pypi: Resource | Projects | Ecosyste.ms: Papers

10.3389/fgene.2020.00363

Novel Immune-Related Gene Signature for Risk Stratification and Prognosis of Survival in Lower-Grade Glioma
Cited by: 114
Author(s): Mingwei Zhang, Xuezhen Wang, Xiaoping Chen, Qiuyu Zhang, Jinsheng Hong
Software Mentions: 12
Published: over 4 years ago

10.7554/eLife.65948

Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments
Cited by: 42
Author(s): Sylvie Estrela, Alicia Sánchez-Gorostiaga, Jean C. C. Vila, Álvaro Sánchez
Software Mentions: 4
Published: over 3 years ago

10.15252/msb.20188323

Genome‐wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy
Cited by: 22
Author(s): Avinash Sahu, Joo S. Lee, Zhiyong Wang, Gao Zhang, Ramiro Iglesias-Bartolomé, Tian Tian, Zhi Wei, Benchun Miao, Nishanth Ulhas Nair, Olga Ponomarova, Adam Friedman, Arnaud Amzallag, Tabea Moll, Gyulnara G. Kasumova, Patricia Greninger, Regina K. Egan, Leah J. Damon, Dennie T. Frederick, Livnat Jerby‐Arnon, Allon Wagner, Kuoyuan Cheng, Seung Gu Park, Welles Robinson, Kevin Gardner, Genevieve M. Boland, Sridhar Hannenhalli, Meenhard Herlyn, Cyril H. Benes, Keith T. Flaherty, Ji Luo, J. Silvio Gutkind, Eytan Ruppin
Software Mentions: 4
Published: over 5 years ago

10.1186/s13073-020-00787-6

Molecular correlates and therapeutic targets in T cell-inflamed versus non-T cell-inflamed tumors across cancer types
Cited by: 21
Author(s): Riyue Bao, Daniel Stapor, Jason J. Luke
Software Mentions: 4
Published: almost 4 years ago

10.3389/fonc.2020.592811

Exploration of the Prognostic and Immunotherapeutic Value of B and T Lymphocyte Attenuator in Skin Cutaneous Melanoma
Cited by: 6
Author(s): Xubin Dong, Jingjing Song, Buran Chen, Yufeng Qi, Wenjie Jiang, Huihui Li, Danni Zheng, Yinghao Wang, Xiaohua Zhang, Haiguang Liu
Software Mentions: 4
Published: over 3 years ago

10.12688/f1000research.25540.1

Population structure of Salmonella enterica serotype Mbandaka reveals similar virulence potential irrespective of source and phylogenomic stratification
Cited by: 2
Author(s): Linto Antony, Gavin Fenske, Radhey S. Kaushik, T. G. Nagaraja, M. G. Thomas, Joy Scaria
Software Mentions: 4
Published: about 4 years ago

10.1186/1471-2229-14-141

Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana
Cited by: 86
Author(s): Yong Ding, Laëtitia Virlouvet, Ning Liu, Jean-Jack M. Riethoven, Michael Fromm, Zoya Avramova
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2020.00549

Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance
Cited by: 45
Author(s): Ashley Cooper, Andrew Low, Adam Koziol, Matthew C. Thomas, Daniel Leclair, Sandeep Tamber, Alex Wong, Burton W. Blais, Catherine D. Carrillo
Software Mentions: 3
Published: over 4 years ago

10.1155/2019/6545210

New Gene Markers of Angiogenesis and Blood Vessels Development in Porcine Ovarian Granulosa Cells during Short-Term Primary Culture In Vitro
Cited by: 20
Author(s): Błażej Chermuła, Maciej Brązert, Dariusz Iżycki, Sylwia Ciesiółka, Wiesława Kranc, Piotr Celichowski, Katarzyna Ożegowska, Mariusz J. Nawrocki, Maurycy Jankowski, Michal Ješeta, Paweł Antosik, Dorota Bukowska, Mariusz T. Skowroński, Klaus‐Peter Brüssow, M Bruska, Leszek Pawełczyk, Maciej Zabel, Michał Nowicki, Bartosz Kempisty
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-8-416

ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information
Cited by: 54
Author(s): Daniel Barthel, Jonathan D. Hirst, Jacek Błażewicz, Edmund K. Burke, Natalio Krasnogor
Software Mentions: 3
Published: almost 17 years ago

10.1186/1471-2105-6-268

MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data
Cited by: 20
Author(s): Mahendra Navarange, Laurence Gamé, Derek Fowler, Vihar Wadekar, H. Stanley Banks, Nicola Cooley, Fatimah Rahman, Justin Hinshelwood, Peter Broderick, Helen C. Causton
Software Mentions: 3
Published: almost 19 years ago

10.3389/fmicb.2016.00901

Reconstruction of the High-Osmolarity Glycerol (HOG) Signaling Pathway from the Halophilic Fungus Wallemia ichthyophaga in Saccharomyces cerevisiae
Cited by: 8
Author(s): Tilen Konte, Ulrich Terpitz, Ana Plemenitaš
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.42866

The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs
Cited by: 36
Author(s): Leah Guthrie, Sarah J. Wolfson, Libusha Kelly
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-8-105

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry
Cited by: 899
Author(s): Tobias Kind, Oliver Fiehn
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2229-9-132

Genome scale transcriptome analysis of shoot organogenesis in Populus
Cited by: 43
Author(s): Yanghuan Bao, Palitha Dharmawardhana, Todd C. Mockler, Steven H. Strauss
Software Mentions: 2
Published: almost 15 years ago

10.3389/fcimb.2020.560240

Systems Biology Approaches for Therapeutics Development Against COVID-19
Cited by: 12
Author(s): Shweta Jaiswal, Mohit Kumar, Mandeep, Sunita Sunita, Yogendra Singh, Pratyoosh Shukla
Software Mentions: 2
Published: almost 4 years ago

10.3389/fimmu.2017.00278

The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design
Cited by: 291
Author(s): Ward Fleri, Sinu Paul, Sandeep Kumar Dhanda, Swapnil Mahajan, Xiaojun Xu, Bjoern Peters, Alessandro Sette
Software Mentions: 2
Published: over 7 years ago

10.3389/fpsyt.2016.00186

What Role Can Avatars Play in e-Mental Health Interventions? Exploring New Models of Client–Therapist Interaction
Cited by: 57
Author(s): Imogen C. Rehm, Emily Foenander, Klaire Wallace, Jo Abbott, Michael Kyrios, Neil Thomas
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12920-018-0411-5

Developing a healthcare dataset information resource (DIR) based on Semantic Web
Cited by: 4
Author(s): Jingyi Shi, Mingna Zheng, Lixia Yao, Yaorong Ge
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1006058

LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions
Cited by: 4
Author(s): Jinbo Chen, Uwe Scholz, Ruonan Zhou, Matthias Lange
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0033617

Identification and Analysis of Conserved cis-Regulatory Regions of the MEIS1 Gene
Cited by: 20
Author(s): José Luis Royo, José Bessa, Carmen Herrera Hidalgo, Ana Fernández-Miñán, Juan J. Tena, Yolanda Roncero, José Luis Gómez-Skármeta, Fernando Casares
Software Mentions: 2
Published: over 12 years ago

10.1093/database/bax047

LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis
Cited by: 19
Author(s): Felipe Guimarães Torres, Raúl Arias‐Carrasco, José Carlos Caris-Maldonado, Aldina Barral, Vinicius Maracaja‐Coutinho, Artur T. L. Queiroz
Software Mentions: 2
Published: over 7 years ago

10.1128/jmbe.00133-21

Development of an Online General Biology Open Educational Resource (OER) Laboratory Manual
Cited by: 0
Author(s): Dmitry Y Brogun, Azure N. Faucette, Kristin Polizzotto, Farshad Tamari
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2148-14-57

Multilocus coalescent analyses reveal the demographic history and speciation patterns of mouse lemur sister species
Cited by: 24
Author(s): Christopher Blair, Kellie L. Heckman, Amy L. Russell, Anne D. Yoder
Software Mentions: 2
Published: over 10 years ago

10.1002/elps.202000121

Physicochemical properties of SARS‐CoV‐2 for drug targeting, virus inactivation and attenuation, vaccine formulation and quality control
Cited by: 93
Author(s): Christin Scheller, Finja Krebs, Robert Minkner, I. Astner, María Gil-Moles, Hermann Wätzig
Software Mentions: 1
Published: over 4 years ago

10.1007/s00259-016-3382-9

Nephrotoxicity after PRRT with 177Lu-DOTA-octreotate
Cited by: 122
Author(s): Hendrik Bergsma, Mark Konijnenberg, Wouter A. van der Zwan, Boen L.R. Kam, Jaap J.M. Teunissen, P. P. M. Kooij, Katya Mauff, Eric P. Krenning, Dik J. Kwekkeboom
Software Mentions: 1
Published: over 8 years ago

10.1002/2211-5463.12849

LCK expression is a potential biomarker for distinguishing primary central nervous system lymphoma from glioblastoma multiforme
Cited by: 2
Author(s): Le Ge, Lixia Xu, Shan Lu, Hua Yan
Software Mentions: 1
Published: over 4 years ago

10.3389/fgene.2020.576442

Integrative Computational Approach Revealed Crucial Genes Associated With Different Stages of Diabetic Retinopathy
Cited by: 2
Author(s): Nidhi Kumari, Aditi Karmakar, Saikat Chakrabarti, Ganesan Senthil Kumar
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmolb.2020.589435

Proteome of the Triatomine Digestive Tract: From Catalytic to Immune Pathways; Focusing on Annexin Expression
Cited by: 8
Author(s): Márcia Gumiel, Débora P Mattos, Cecília Stahl Vieira, Caroline S. Moraes, Carlos José de Carvalho Moreira, Marcelo S. Gonzalez, André Teixeira-Ferreira, Mariana Caldas Waghabi, Patrı́cia Azambuja, Nicolas Carels
Software Mentions: 1
Published: almost 4 years ago

10.1128/genomeA.01472-17

Completed Genome Sequences of Strains from 36 Serotypes of Salmonella
Cited by: 1
Author(s): James A. Robertson, Catherine Yoshida, Simone Gurnik, John H. E. Nash
Software Mentions: 1
Published: over 6 years ago

10.9745/GHSP-D-20-00556

Expanding Contraceptive Method Choice With a Hormonal Intrauterine System: Results From Mixed Methods Studies in Kenya and Zambia
Cited by: 5
Author(s): Deborah Sitrin, Anne Pfitzer, Gathari Ndirangu, Ameck Kamanga, Brenda Onguti, Susan Ontiri, J. Chilambwe, Victor Kabwe, Lola Aladesanmi, Leah Elliott, Neeta Bhatnagar
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.ppat.1007375

An anti-Gn glycoprotein antibody from a convalescent patient potently inhibits the infection of severe fever with thrombocytopenia syndrome virus
Cited by: 36
Author(s): Ki–Hyun Kim, Jinhee Kim, Meehyun Ko, June Young Chun, Hyori Kim, Seungtaek Kim, Ji Young Min, Sang-Won Park, Myoung Don Oh, Junho Chung
Software Mentions: 1
Published: over 5 years ago

10.1186/1477-5956-6-18

Identification of differentially expressed proteins in spontaneous thymic lymphomas from knockout mice with deletion of p53
Cited by: 13
Author(s): Bent Honoré, Søren Buus, Mogens H. Claësson
Software Mentions: 1
Published: over 16 years ago

10.1038/s41598-018-35149-1

Gene prioritization, communality analysis, networking and metabolic integrated pathway to better understand breast cancer pathogenesis
Cited by: 24
Author(s): Andrés López‐Cortés, César Paz‐y‐Miño, Alejandro Cabrera-Andrade, Stephen J. Barigye, Cristian R. Munteanu, Humberto González-Dı́az, Alejandro Pazos, Yunierkis Pérez-Castillo, Eduardo Tejera
Software Mentions: 1
Published: almost 6 years ago

10.2196/21648

Toward Preparing a Knowledge Base to Explore Potential Drugs and Biomedical Entities Related to COVID-19: Automated Computational Approach
Cited by: 6
Author(s): Junaed Younus Khan, Md. Tawkat Islam Khondaker, Iram Tazim Hoque, Hamada R. H. Al-Absi, M. Sohel Rahman, Reto Guler, Tanvir Alam
Software Mentions: 1
Published: almost 4 years ago

10.3390/ijms13067109

Structural Analysis of Hypothetical Proteins from Helicobacter pylori: An Approach to Estimate Functions of Unknown or Hypothetical Proteins
Cited by: 15
Author(s): Sung Jean Park, Woo Sung Son, Bong-Jin Lee
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-9-419

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm
Cited by: 43
Author(s): Sheila Podell, Terry Gaasterland, Eric E. Allen
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-9-568

Genome-wide transcriptional response of an avian pathogenic Escherichia coli (APEC) pst mutant
Cited by: 33
Author(s): Sébastien Crépin, Martin G. Lamarche, Philippe Garneau, Julie Séguin, Julie Proulx, Charles M. Dozois, Josée Harel
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-9-217

Biocomputational prediction of small non-coding RNAs in Streptomyces
Cited by: 61
Author(s): Josef Pánek, Jan Bobek, Karel Mikulı́k, Marek Basler, Jiřı́ Vohradský
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2180-10-37

Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales
Cited by: 82
Author(s): Fabíola Marques de Carvalho, Rangel Celso Souza, Fernando Gomes Barcellos, Mariangela Hungría, Ana Tereza Ribeiro de Vasconcelos
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2180-8-99

A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes
Cited by: 41
Author(s): Young-Su Seo, Malinee Sriariyanun, Li Wang, Janice Pfeiff, Jirapa Phetsom, Lin Ye, Ki‐Hong Jung, Hui Hsien Chou, Adam J. Bogdanove, Pamela C. Ronald
Software Mentions: 1
Published: about 16 years ago

10.1186/s12888-016-0993-4

Linear and non-linear analyses of Conner’s Continuous Performance Test-II discriminate adult patients with attention deficit hyperactivity disorder from patients with mood and anxiety disorders
Cited by: 23
Author(s): Ole Bernt Fasmer, Kristin Mjeldheim, Wenche Førland, Anita L. Hansen, Vigdis Elin Giæver Syrstad, Ketil J. Oedegaard, Jan Øystein Berle
Software Mentions: 1
Published: about 8 years ago

10.1186/s12917-019-2204-2

High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea
Cited by: 17
Author(s): Martı́ Cortey, Iván Díaz, Àlvar Martínez Vidal, Gerard Martín‐Valls, Giovanni Franzo, Pedro J. G. de Nova, Laila Darwich, Héctor Puente, Ana Carvajal, M. Martín, Enric Mateu
Software Mentions: 1
Published: almost 5 years ago

10.1042/BSR20201920

Prognostic and immunological role of Fam20C in pan-cancer
Cited by: 17
Author(s): Xinpeng Liu, Yuanbo Zhan, Wenxia Xu, Xiaoyao Liu, Yawei Geng, Lixue Liu, Junlong Da, Jianqun Wang, Xinjian Zhang, Han Jin, Zhongshuang Liu, Shouli Guo, Bin Zhang, Ying Li
Software Mentions: 1
Published: over 3 years ago

10.1186/1475-2859-12-30

New insights on the reorganization of gene transcription in Pseudomonas putida KT2440 at elevated pressure
Cited by: 34
Author(s): Stéphanie Follonier, Isabel F. Escapa, Pilar Fonseca, Bernhard Henes, Sven Panke, Manfred Zinn, M. Prieto
Software Mentions: 1
Published: over 11 years ago

10.1099/mgen.0.000151

Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella in silico Typing Resource (SISTR)
Cited by: 39
Author(s): James A. Robertson, Catherine Yoshida, Peter Kruczkiewicz, Céline Nadon, Anil Nichani, Eduardo N. Taboada, John H. E. Nash
Software Mentions: 1
Published: over 6 years ago

10.1017/S0031182019001768

Bioinformatic analysis of eosinophil activity and its implications for model and target species
Cited by: 3
Author(s): Caitlin J. Jenvey, Dalal Alenizi, Fazel Almasi, Callum Cairns, Andrew Holmes, Sarah Sloan, M. J. Stear
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13071-015-1176-8

A cecropin-like antimicrobial peptide with anti-inflammatory activity from the black fly salivary glands
Cited by: 26
Author(s): Jing Wu, Lingli Mu, Zhuang Li, Yamei Han, Tong Liu, Jun Li, Yadong Yuan, Hailong Yang, Wei Lin
Software Mentions: 1
Published: almost 9 years ago

10.3390/pharmaceutics11030119

Computational Approaches in Theranostics: Mining and Predicting Cancer Data
Cited by: 18
Author(s): Tânia F.G.G. Cova, Daniel Jorge Silva Bento, Sandra C.C. Nunes
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.3000665

ORANGE: A CRISPR/Cas9-based genome editing toolbox for epitope tagging of endogenous proteins in neurons
Cited by: 95
Author(s): Jelmer Willems, Arthure Jong, Nicky Scheefhals, Eline J. Mertens, Lisa A.E. Catsburg, Rogier B. Poorthuis, Fred de Winter, Joost Verhaagen, Frank J. Meye, Harold D. MacGillavry
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pcbi.1003849

A Reappraisal of How to Build Modular, Reusable Models of Biological Systems
Cited by: 46
Author(s): Maxwell Lewis Neal, Michael T. Cooling, Lucian P. Smith, Christopher T. Thompson, Herbert M. Sauro, Brian E. Carlson, Daniel L. Cook, John H. Gennari
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pcbi.1002492

Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses
Cited by: 26
Author(s): Lars Steinbrück, Alice C. McHardy
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pntd.0007169

The diversity, evolution and ecology of Salmonella in venomous snakes
Cited by: 17
Author(s): Caisey V Pulford, Nicolas Wenner, Martha L. Redway, Ella V Rodwell, Hermione J. Webster, Roberta Escudero, Carsten Kröger, Rocı́o Canals, Will Rowe, Javier López, Neil Hall, Paul D. Rowley, Dorina Timofte, Robert A. Harrison, Kate S. Baker, Jay C. D. Hinton
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0127108

Analysis of Human RSV Immunity at the Molecular Level: Learning from the Past and Present
Cited by: 3
Author(s): Kerrie Vaughan, Julia Ponomarenko, Bjoern Peters, Alessandro Sette
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0159887

Novel Anthropometry Based on 3D-Bodyscans Applied to a Large Population Based Cohort
Cited by: 40
Author(s): Henry Löffler-Wirth, Edith Willscher, Peter Ahnert, Kerstin Wirkner, Christoph Engel, Markus Loeffler, Hans Binder
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0145124

Novel Genes Affecting the Interaction between the Cabbage Whitefly and Arabidopsis Uncovered by Genome-Wide Association Mapping
Cited by: 11
Author(s): Colette Broekgaarden, Johan Bucher, Johanna A. Bac-Molenaar, Joost J. B. Keurentjes, Willem Kruijer, Roeland E. Voorrips, Ben Vosman
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0086309

Integrative Gene Network Construction to Analyze Cancer Recurrence Using Semi-Supervised Learning
Cited by: 46
Author(s): Chihyun Park, Jaegyoon Ahn, Hyun‐Jin Kim, Sang‐Hyun Park
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0089574

Actigraphic Assessment of Motor Activity in Acutely Admitted Inpatients with Bipolar Disorder
Cited by: 92
Author(s): Karoline Krane-Gartiser, Tone Elise Gjøtterud Henriksen, Gunnar Morken, Arne Vaaler, Ole Bernt Fasmer
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0075601

New Pyrazolopyrimidine Inhibitors of Protein Kinase D as Potent Anticancer Agents for Prostate Cancer Cells
Cited by: 28
Author(s): Manuj Tandon, J. Karl Johnson, Zhihong Li, Shaohua Xu, Peter Wipf, Qiming J. Wang
Software Mentions: 1
Published: almost 11 years ago

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