sejoon Lee, Hyun Joo An, Dong Man Jang, Byung Woo Han, Hye Seung Lee, Seung Joo Kang, Sang Woo Kim, Dong Hoon Lee
Software Mentions: 3
Published: about 6 years ago

10.1002/ece3.646

Environmental effects on molecular and phenotypic variation in populations of<i>Eruca sativa</i>across a steep climatic gradient
Cited by: 31
Author(s): Erik Westberg, Shachar Ohali, Anatoly Shevelevich, Pinchas Fine, Oz Barazani
Software Mentions: 3
Published: about 13 years ago

10.1186/bcr2632

Expression levels of uridine 5'-diphospho-glucuronosyltransferase genes in breast tissue from healthy women are associated with mammographic density
Cited by: 37
Author(s): Vilde Drageset Haakensen, Margarethe Biong, Ole Christian Lingjærde, Marit Muri Holmen, Jan Ole Frantzen, Ying Chen, Dina Navjord, Linda Romundstad, Torben Lüders, Ida K. Bukholm, Hiroko Kato Solvang, Vessela N. Kristensen, Giske Ursin, Anne‐Lise Børresen‐Dale, Åslaug Helland
Software Mentions: 3
Published: about 16 years ago

10.1002/ece3.498

New-old hemoglobin-like proteins of symbiotic dinoflagellates
Cited by: 11
Author(s): Nedeljka Rosic, William Leggat, Paulina Kaniewska, Sophie Dove, Ove Hoegh‐Guldberg
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0173664

The miR-200 family is increased in dysplastic lesions in ulcerative colitis patients
Cited by: 14
Author(s): Amy Lewis, Carla Felice, Tomoko Kumagai, Claudia K. Y. Lai, Kriti Singh, Rosemary Jeffery, Roger Feakins, Eleni Giannoulatou, Alessandro Armuzzi, Noor Jawad, James O. Lindsay, Andrew Silver
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2016.01528

Invasive Shrub Mapping in an Urban Environment from Hyperspectral and LiDAR-Derived Attributes
Cited by: 29
Author(s): Curtis M. Chance, Nicholas C. Coops, Andrew Plowright, Thoreau Rory Tooke, Andreas Christen, Neal W. Aven
Software Mentions: 3
Published: almost 10 years ago

10.3389/fphar.2019.01690

SAMbinder: A Web Server for Predicting S-Adenosyl-L-Methionine Binding Residues of a Protein From Its Amino Acid Sequence
Cited by: 3
Author(s): Piyush Agrawal, Gaurav Mishra, Gajendra P. S. Raghava
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0244433

A sound coding strategy based on a temporal masking model for cochlear implants
Cited by: 6
Author(s): E Kludt, Waldo Nogueira, Thomas Lenarz, Andreas Buechner
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0213502

Comparative metabolomic profiling in the roots and leaves in contrasting genotypes reveals complex mechanisms involved in post-anthesis drought tolerance in wheat
Cited by: 60
Author(s): Zhiyu Kang, Ali Babar, Naeem Khan, Jia Guo, Jahangir Khan, Shafiqul Islam, Sumit Shrestha, Dipendra Shahi
Software Mentions: 3
Published: over 7 years ago

10.1007/s13361-016-1544-4

Prognostic Metabolite Biomarkers for Soft Tissue Sarcomas Discovered by Mass Spectrometry Imaging
Cited by: 37
Author(s): Sha Lou, Benjamin Balluff, Arjen H.G. Cleven, Judith V.M.G. Bovée, Liam A. McDonnell
Software Mentions: 3
Published: almost 10 years ago

10.1120/jacmp.v17i3.6370

2016 AAPM Spring Clinical Meeting - Abstracts
Cited by: 0
Author(s):
Software Mentions: 3
Published: over 10 years ago

10.1155/2013/610297

Power and Stability Properties of Resampling-Based Multiple Testing Procedures with Applications to Gene Oncology Studies
Cited by: 12
Author(s): Dongmei Li, Timothy D. Dye
Software Mentions: 3
Published: over 13 years ago

10.1155/2020/3158108

Danhong Injection Alleviates Cardiac Fibrosis via Preventing the Hypermethylation of Rasal1 and Rassf1 in TAC Mice
Cited by: 7
Author(s): Sinai Li, Ping Li, Weihong Liu, Juju Shang, Sheng-Lei Qiu, Xiang Li, Wei Liu, Haoyue Shi, Mingxue Zhou, Hongxu Liu
Software Mentions: 3
Published: over 5 years ago

10.1093/jxb/erx010

Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation
Cited by: 48
Author(s): Lekha T. Pazhamala, Shilp Purohit, Rachit K. Saxena, Vanika Garg, L. Krishnamurthy, Jérôme Verdier, Rajeev K. Varshney
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0086869

CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding
Cited by: 46
Author(s): Yong-Chao Liu, Bernt Popp, Bertil Schmidt
Software Mentions: 3
Published: over 12 years ago

10.7554/eLife.32920

Association mapping from sequencing reads using k-mers
Cited by: 82
Author(s): Atif Rahman, Ingileif B. Hallgrímsdóttir, Michael B. Eisen, Lior Pachter
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.ppat.1005943

Cathelicidin Insufficiency in Patients with Fatal Leptospirosis
Cited by: 21
Author(s): Janet C. Lindow, Elsio A. Wunder, Stephen J. Popper, Jinsoo Min, Praveen Mannam, Anup Srivastava, Yi Yao, Kathryn P. Hacker, Khadir Raddassi, Patty J Lee, Ruth R. Montgomery, Albert C. Shaw, José E. Hagan, Guilherme C. Araújo, Nívison Nery, David A. Relman, Charles C. Kim, Mitermayer Galvão dos Reis, Albert I. Ko
Software Mentions: 3
Published: almost 10 years ago

10.1186/s41687-020-00193-x

Advances in Patient Reported Outcomes: Integration and Innovation
Cited by: 5
Author(s):
Software Mentions: 3
Published: over 6 years ago

10.1016/j.csbj.2021.04.068

Refinement of bamboo genome annotations through integrative analyses of transcriptomic and epigenomic data
Cited by: 3
Author(s): Xuelian Ma, Hansheng Zhao, Hengyu Yan, Minghao Sheng, Yaxin Cao, Kebin Yang, Hao Xu, Wenying Xu, Zhimin Gao, Zhen Su
Software Mentions: 3
Published: over 5 years ago

10.3390/jpm11020062

Modified Significance Analysis of Microarrays in Heterogeneous Diseases
Cited by: 2
Author(s): I‐Shiang Tzeng
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.22345

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition
Cited by: 83
Author(s): Yun Huang, Jong Kim, Dang Vinh, Caroline Lee, Christopher A. Penfold, J. Ż̷ylicz, John C. Marioni, Jim Hackett, M. Azim Surani
Software Mentions: 3
Published: over 9 years ago

10.1029/2019RG000686

Spaceborne Cloud and Precipitation Radars: Status, Challenges, and Ways Forward
Cited by: 65
Author(s): Alessandro Battaglia, Pavlos Kollias, Ranvir Dhillon, Richard Roy, Simone Tanelli, Katia Lamer, Mircea Grecu, Matthew Lebsock, Daniel Watters, Kamil Mróz, Gerald M. Heymsfield, Lihua Li, Katsuko Furukawa
Software Mentions: 3
Published: about 6 years ago

10.3758/s13421-020-01082-w

The simultaneous recognition of multiple words: A process analysis
Cited by: 4
Author(s): Anne Voormann, Mikhail S. Spektor, Karl Christoph Klauer
Software Mentions: 3
Published: over 5 years ago

10.1515/jib-2018-0080

Gene Expression Studies to Identify Significant Genes in AR, MTOR, MAPK Pathways and their Overlapping Regulatory Role in Prostate Cancer
Cited by: 0
Author(s): Nimisha Asati, Abhinav Mishra, Ayush Shukla, Tiratha Raj Singh
Software Mentions: 3
Published: over 7 years ago

10.1186/1476-9255-7-50

TNFRSF11B computational development network construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-control patients
Cited by: 26
Author(s): Ju X Huang, Lin Wang, Meng Ji
Software Mentions: 3
Published: almost 16 years ago

10.3892/ijo.2014.2648

Microarray phosphatome profiling of breast cancer patients unveils a complex phosphatase regulatory role of the MAPK and PI3K pathways in estrogen receptor-negative breast cancers
Cited by: 13
Author(s): Ramón González Manzano, E. Martinez-Navarro, Jerónimo Forteza, Antonio Brugarolas
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0163832

The Role of Vitamin D in the Transcriptional Program of Human Pregnancy
Cited by: 30
Author(s): Amal Al-Garawi, Vincent J. Carey, Divya Chhabra, Hooman Mirzakhani, Jarrett Morrow, Jessica Lasky‐Su, Weiliang Qiu, Nancy Laranjo, Augusto A. Litonjua, Scott T. Weiss
Software Mentions: 3
Published: almost 10 years ago

10.7150/ijms.51743

Identifying daily changes in circRNAs and circRNA-associated-ceRNA networks in the rat pineal gland
Cited by: 5
Author(s): Yi Zheng, Hao Jiang, Hao-Qi Wang, Haixiang Guo, Dong-Xu Han, Yongping Huang, Yan Gao, Bao Yuan
Software Mentions: 3
Published: over 5 years ago

10.1029/2020MS002138

Clouds and Convective Self‐Aggregation in a Multimodel Ensemble of Radiative‐Convective Equilibrium Simulations
Cited by: 69
Author(s): Allison A. Wing, Catherine L. Stauffer, Tobias Becker, Kevin A. Reed, Min‐Seop Ahn, Nathan Arnold, Sandrine Bony, Mark Branson, G. H. Bryan, Jean‐Pierre Chaboureau, Stephan R. de Roode, Gayatri Kulkarni, Cathy Hohenegger, I‐Kuan Hu, Fredrik Jansson, Todd R. Jones, Marat Khairoutdinov, Dae Hyun Kim, Zane Martin, Shuhei Matsugishi, Brian Medeiros, Hiroaki Miura, Yumin Moon, Sebastian K. Müller, Tomoki Ohno, Max Popp, Thara Prabhakaran, David A. Randall, Rosimar Ríos-Berríos, Nicolas Rochetin, Romain Roehrig, David M. Romps, James H. Ruppert, Masaki Satoh, Levi G. Silvers, Martin S. Singh, Björn Stevens, Lorenzo Tomassini, Chiel C. van Heerwaarden, Shuguang Wang, Ming Zhao
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0103515

Characterisation of Adaptive Genetic Diversity in Environmentally Contrasted Populations of Eucalyptus camaldulensis Dehnh. (River Red Gum)
Cited by: 40
Author(s): Shannon Dillon, Rachel McEvoy, Darren S. Baldwin, Gavin N. Rees, Y. M. Parsons, Simon G. Southerton
Software Mentions: 3
Published: about 12 years ago

10.1038/s41598-018-23641-7

Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol
Cited by: 43
Author(s): Joseph A. Russell, Brittany Campos, Jennifer Stone, Erik M. Blosser, Nathan D. Burkett‐Cadena, Jonathan L. Jacobs
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1006571

Enhancer of polycomb coordinates multiple signaling pathways to promote both cyst and germline stem cell differentiation in the Drosophila adult testis
Cited by: 25
Author(s): Lijuan Feng, Zhen Shi, Xin Chen
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-019-43141-6

CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement
Cited by: 62
Author(s): Joshua K. Young, Gina Zastrow-Hayes, Stéphane Deschamps, Sergei Svitashev, Mindaugas Zaremba, Ananta Acharya, Sushmitha Paulraj, Brooke D. Peterson-Burch, Chris Schwartz, Vesna Djukanovic, Brian Lenderts, Lanie Feigenbutz, Limin Wang, Clara M. Alarcon, Virginijus Šikšnys, Gregory D. May, N. Doane Chilcoat, Sandeep Kumar
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-31064-7

Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis
Cited by: 33
Author(s): Johnny A. Sena, Giulia Galotto, Nico Devitt, Melanie C. Connick, Jennifer L. Jacobi, Pooja Umale, Luis Vidali, Callum J. Bell
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-019-43512-z

Melanoma proteomics suggests functional differences related to mutational status
Cited by: 9
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara, Enrique Espinosa
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-41625-z

Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data
Cited by: 12
Author(s): Lázaro Betancourt, Krzysztof Pawłowski, Jonatan Eriksson, Attila Marcell Szász, Shamik Mitra, Indira Pla, Charlotte Welinder, Henrik Ekedahl, Per Broberg, Roger Appelqvist, Maria Yakovleva, Y. Sugita, Kenichi Miharada, Christian Ingvar, Lotta Lundgren, Bo Baldetorp, Håkan Olsson, Melinda Rezeli, Elisabet Wieslander, Péter Horvatovich, Johan Malm, Göran Jönsson, György Markó-Varga
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0022226

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology
Cited by: 70
Author(s): Xun Lan, Christopher M. Adams, Mark Landers, Miroslav Dudas, Daniel Krissinger, George Marnellos, Russell Bonneville, Maoxiong Xu, Junbai Wang, Tim H-M. Huang, Gavin Meredith, Victor X. Jin
Software Mentions: 3
Published: about 15 years ago

10.1038/s41598-020-59541-y

Chronic circadian misalignment accelerates immune senescence and abbreviates lifespan in mice
Cited by: 78
Author(s): Hitoshi Inokawa, Yasuhiro Umemura, Akihiro Shimba, Eiryo Kawakami, Nobuya Koike, Yoshiki Tsuchiya, Masaru Ohashi, Yoichi Minami, Guangwei Cui, T. Asahi, Ryutaro Ono, Yuh Sasawaki, Eiichi Konishi, Seung-Hee Yoo, Chen Zheng, Satoshi Teramukai, Koichi Ikuta, Kazuhiro Yagita
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-51645-4

Predicting low-concentration effects of pesticides
Cited by: 17
Author(s): Matthias Liess, Sebastian Henz, Saskia Knillmann
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-21484-w

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias
Cited by: 56
Author(s): Raga Krishnakumar, Anupama Sinha, Sara W. Bird, Harikrishnan Jayamohan, Harrison Edwards, Joseph S. Schoeniger, Kamlesh D. Patel, Steven S. Branda, Michael Bartsch
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1000812

Altered Gene Expression and DNA Damage in Peripheral Blood Cells from Friedreich's Ataxia Patients: Cellular Model of Pathology
Cited by: 95
Author(s): Astrid C. Haugen, Nicholas A. Di Prospero, Joel S. Parker, Rick D. Fannin, Jeff W. Chou, Joel N. Meyer, Christopher Halweg, Jennifer B. Collins, Alexandra Dürr, Kenneth H. Fischbeck, Bennett Van Houten
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pone.0010770

Integrative Genome Comparison of Primary and Metastatic Melanomas
Cited by: 159
Author(s): Omar Kabbarah, Cristina Nogueira, Bin Feng, Rosalynn M. Nazarian, Marcus W. Bosenberg, Min Wu, Kenneth L. Scott, Lawrence N. Kwong, Yonghong Xiao, Carlos Cordón-Cardo, Scott R. Granter, Sridhar Ramaswamy, Todd R. Golub, Lyn M. Duncan, Stephan N. Wagner, Cameron Brennan, Lynda Chin
Software Mentions: 3
Published: over 16 years ago

10.1038/s41598-019-45898-2

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor
Cited by: 19
Author(s): Rajesh Kumar Gazara, Eduardo Alves Gamosa de Oliveira, B. Calderan Rodrigues, Rodrigo Nunes da Fonseca, Antônia Elenir Amâncio Oliveira, Thiago M. Venancio
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-39880-1

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Cited by: 25
Author(s): Bruno Arcà, Alessio Colantoni, Carmine Fiorillo, Francesco Severini, Vladimír Beneš, Marco Di Luca, Raffaele Calogero, Fabrizio Lombardo
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1007949

Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
Cited by: 38
Author(s): Dmytro Kryvokhyzha, Adriana Salcedo, Mimmi C. Eriksson, Tianlin Duan, Nilesh R. Tawari, Jun Chen, Maria Guerrina, Julia M. Kreiner, Tyler V. Kent, Ulf Lagercrantz, John R. Stinchcombe, Sylvain Glémin, Stephen I. Wright, Martin Lascoux
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-31093-2

Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing
Cited by: 23
Author(s): David Jebb, Nicole M. Foley, Conor V. Whelan, Frédéric Touzalin, Sébastien J. Puechmaille, Emma C. Teeling
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0015595

A Novel Statistical Algorithm for Gene Expression Analysis Helps Differentiate Pregnane X Receptor-Dependent and Independent Mechanisms of Toxicity
Cited by: 8
Author(s): M. Ann Mongan, Robert T. Dunn, Steven Vonderfecht, Nancy E. Everds, Guang Chen, Cheng Su, Marnie Higgins-Garn, Yuan Chen, Cynthia A. Afshari, Toni Williamson, Linda L. Carlock, Christopher DiPalma, Suzanne T. Moss, Jeanine L. Bussiere, Charles W. Qualls, Yudong He, Hisham K. Hamadeh
Software Mentions: 3
Published: over 15 years ago

10.1038/s41598-017-14418-5

Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis
Cited by: 10
Author(s): Emiko Yoshida, Yasuhisa Terao, Noriko Hayashi, Kaoru Mogushi, Atsushi Arakawa, Yuji Tanaka, Yoshiaki Ito, Hiroko Ohmiya, Yoshihide Hayashizaki, Satoru Takeda, Masayoshi Itoh, Hideya Kawaji
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1004142

Genetic Basis of Metabolome Variation in Yeast
Cited by: 50
Author(s): J. Scott Breunig, Sean R. Hackett, Joshua D. Rabinowitz, Leonid Kruglyak
Software Mentions: 3
Published: over 12 years ago

10.1186/2049-3002-2-13

Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer
Cited by: 27
Author(s): Debarshi Roy, Susmita Mondal, Chen Wang, Xiaoping He, Ashwani Khurana, Shailendra Giri, Robert Hoffmann, Deok‐Beom Jung, Sung Hyun Kim, Eduardo N. Chini, Juliana Camacho Periera, Clifford D.L. Folmes, Andrea Mariani, Sean C. Dowdy, Jamie N. Bakkum-Gamez, Shaun M. Riska, Ann L. Oberg, Edward D. Karoly, Lauren N. Bell, Jeremy Chien, Viji Shridhar
Software Mentions: 3
Published: about 12 years ago

10.1038/s41598-017-04786-3

sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide
Cited by: 25
Author(s): Julie Bronsard, Gaëtan Pascreau, Mohamed Sassi, Tony Mauro, Yoann Augagneur, Brice Felden
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-019-52395-z

Environmental and ecological factors mediate taxonomic composition and body size of polyplacophoran assemblages along the Peruvian Province
Cited by: 6
Author(s): Christian M. Ibáñez, Melany Waldisperg, Felipe I. Torres, Sergio A. Carrasco, Javier Sellanes, M. Cecilia Pardo‐Gandarillas, Julia D. Sigwart
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-017-02329-4

Expression Profiling of mRNAs and Long Non-Coding RNAs in Aged Mouse Olfactory Bulb
Cited by: 11
Author(s): Ming Wang, Wei Liu, Jian Jiao, Jingyun Li, Chengshuo Wang, Luo Zhang
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0084231

Identification of the Third Binding Site of Arsenic in Human Arsenic (III) Methyltransferase
Cited by: 12
Author(s): Xiangli Li, Zhirong Geng, Jiayin Chang, Shuping Wang, Xiaoli Song, Xin Hu, Zhilin Wang
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pgen.1001135

Analysis of the Basidiomycete Coprinopsis cinerea Reveals Conservation of the Core Meiotic Expression Program over Half a Billion Years of Evolution
Cited by: 34
Author(s): Claire Burns, Jason E. Stajich, Andreas Rechtsteiner, Lorna A. Casselton, Sean E. Hanlon, Sarah K. Wilke, Oleksandr P. Savytskyy, Allen C. Gathman, Walt W. Lilly, Jason D. Lieb, Miriam E. Zolan, Patricia J. Pukkila
Software Mentions: 3
Published: almost 16 years ago

10.1038/s41598-017-02824-8

High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor
Cited by: 8
Author(s): Masahito Yoshihara, Yuzuru Sasamoto, Ryuhei Hayashi, Yuki Ishikawa, Motokazu Tsujikawa, Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji, Kohji Nishida
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.1009600

Antagonistic fungal enterotoxins intersect at multiple levels with host innate immune defences
Cited by: 10
Author(s): Xing Zhang, Benjamin W. Harding, Dina Aggad, Damien Courtine, Jia‐Xuan Chen, Nathalie Pujol, Jonathan J. Ewbank
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-53901-z

Blood transcriptome analysis in a buck-ewe hybrid and its parents
Cited by: 1
Author(s): Clemens Falker‐Gieske, C. Knorr, Jens Tetens
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.0010016

Glucocorticoid Receptor-Dependent Gene Regulatory Networks
Cited by: 194
Author(s): Panin Le, Joshua R. Friedman, Jonathan Schug, John Brestelli, J. Brandon Parker, Irina M. Bochkis, Klaus H. Kaestner
Software Mentions: 3
Published: about 21 years ago

10.3390/metabo11090627

Comparative Untargeted Metabolomic Profiling of Induced Mitochondrial Fusion in Pancreatic Cancer
Cited by: 0
Author(s): Nathalie Nguyen, Meifang Yu, Vinit Y. Reddy, Ariana Carolina Acevedo-Diaz, Enzo C. Mesarick, Joseph Abi Jaoude, Min Yuan, John M. Asara, Cullen M. Taniguchi
Software Mentions: 3
Published: almost 5 years ago

10.1002/prot.25697

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13
Cited by: 142
Author(s): Jie Hou, Tai Tsun Wu, Renzhi Cao, Jianlin Cheng
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.29736

CDK9-dependent RNA polymerase II pausing controls transcription initiation
Cited by: 157
Author(s): Saskia Gressel, Björn Schwalb, Tim-Michael Decker, Weihua Qin, Heinrich Leonhardt, Dirk Eick, Patrick Cramer
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.17903

A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading
Cited by: 32
Author(s): Chun-Min Shan, Jiyong Wang, Ke Xu, Huijie Chen, Jia-Xing Yue, Stuart Andrews, James J. Moresco, John R. Yates, Péter L. Nagy, Liang Tong, Songtao Jia
Software Mentions: 3
Published: almost 10 years ago

10.1073/pnas.1921055117

ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in <i>Arabidopsis</i>
Cited by: 54
Author(s): Christophe Lambing, Pallas Kuo, Andrew J. Tock, Stephanie D. Topp, Ian Henderson
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0142864

Evolutionary Quantitative Genomics of Populus trichocarpa
Cited by: 24
Author(s): Ilga Porth, Jaroslav Klápště, Athena D. McKown, Jonathan La Mantia, Robert D. Guy, Pär K. Ingvarsson, Richard Hamelin, Shawn D. Mansfield, Jürgen Ehlting, Carl J. Douglas, Yousry A. El‐Kassaby
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.ppat.1009175

Escalation in the host-pathogen arms race: A host resistance response corresponds to a heightened bacterial virulence response
Cited by: 5
Author(s): Qi Wang, Nadia Shakoor, Adam Boyher, Kira M. Veley, Jeffrey C. Berry, Todd C. Mockler, Rebecca Bart
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0046847

lociNGS: A Lightweight Alternative for Assessing Suitability of Next-Generation Loci for Evolutionary Analysis
Cited by: 6
Author(s): Sarah M. Hird
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.ppat.1006510

Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection
Cited by: 50
Author(s): Gustavo H. Kijak, Eric Sanders‐Buell, Agnès‐Laurence Chenine, Michael A. Eller, Nilu Goonetilleke, Rasmi Thomas, Sivan Leviyang, Elizabeth A. Harbolick, Meera Bose, Phuc Pham, Celina Oropeza, Kultida Poltavee, Anne Marie O’Sullivan, Erik Billings, Mélanie Merbah, Margaret C. Costanzo, Joanna Warren, Bonnie M. Slike, Hui Li, Kristina K. Peachman, Will Fischer, Feng Gao, Claudia Cicala, James Arthos, Leigh Anne Eller, Robert J. O’Connell, Samuel Sinei, Lucas Maganga, Hannah Kibuuka, Sorachai Nitayaphan, Mangala Rao, Mary Marovich, Shelly J. Krebs, Morgane Rolland, Bette T. Korber, George M. Shaw, Nelson L. Michael, Merlin L. Robb, Sodsai Tovanabutra, Jerome H. Kim
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0238311

Length of stay to recover from severe acute malnutrition and associated factors among under-five years children admitted to public hospitals in Aksum, Ethiopia
Cited by: 10
Author(s): Wagnew Tesfay, Mebrahtu Abay, Solomon Hintsa, Tekia Zafu
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1003820

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
Cited by: 80
Author(s): Stefanie Traeger, Florian Altegoer, Michael Freitag, Toni Gabaldón, Frank Kempken, Abhishek Kumar, Marina Marcet‐Houben, Stefanie Pöggeler, Jason E. Stajich, Minou Nowrousian
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.ppat.1003341

Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy
Cited by: 132
Author(s): Michael J. Strong, Guiyin Xu, Joseph Coco, Carl Baribault, Dass S. Vinay, Michelle Lacey, Amy L. Strong, Teresa A. Lehman, Michael Seddon, Zhen Lin, Monica Concha, Melody Baddoo, MaryBeth Ferris, Kenneth F. Swan, Deborah E. Sullivan, Matthew E. Burow, Christopher M. Taylor, Erik K. Flemington
Software Mentions: 3
Published: over 13 years ago

10.7554/eLife.23468

A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation
Cited by: 29
Author(s): Meng Amy Li, Paulo Amaral, Priscilla Cheung, Jan H. Bergmann, Masaki Kinoshita, Tüzer Kalkan, Markus Ralser, Sam Robson, Ferdinand von Meyenn, Maike Paramor, Fengtang Yang, Caifu Chen, Jennifer Nichols, David L. Spector, Tony Kouzarides, Lin He, Austin Smith
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pgen.1005265

The Developmental Intestinal Regulator ELT-2 Controls p38-Dependent Immune Responses in Adult C. elegans
Cited by: 42
Author(s): Dena H. S. Block, Kwame Twumasi-Boateng, Hae Sung Kang, Jolie A Carlisle, Alexandru Hanganu, Ty Yu-Jen Lai, Michael Y. Shapira
Software Mentions: 3
Published: over 11 years ago

10.1186/1479-5876-6-69

Gene expression profiling for molecular distinction and characterization of laser captured primary lung cancers
Cited by: 55
Author(s): Astrid Rohrbeck, Judith Neukirchen, Michael Rosskopf, Guillermo G Pardillos, Helene Geddert, Andreas Schwalen, Helmut E. Gabbert, Arndt von Haeseler, Gerald Pitschke, M. Schott, Ralf Kronenwett, Rainer Haas, Ulrich-Peter Rohr
Software Mentions: 3
Published: almost 18 years ago

10.1186/1479-5876-9-155

SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document: Online resources and useful tools - a compass in the land of biomarker discovery
Cited by: 26
Author(s): Davide Bedognetti, James M Balwit, Ena Wang, Mary L. Disis, Cedrik M. Britten, Lucia Gemma Delogu, Sara Tomei, Bernard A. Fox, Thomas F. Gajewski, Francesco M. Marincola, Lisa H. Butterfield
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pone.0086214

Protection Genes in Nucleus Accumbens Shell Affect Vulnerability to Nicotine Self-Administration across Isogenic Strains of Adolescent Rat
Cited by: 10
Author(s): Hao Chen, Rui Luo, Shusheng Gong, Shannon G. Matta, Burt M. Sharp
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pmed.0030047

Gene Expression Programs in Response to Hypoxia: Cell Type Specificity and Prognostic Significance in Human Cancers
Cited by: 549
Author(s): Jen‐Tsan Chi, Zhen Wang, Dimitry S.A. Nuyten, Edwin H. Rodriguez, Marci E. Schaner, Ali Salim, Yun Wang, Gunnar B. Kristensen, Åslaug Helland, Anne Lise Børresen-Dale, Amato J. Giaccia, Michael T. Longaker, Trevor Hastie, George P. Yang, Marc J. van de Vijver, Patrick O. Brown
Software Mentions: 3
Published: over 20 years ago

Projects: cran: SAM

Science Score: 85/100

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Papers Mentioning SAM 4,566