Ecosyste.ms: Papers

10.3389/fmicb.2021.634503

Cottonseed Press Cake as a Potential Diet for Industrially Farmed Black Soldier Fly Larvae Triggers Adaptations of Their Bacterial and Fungal Gut Microbiota
Cited by: 26
Author(s): Dorothee Tegtmeier, Sabine Hurka, Patrick Klüber, Karina Brinkrolf, Philipp Heise, Andreas Vilcinskas
Software Mentions: 10
Published: over 3 years ago

10.3389/fmicb.2020.01190

Genetic Organization of the aprX-lipA2 Operon Affects the Proteolytic Potential of Pseudomonas Species in Milk
Cited by: 14
Author(s): Christopher Maier, Christopher Huptas, Mario von Neubeck, Stephen W. Scherer, Mareike Wenning, Genia Lücking
Software Mentions: 10
Published: over 4 years ago

10.7717/peerj.9624

Genome‐wide identification of CpG island methylator phenotype related gene signature as a novel prognostic biomarker of gastric cancer
Cited by: 12
Author(s): Zhi Zeng, Daxing Xie, Jianping Gong
Software Mentions: 10
Published: over 4 years ago

10.1186/s12859-016-0997-6

Unaccounted uncertainty from qPCR efficiency estimates entails uncontrolled false positive rates
Cited by: 5
Author(s): Anders Ellern Bilgrau, Steffen Falgreen, Anders Petersen, Malene Krag Kjeldsen, Julie Støve Bødker, Hans Erik Johnsen, Karen Dybkær, Martin Bøgsted
Software Mentions: 10
Published: over 8 years ago

10.3390/insects10030065

Multi-Scenario Species Distribution Modeling
Cited by: 12
Author(s): Senait D. Senay, Susan P. Worner
Software Mentions: 10
Published: almost 6 years ago

10.1186/s12864-016-2737-8

Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery
Cited by: 55
Author(s): Zhilong Jia, Ying Liu, Naiyang Guan, Xiaochen Bo, Zhi-Gang Luo, Michael R. Barnes
Software Mentions: 10
Published: over 8 years ago

10.3389/fpsyg.2021.620307

No Evidence for a Decrease in Physical Activity Among Swiss Office Workers During COVID-19: A Longitudinal Study
Cited by: 19
Author(s): Andrea Martina Aegerter, Manja Deforth, Gisela Sjøgaard, Venerina Johnston, Thomas Volken, Hannu Luomajoki, Julia Dratva, Holger Dressel, Oliver Distler, Markus Melloh, Achim Elfering
Software Mentions: 10
Published: almost 4 years ago

10.1155/2020/1468980

Construction and Analysis of lncRNA-Mediated ceRNA Network in Nasopharyngeal Carcinoma Based on Weighted Correlation Network Analysis
Cited by: 7
Author(s): Zhenning Zou, Shuguang Liu, Yanping Ha, Bowan Huang
Software Mentions: 10
Published: about 4 years ago

10.1186/s12920-020-00754-5

Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis
Cited by: 15
Author(s): Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye, Guowei Li
Software Mentions: 10
Published: over 4 years ago

10.1186/s12935-021-01965-1

Elevated expression of LPCAT1 predicts a poor prognosis and is correlated with the tumour microenvironment in endometrial cancer
Cited by: 9
Author(s): Tianyi Zhao, Min Han, Xiaohong Ma, Lina Wei, Yixin Hou, Rui Sun, Jie Jiang
Software Mentions: 10
Published: over 3 years ago

10.1186/s13059-020-02034-y

APEC: an accesson-based method for single-cell chromatin accessibility analysis
Cited by: 11
Author(s): Bin Li, Young Li, Kun Li, Lianbang Zhu, Qiaoni Yu, Pengfei Cai, Jingwen Fang, Wen Zhang, Pengcheng Du, Chen Jiang, Jun Lin, Kun Qu
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pgen.1009376

Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae
Cited by: 46
Author(s): Wei Zhang, Jun Huang, David E. Cook
Software Mentions: 10
Published: almost 4 years ago

10.3389/fimmu.2021.641495

Mitochondrial Reactive Oxygen Species Regulate Immune Responses of Macrophages to Aspergillus fumigatus
Cited by: 15
Author(s): Rémi Hatinguais, Arnab Pradhan, Gordon D. Brown, Alistair J. P. Brown, Adilia Warris, Elena Shekhova
Software Mentions: 10
Published: over 3 years ago

10.1007/s10456-020-09743-9

Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cells
Cited by: 16
Author(s): Carlotta Tacconi, Yuliang He, Luca Ducoli, Michael Detmar
Software Mentions: 10
Published: about 4 years ago

10.1371/journal.pone.0256016

Integration of chronological omics data reveals mitochondrial regulatory mechanisms during the development of hepatocellular carcinoma
Cited by: 2
Author(s): J. Noé García-Chávez, Verónica Rocío Vásquez-Garzón, Mercedes G. López, Saúl Villa‐Treviño, Rafaél Montiel
Software Mentions: 10
Published: over 3 years ago

10.1186/s13148-019-0795-x

DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis
Cited by: 50
Author(s): Ieva Rauluševičiūtė, Finn Drabløs, Morten Rye
Software Mentions: 10
Published: about 5 years ago

10.1002/ece3.4550

Size does matter: Parallel evolution of adaptive thermal tolerance and body size facilitates adaptation to climate change in domestic cattle
Cited by: 20
Author(s): Muhammed Elayadeth-Meethal, Aravindakshan Thazhathu Veettil, Shane K. Maloney, N. J. Hawkins, Tom Misselbrook, Veerasamy Sejian, M. Jordana Rivero, Michael R. F. Lee
Software Mentions: 10
Published: about 6 years ago

10.15252/msb.20188339

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks
Cited by: 31
Author(s): Jan‐Philipp Mallm, Murat Iskar, Naveed Ishaque, Lara Klett, Sabrina J. Kugler, Jose M. Muiño, Vladimir B. Teif, Alexandra M Poos, Sebastian Großmann, Fabian Erdel, Daniele Tavernari, Sandra D. Koser, Sabrina Schumacher, Benedikt Brors, Rainer König, Daniel Remondini, Martin Vingron, Stephan Stilgenbauer, Peter Lichter, Marc Zapatka, Daniel Mertens, Karsten Rippe
Software Mentions: 10
Published: over 5 years ago

10.3389/fmicb.2021.657508

Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas
Cited by: 3
Author(s): Fernando Igne Rocha, Thiago Gonçalves Ribeiro, Marcelo Antoniol Fontes, Stefan Schwab, Márcia Reed Rodrigues Coelho, J. F. Lumbreras, P. E. F. da Motta, W. G. Teixeira, James R. Cole, Ana Carolina Borsanelli, Iveraldo S. Dutra, Adina Howe, Aline Pacobahyba de Oliveira, Ederson da Conceição Jesus
Software Mentions: 10
Published: over 3 years ago

10.1007/s00401-020-02224-9

Altered DNA methylation profiles in blood from patients with sporadic Creutzfeldt–Jakob disease
Cited by: 14
Author(s): Luke C. Dabin, Fernando Guntoro, Tracy Campbell, Tony Bélicard, Adam R. Smith, Rebecca G. Smith, Rachel Raybould, Jonathan M. Schott, Katie Lunnon, Peter Sarkies, John Collinge, Simon Mead, Emmanuelle Viré
Software Mentions: 10
Published: about 4 years ago

10.1186/s12859-021-04037-3

InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification
Cited by: 8
Author(s): Dominik J. E. Waibel, Sayedali Shetab Boushehri, Carsten Marr
Software Mentions: 10
Published: almost 4 years ago

10.12688/f1000research.13925.3

BED: a Biological Entity Dictionary based on a graph data model
Cited by: 1
Author(s): Patrice Godard, Jonathan van Eyll
Software Mentions: 10
Published: over 6 years ago

10.1038/s42003-021-02407-4

Social familiarity improves fast-start escape performance in schooling fish
Cited by: 8
Author(s): Lauren E. Nadler, Mark I. McCormick, Jacob L. Johansen, Paolo Domenici
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0128124

Oceanographic Conditions Limit the Spread of a Marine Invader along Southern African Shores
Cited by: 57
Author(s): Jorge Assis, Mirta Zupan, Katy R. Nicastro, Gerardo I. Zardi, Christopher D. McQuaid, Ester Á. Serrão
Software Mentions: 10
Published: over 9 years ago

10.1016/j.cell.2019.10.007

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
Cited by: 375
Author(s): David Clark, Saravana M. Dhanasekaran, Francesca Petralia, Jianbo Pan, Xiaoyu Song, Yingwei Hu, Felipe da Veiga Leprevost, Boris Reva, Tung-Shing Mamie Lih, Hui-Yin Chang, Wanli Ma, Chen Huang, Christopher J. Ricketts, Lijun Chen, Azra Krek, Yize Li, Dmitry Rykunov, Qing Kay Li, Lin S. Chen, Umut Özbek, Suhas Vasaikar, Yige Wu, Seungyeul Yoo, Shrabanti Chowdhury, Matthew A. Wyczalkowski, Jiayi Ji, Michael Schnaubelt, Andy T. Kong, Sunantha Sethuraman, Dmitry M. Avtonomov, Minghui Ao, Antonio Colaprico, Song Cao, Kyung-Cho Cho, Selim Kalayci, Shiyong Ma, Wenke Liu, Kelly V. Ruggles, Anna Calinawan, Zeynep H. Gümüş, Daniel Geiszler, Emily Kawaler, Guo Ci Teo, Bo Wen, Yuping Zhang, Sarah Keegan, Kai Li, Feng Chen, Nathan Edwards, Phillip M. Pierorazio, Xi Steven Chen, Christian P. Pavlovich, A. Ari Hakimi, Gabriel Bromiński, James J. Hsieh, Andrzej Antczak, Tatiana Omelchenko, Jan Lubiński, Maciej Wiznerowicz, W. Marston Linehan, Christopher R. Kinsinger, Mathangi Thiagarajan, Emily S. Boja, Mehdi Mesri, Tara Hiltke, Ana I. Robles, Henry Rodriguez, Jiang Qian, David Fenyö, Bing Zhang, Ding Li, Eric E. Schadt, Arul M. Chinnaiyan, Zhen Zhang, Gilbert S. Omenn, Marcin Cieślik, Daniel W. Chan, Alexey I. Nesvizhskii, Pei Wang, Hui Zhang, A. Samad Hashimi, Alexander Pico, Alla Karpova, Alyssa Charamut, Amanda G. Paulovich, Amy M. Perou, Anna Malovannaya, Annette Marrero-Oliveras, Anupriya Agarwal, Barbara Hindenach, Barbara L. Pruetz, Beom-Jun Kim, Brian J. Druker, Chelsea J. Newton, Chet Birger, Corbin D. Jones, Cristina E. Tognon, D. R. Mani, Dana R. Valley, Daniel C. Rohrer, Daniel Cui Zhou, Darlene Tansil, David Chesla, David I. Heiman, David A. Wheeler, Donghui Tan, Doug W. Chan, Emek Demir, Ewa Malc, Francesmary Modugno, Gaddy Getz, Galen Hostetter, George Wilson, Gerald W. Hart, Heng Zhu, Hongwei Liu, Houston Culpepper, Hua Sun, Hua Zhou, Jacob Day, James Suh, Jasmine Huang, Jason McDermott, Jeffrey R. Whiteaker, Jeffrey W. Tyner, Jennifer Eschbacher, Jin Chen, John P. McGee, Jun Zhu, Karen A. Ketchum, Karin D. Rodland, Karl R. Clauser, Karna Robinson, Karsten Krug, Katherine A. Hoadley, Ki Sung Um, Kim Elburn, Kimberly Holloway, Liang-Bo Wang, Lili M. Blumenberg, Linda Hannick, Liqun Qi, Lori J. Sokoll, MacIntosh Cornwell, Marc Loriaux, Marcin J. Domagalski, Marina Gritsenko, Matthew L. Anderson, Matthew E. Monroe, Matthew J. Ellis, Maureen A. Dyer, Meenakshi Anurag, Meghan C. Burke, Melissa Borucki, Michael A. Gillette, Michael J. Birrer, Michael R. Lewis, Michael Ittmann, Michael J. Smith, Michael Vernon, Michelle Chaikin, Milan G. Chheda, Munziba Khan, Nancy Roche, Nathan Edwards, Negin Vatanian, Nicole Tignor, Noam D. Beckmann, Pamela Grady, Patricia Castro, Paul Piehowski, Peter B. McGarvey, Piotr A. Mieczkowski, Pushpa Hariharan, Qingsong Gao, Rajiv Dhir, Ramani B. Kothadia, Ratna R. Thangudu, Rebecca Montgomery, Reyka G. Jayasinghe, Richard Smith, Robert A. Edwards, Robert Zelt, Ross M. Bremner, Ruiyang Liu, Runyu Hong, Sailaja Mareedu, Samuel H. Payne, Sandra Cottingham, Sanford P. Markey, Scott D. Jewell, Shalin Patel, Shankha Satpathy, Shannon Richey, Sherri R. Davies, Shuang Cai, Simina M. Boca, Snehal Patil, Sohini Sengupta, Sonya Carter, Stacey Gabriel, Stefani N. Thomas, Stephanie Young, Stephen E. Stein, Steven A. Carr, Steven M. Foltz, S. G. Hilsenbeck, Tanya Krubit, Tao Liu, Tara Skelly, Thomas F. Westbrook, Uma Borate, Uma Velvulou, Vladislav Petyuk, William Bocik, Xi Chen, Yan Shi, Yifat Geffen, Yihao Lu, Ying Wang, Yosef E. Maruvka, Zhi Li, Zhiao Shi, Zhidong Tu
Software Mentions: 10
Published: about 5 years ago

10.1534/g3.120.401174

Sirt4 Modulates Oxidative Metabolism and Sensitivity to Rapamycin Through Species-Dependent Phenotypes in <i>Drosophila</i> mtDNA Haplotypes
Cited by: 3
Author(s): Richard Sejour, Roger A. Sanguino, Monika Mikolajczak, Walishah Ahmadi, Eugenia Villa-Cuesta
Software Mentions: 10
Published: over 4 years ago

10.3389/fchem.2021.722087

PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems
Cited by: 0
Author(s): Matej Medvecký, Manolis Mandalakis
Software Mentions: 10
Published: over 3 years ago

10.15252/msb.20209923

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis
Cited by: 122
Author(s): Dénes Türei, Alberto Valdeolivas, Lejla Gul, Nicolàs Palacio-Escat, Michal Klein, Olga Ivanova, Márton Ölbei, Attila Gábor, Fabian J. Theis, Dezső Módos, Tamás Korcsmáros, Julio Sáez-Rodríguez
Software Mentions: 10
Published: almost 4 years ago

10.1186/s12859-017-1770-1

CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction
Cited by: 24
Author(s): Carlos Guzmán, Iván D’Orso
Software Mentions: 10
Published: over 7 years ago

10.1371/journal.pone.0185171

Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes
Cited by: 29
Author(s): Tuulia Mali, Jaana Kuuskeri, Firoz Shah, Taina Lundell
Software Mentions: 10
Published: about 7 years ago

10.1371/journal.pntd.0009540

Sexual selection theory meets disease vector control: Testing harmonic convergence as a “good genes” signal in Aedes aegypti mosquitoes
Cited by: 6
Author(s): Garrett P. League, Laura C. Harrington, Sylvie A. Pitcher, Julie K. Geyer, Lindsay L. Baxter, Julian Montijo, John G. Rowland, Lynn M. Johnson, Courtney C. Murdock, Lauren J. Cator
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pgen.1008530

Genetic variation in GC and CYP2R1 affects 25-hydroxyvitamin D concentration and skeletal parameters: A genome-wide association study in 24-month-old Finnish children
Cited by: 12
Author(s): Anders Kämpe, Maria Enlund-Cerullo, Saara Valkama, Elisa Holmlund-Suila, Jenni Rosendahl, Helena Hauta-alus, Minna Pekkinen, Sture Andersson, Outi Mäkitie
Software Mentions: 10
Published: almost 5 years ago

10.1371/journal.pone.0029018

Python as a Federation Tool for GENESIS 3.0
Cited by: 26
Author(s): Hugo Cornelis, Antony Rodríguez, Allan D Coop, James M. Bower
Software Mentions: 10
Published: almost 13 years ago

10.1186/s12915-021-01029-w

Global population genetic structure and demographic trajectories of the black soldier fly, Hermetia illucens
Cited by: 36
Author(s): Cengiz Kaya, Tomas N Generalovic, Gunilla Ståhls, Martin Hauser, Ana Clariza Samayoa, Carlos Gustavo Nunes-Silva, Heather Roxburgh, Jens Wohlfahrt, Ebenezer Ato Ewusie, Marc Kenis, Yupa Hanboonsong, Jesús Orozco, Nancy Carrejo, Satoshi Nakamura, Laura Gasco, Santos Rojo, Chrysantus M. Tanga, Rudolf Meier, Clint Rhode, Christine Picard, Chris D. Jiggins, Florian Leiber, Jeffery K. Tomberlin, Martin Hasselmann, Wolf U. Blanckenhorn, Martin Kapun, Christoph Sandrock
Software Mentions: 10
Published: over 3 years ago

10.1186/s12864-021-07388-6

Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential
Cited by: 3
Author(s): Niels A. Zondervan, Vítor A. P. Martins dos Santos, María Suárez-Diez, Edoardo Saccenti
Software Mentions: 10
Published: almost 4 years ago

10.3390/jcm8091298

Comparison of Machine Learning Techniques for Prediction of Hospitalization in Heart Failure Patients
Cited by: 32
Author(s): Giulia Lorenzoni, Stefano Santo Sabato, Corrado Lanera, Daniele Bottigliengo, Clara Minto, Honoria Ocagli, Paola De Paolis, Darío Gregori, Sabino Iliceto, Franco Pisanò
Software Mentions: 10
Published: over 5 years ago

10.3897/zookeys.1044.62340

Carabid beetle (Coleoptera, Carabidae) richness, diversity, and community structure in the understory of temporarily flooded and non-flooded Amazonian forests of Ecuador
Cited by: 2
Author(s): Kathryn N. Riley Peterson, Robert A. Browne, Terry L. Erwin
Software Mentions: 10
Published: over 3 years ago

10.1186/s13071-020-04461-z

Oviposition of Aedes japonicus japonicus (Diptera: Culicidae) and associated native species in relation to season, temperature and land use in western Germany
Cited by: 12
Author(s): Linus Früh, Helge Kampen, Marcel B. Koban, Nadja Pernat, Günter A. Schaub, Doreen Werner
Software Mentions: 10
Published: about 4 years ago

10.1093/aje/kwaa127

Conditional Cash Transfer Program and Leprosy Incidence: Analysis of 12.9 Million Families From the 100 Million Brazilian Cohort
Cited by: 15
Author(s): Júlia Moreira Pescarini, Elizabeth Williamson, Maria Yury Ichihara, Rosemeire Leovigildo Fiaccone, Laura Forastiere, Anna Ramond, Joilda Silva Nery, Maria Lúcia Fernandes Penna, Agostino Strina, Sandra Reis, Liam Smeeth, Laura C. Rodrigues, Elizabeth B Brickley, Gerson Oliveira Penna, Marcos Barreto
Software Mentions: 10
Published: over 4 years ago

10.1038/s42003-021-02009-0

Pests, diseases, and aridity have shaped the genome of Corymbia citriodora
Cited by: 15
Author(s): Adam Healey, Mervyn Shepherd, Graham J. King, Jakob B. Butler, Jules S. Freeman, David J Lee, Brad M. Potts, Orzenil B. Silva‐Junior, Abdul Baten, Jerry Jenkins, Shengqiang Shu, John T. Lovell, Avinash Sreedasyam, Jane Grimwood, Agnelo Furtado, Dário Grattapaglia, Kerrie Barry, Hope Hundley, Blake A. Simmons, Jeremy Schmutz, René E. Vaillancourt, Robert J. Henry
Software Mentions: 10
Published: over 3 years ago

10.1186/s13059-021-02484-y

Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implications
Cited by: 5
Author(s): Benjamin Planterose Jiménez, Manfred Kayser, Athina Vidaki
Software Mentions: 10
Published: about 3 years ago

10.1371/journal.pone.0191601

Highly multiplexed single-cell quantitative PCR
Cited by: 12
Author(s): Michael VanInsberghe, Hans Zahn, Alexander D. White, Oleh I. Petriv, Carl L. Hansen
Software Mentions: 10
Published: almost 7 years ago

10.3390/v12111229

RNAseq of Deformed Wing Virus and Other Honey Bee-Associated Viruses in Eight Insect Taxa with or without Varroa Infestation
Cited by: 17
Author(s): Laura E. Brettell, Declan C. Schroeder, Stephen J. Martin
Software Mentions: 10
Published: about 4 years ago

10.1093/gigascience/giz146

Systematic processing of ribosomal RNA gene amplicon sequencing data
Cited by: 45
Author(s): Julien Tremblay, Étienne Yergeau
Software Mentions: 10
Published: about 5 years ago

10.3390/ani9050215

Waste Disposal Sites as All-You-Can Eat Buffets for Carrion Crows (Corvus corone)
Cited by: 14
Author(s): Doris Preininger, Bjoern Schoas, Diether Kramer, Markus Boeckle
Software Mentions: 10
Published: over 5 years ago

10.1186/1472-6785-10-12

The world's richest tadpole communities show functional redundancy and low functional diversity: ecological data on Madagascar's stream-dwelling amphibian larvae
Cited by: 54
Author(s): Axel Strauß, Erik Reeve, Roger-Daniel Randrianiaina, Miguel Vences, Julian Glos
Software Mentions: 10
Published: almost 15 years ago

10.1186/s12916-020-01595-w

Serum metabolite profiles are associated with the presence of advanced liver fibrosis in Chinese patients with chronic hepatitis B viral infection
Cited by: 30
Author(s): Guoxiang Xie, Xiaoning Wang, Runmin Wei, Jingye Wang, Aihua Zhao, Tianlu Chen, Yixing Wang, Hua Zhang, Zhun Xiao, Xin-Zhu Liu, Youping Deng, Linda L. Wong, Cynthia Rajani, Sandi A. Kwee, Hua Bian, Xin Gao, Ping Liu, Jia Wang
Software Mentions: 10
Published: over 4 years ago

10.1128/mSystems.00571-21

Pathogenic <i>Vibrio</i> Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes
Cited by: 11
Author(s): Rachel E. Diner, Drishti Kaul, Ariel Rabines, Hong Zheng, Joshua A. Steele, John F. Griffith, Andrew E. Allen
Software Mentions: 10
Published: over 3 years ago

10.1186/s12864-015-2356-9

QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization
Cited by: 33
Author(s): Shanrong Zhao, Li Xi, Jie Quan, Hualin Simon Xi, Ying Zhang, David von Schack, Michael S. Vincent, Baohong Zhang
Software Mentions: 10
Published: almost 9 years ago

10.3389/fimmu.2021.622563

9-Gene Signature Correlated With CD8+ T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in Melanoma
Cited by: 17
Author(s): Kexin Yan, Yuxiu Lu, Zhangyong Yan, Yutao Wang
Software Mentions: 10
Published: over 3 years ago

10.3389/fonc.2018.00659

The Role of COL5A2 in Patients With Muscle-Invasive Bladder Cancer: A Bioinformatics Analysis of Public Datasets Involving 787 Subjects and 29 Cell Lines
Cited by: 28
Author(s): Xiangyu Meng, Mingjun Shi, Zhao-Yi Zeng, Chen Chen, Tong-Zu Liu, Qiuji Wu, Shuo Li
Software Mentions: 10
Published: almost 6 years ago

10.1371/journal.pone.0216723

A metadata approach to evaluate the state of ocean knowledge: Strengths, limitations, and application to Mexico
Cited by: 10
Author(s): Juliano Palacios‐Abrantes, Andrés M. Cisneros‐Montemayor, Miguel Á. Cisneros-Mata, Laura Rodríguez, Francisco Arreguı́n-Sánchez, Verónica Aguilar, Santiago Domínguez-Sánchez, Stuart Fulton, Raquel López-Sagástegui, Héctor Reyes‐Bonilla, Rocío Rivera-Campos, Silvia Salas, Nuno Simões, William W. L. Cheung
Software Mentions: 10
Published: over 5 years ago

10.1186/s40168-020-00895-w

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota
Cited by: 32
Author(s): Shashank Gupta, Mathis Hjort Hjelmsø, Jenni Lehtimäki, Xuanji Li, Martin Steen Mortensen, Jakob Russel, Urvish Trivedi, Morten Arendt Rasmussen, Jakob Stokholm, Hans Bisgaard, Søren J. Sørensen
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pone.0218773

Demand and level of service inflation in Floating Catchment Area (FCA) methods
Cited by: 34
Author(s): Antonio Páez, Christopher D. Higgins, Salvatore Vivona
Software Mentions: 10
Published: over 5 years ago

10.1186/cc13914

Higher clinical success in patients with ventilator-associated pneumonia due to methicillin-resistant Staphylococcus aureus treated with linezolid compared with vancomycin: results from the IMPACT-HAP study
Cited by: 37
Author(s): Paula Peyrani, Timothy Wiemken, Robert Kelley, Marcus J. Zervos, Daniel H. Kett, Thomas M. File, Gary E. Stein, Kimbal D. Ford, Ernesto G. Scerpella, Verna L Welch, Julio A. Ramirez
Software Mentions: 10
Published: almost 11 years ago

10.1371/journal.pone.0034594

Heterogeneity of Inflammatory and Cytokine Networks in Chronic Plaque Psoriasis
Cited by: 71
Author(s): William R. Swindell, Xianying Xing, Philip E. Stuart, Cynthia S. Chen, Abhishek Aphale, Rajan P. Nair, John J. Voorhees, James T. Elder, Andrew Johnston, Jóhann E. Guðjónsson
Software Mentions: 10
Published: over 12 years ago

10.1186/s40360-021-00505-x

Causal inference multiple imputation investigation of the impact of cannabinoids and other substances on ethnic differentials in US testicular cancer incidence
Cited by: 26
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 10
Published: over 3 years ago

10.3389/fgene.2021.682638

Scalable and Robust Regression Methods for Phenome-Wide Association Analysis on Large-Scale Biobank Data
Cited by: 2
Author(s): Wenjian Bi, Seunggeun Lee
Software Mentions: 10
Published: over 3 years ago

10.3390/md16100379

Fatty Acid Composition and Fatty Acid Associated Gene-Expression in Gilthead Sea Bream (Sparus aurata) are Affected by Low-Fish Oil Diets, Dietary Resveratrol, and Holding Temperature
Cited by: 18
Author(s): Claudia Torno, Stefanie Staats, Stéphanie Céline Michl, Sonia de Pascual‐Teresa, Marisol Izquierdo, Gerald Rimbach, Carsten Schulz
Software Mentions: 10
Published: about 6 years ago

10.3389/fgene.2019.00279

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis
Cited by: 46
Author(s): Verónica Jiménez-Jacinto, Alejandro Sánchez-Flores, Leticia Vega‐Alvarado
Software Mentions: 10
Published: over 5 years ago

10.1186/s13059-018-1466-5

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data
Cited by: 40
Author(s): Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele
Software Mentions: 10
Published: over 6 years ago

10.3389/fmicb.2018.01598

Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility
Cited by: 60
Author(s): Kristopher D. Parker, Shannon E. Albeke, Jason P. Gigley, Allan M. Goldstein, Naomi Ward
Software Mentions: 10
Published: over 6 years ago

10.1038/s41598-020-70722-7

Active and social life is associated with lower non-social fearfulness in pet dogs
Cited by: 15
Author(s): Emma Hakanen, Salla Mikkola, Milla Salonen, Jenni Puurunen, Sini Sulkama, Cynthia Gobbi Alves Araújo, Hannes Lohi
Software Mentions: 10
Published: over 4 years ago

10.1186/s12864-019-6324-7

Identification of genetic loci and candidate genes related to soybean flowering through genome wide association study
Cited by: 9
Author(s): Minmin Li, Ying Liu, Yahan Tao, Chongjing Xu, Xin Li, Xiaoming Zhang, Yingpeng Han, Xue Yang, Jingzhe Sun, Wenbin Li, Dongmei Li, Xue Zhao, Lin Zhao
Software Mentions: 10
Published: about 5 years ago

10.1186/s13059-016-0999-8

Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia
Cited by: 64
Author(s): Syed Haider, Alan McIntyre, Ruud G.P.M. van Stiphout, Laura Winchester, Simon Wigfield, Adrian L. Harris, Francesca M. Buffa
Software Mentions: 10
Published: over 8 years ago

10.1186/s12917-018-1331-5

A large-scale study of a poultry trading network in Bangladesh: implications for control and surveillance of avian influenza viruses
Cited by: 32
Author(s): Natalie Moyen, Graba Ahmed, Suman Das Gupta, Tenzin Tenzin, Rasheda Khan, Tooba Khan, Nitish Debnath, Mat Yamage, Dirk U. Pfeiffer, Guillaume Fournié
Software Mentions: 10
Published: almost 7 years ago

10.3389/fcell.2021.731790

Identification and Validation of a Nine-Gene Amino Acid Metabolism-Related Risk Signature in HCC
Cited by: 34
Author(s): Yajuan Zhao, Junli Zhang, Shuhan Wang, Qianqian Jiang, Ke Xu
Software Mentions: 10
Published: about 3 years ago

10.1002/ece3.6594

A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses
Cited by: 36
Author(s): Devon O’Rourke, Nicholas A. Bokulich, Michelle A. Jusino, Matthew D. MacManes, Jeffrey T. Foster
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pone.0247535

Tools for mapping multi-scale settlement patterns of building footprints: An introduction to the R package foot
Cited by: 21
Author(s): Warren C. Jochem, Andrew J. Tatem
Software Mentions: 10
Published: almost 4 years ago

10.1002/cam4.4117

A comprehensive analysis of immune infiltration in the tumor microenvironment of osteosarcoma
Cited by: 17
Author(s): Hao Yang, Liang Zhao, Yang Zhang, Fangfang Li
Software Mentions: 10
Published: over 3 years ago

10.3389/fmicb.2020.545419

Species Dependence of SYTO 9 Staining of Bacteria
Cited by: 20
Author(s): Cushla McGoverin, Julia Robertson, Yaqub Jonmohamadi, Simon Swift, Frédérique Vanholsbeeck
Software Mentions: 10
Published: about 4 years ago

10.1002/sim.7582

Dynamic prediction in functional concurrent regression with an application to child growth
Cited by: 13
Author(s): Andrew Leroux, Luo Xiao, Ciprian M. Crainiceanu, William Checkley
Software Mentions: 10
Published: almost 7 years ago

10.1186/s12859-021-04254-w

ORFik: a comprehensive R toolkit for the analysis of translation
Cited by: 13
Author(s): Håkon Tjeldnes, Kornel Labun, Yamila Torres Cleuren, Katarzyna Chyżyńska, Michał Świrski, Eivind Valen
Software Mentions: 10
Published: over 3 years ago

10.1016/S2213-2600(21)00175-2

Changes in in-hospital mortality in the first wave of COVID-19: a multicentre prospective observational cohort study using the WHO Clinical Characterisation Protocol UK
Cited by: 71
Author(s): Annemarie B Docherty, Rachel Mulholland, Nazir Lone, Christopher P. Cheyne, Daniela De Angelis, Karla Díaz-Ordaz, Cara Donegan, Thomas M Drake, Jake Dunning, Sebastian Funk, Marta García‐Fiñana, Michelle Girvan, Hayley Hardwick, Janet Harrison, Antonia Ho, David Hughes, Ruth H. Keogh, Peter Kirwan, Gary Leeming, J. Van-Tam, Riinu Pius, Clark D Russell, Rebecca G. Spencer, Brian D. M. Tom, Lance Turtle, Peter Openshaw, J Kenneth Baillie, Ewen M Harrison, Malcolm G Semple
Software Mentions: 10
Published: over 3 years ago

10.1186/s13059-021-02368-1

treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses
Cited by: 4
Author(s): Ronald Huang, Charlotte Soneson, Pierre‐Luc Germain, Thomas Schmidt, Christian von Mering, Mark D. Robinson
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pbio.3001053

Identification of 3′ UTR motifs required for mRNA localization to myelin sheaths in vivo
Cited by: 13
Author(s): Katie M. Yergert, Caleb A. Doll, Rebecca O’Rouke, Jacob H. Hines, Bruce Appel
Software Mentions: 10
Published: almost 4 years ago

10.3390/cells9030779

Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea (Pisum sativum L.)
Cited by: 12
Author(s): Yury V. Malovichko, O. Y. Shtark, Ekaterina N. Vasileva, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pcbi.1008947

Chromosomal neighbourhoods allow identification of organ specific changes in gene expression
Cited by: 1
Author(s): Rishi Das Roy, Outi Hallikas, Mona M. Christensen, Élodie Renvoisé, Jukka Jernvall
Software Mentions: 10
Published: about 3 years ago

10.1371/journal.pone.0216611

Combined effects of nutritional, biochemical and environmental stimuli on growth performance and fatty acid composition of gilthead sea bream (Sparus aurata)
Cited by: 3
Author(s): Claudia Torno, Stefanie Staats, Anna Fickler, Sonia de Pascual‐Teresa, M.S. Izquierdo, Gerald Rimbach, Carsten Schulz
Software Mentions: 10
Published: over 5 years ago

10.1038/s41416-020-0764-3

A common polymorphism in the retinoic acid pathway modifies adrenocortical carcinoma age-dependent incidence
Cited by: 7
Author(s): Mirvat Surakhy, Marsha D. Wallace, Elisabeth E. Bond, Lukasz F. Grochola, Husein Perez, Matteo Di Giovannantonio, Ping Zhang, David Malkin, Hannah Carter, Ivy Zortéa S Parise, Gerard P. Zambetti, Heloísa Komechen, Mariana M Paraizo, Meghana Pagadala, Emília M. Pinto, Enzo Lalli, Bonald C. Figueiredo, Gareth L. Bond
Software Mentions: 10
Published: over 4 years ago

10.1002/advs.201901850

<i>Mesostigma viride</i> Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta
Cited by: 29
Author(s): Zhe Liang, Yuke Geng, Changmian Ji, Hongwu Du, Chui Eng Wong, Qian Zhang, Ye Zhang, Pingxian Zhang, Adeel Riaz, Sadaruddin Chachar, Yike Ding, Jing Wen, Yun-Wen Wu, Mingcheng Wang, Hongkun Zheng, Yanmin Wu, Viktor Demko, Lisha Shen, Han Xiao, Pengpeng Zhang, Xiaofeng Gu, Hao Yu
Software Mentions: 10
Published: about 5 years ago

10.1080/19336896.2020.1751574

Estimation of amyloid aggregate sizes with semi-denaturing detergent agarose gel electrophoresis and its limitations
Cited by: 10
Author(s): Polina Drozdova, Yury A. Barbitoff, М. В. Белоусов, Rostislav K. Skitchenko, Tatyana Rogoza, Jeremy Y Leclercq, Andrey V. Kajava, Andrew G. Matveenko, Galina A. Zhouravleva, Stanislav A. Bondarev
Software Mentions: 10
Published: almost 5 years ago

10.1007/s00228-020-03052-2

Potentially inappropriate prescribing in older hospitalized Dutch patients according to the STOPP/START criteria v2: a longitudinal study
Cited by: 9
Author(s): Birgit A. Damoiseaux-Volman, Stephanie Medlock, Kimmy Raven, Danielle Sent, Johannes A. Romijn, Nathalie van der Velde, Ameen Abu‐Hanna
Software Mentions: 10
Published: almost 4 years ago

10.3390/jcm9051572

Eye-Catching Microbes—Polyphasic Analysis of the Microbiota on Microscope Oculars Verifies Their Role as Fomites
Cited by: 3
Author(s): Birgit Fritz, Karin Schäfer, Melanie März, Siegfried Wahl, Focke Ziemssen, Markus Egert
Software Mentions: 10
Published: over 4 years ago

10.1186/s12935-019-0890-2

Comprehensive bioinformatics analysis reveals potential lncRNA biomarkers for overall survival in patients with hepatocellular carcinoma: an on-line individual risk calculator based on TCGA cohort
Cited by: 19
Author(s): Zhiqiao Zhang, Yanling Ouyang, Yiyan Huang, Peng Wang, Jing Li, Tingshan He, Qingbo Liu
Software Mentions: 10
Published: over 5 years ago

10.3390/s21020436

A Methodology for Discriminant Time Series Analysis Applied to Microclimate Monitoring of Fresco Paintings
Cited by: 8
Author(s): Sandra Ramírez, Manuel Zarzo, Ángel Perles, Fernando-Juan García-Diego
Software Mentions: 10
Published: almost 4 years ago

10.1155/2020/6539398

Distinguishing Kawasaki Disease from Febrile Infectious Disease Using Gene Pair Signatures
Cited by: 1
Author(s): Jiayong Zhong, Qingsheng Huang, Yanfei Wang, Huan Gao, Hongling Jia, Jun Fan, Huiying Liang
Software Mentions: 10
Published: over 4 years ago

10.1186/s12957-021-02162-0

The preoperative prognostic value of the radiomics nomogram based on CT combined with machine learning in patients with intrahepatic cholangiocarcinoma
Cited by: 16
Author(s): Youyin Tang, Tao Zhang, Xianghong Zhou, Ying Zhao, Hanyue Xu, Yichun Liu, Hang Wang, Zheyu Chen, Xuelei Ma
Software Mentions: 10
Published: over 3 years ago

10.3390/brainsci10100715

Attention Networks in ADHD Adults after Working Memory Training with a Dual n-Back Task
Cited by: 7
Author(s): Masashi Dotare, Michel Bader, Sarah K. Mesrobian, Yoshiyuki Asai, Alessandro E. P. Villa, Alessandra Lintas
Software Mentions: 10
Published: about 4 years ago

10.1002/cam4.3919

Competing‐risks nomograms for predicting cause‐specific mortality in parotid‐gland carcinoma: A population‐based analysis
Cited by: 6
Author(s): Fengshuo Xu, Feng Xue, Fanfan Zhao, Qiao Huang, Didi Han, Chengzhuo Li, Shuai Zheng, Jun Lyu
Software Mentions: 10
Published: over 3 years ago

10.3390/ijerph17218164

Differences in the Estimation of Wildfire-Associated Air Pollution by Satellite Mapping of Smoke Plumes and Ground-Level Monitoring
Cited by: 9
Author(s): Raj P. Fadadu, John R. Balmes, Stephanie M. Holm
Software Mentions: 10
Published: about 4 years ago

10.7554/eLife.55993

Combining agent-based, trait-based and demographic approaches to model coral-community dynamics
Cited by: 7
Author(s): Bruno Carturan, Jason Pither, Jean‐Philippe Maréchal, Corey J. A. Bradshaw, Lael Parrott
Software Mentions: 10
Published: over 4 years ago

10.7554/eLife.66036

A new Heterodontosaurus specimen elucidates the unique ventilatory macroevolution of ornithischian dinosaurs
Cited by: 8
Author(s): Viktor J. Radermacher, Vincent Fernández, Emma R. Schachner, Richard J. Butler, Emese M. Bordy, Michael Naylor Hudgins, William J. De Klerk, Kimberley E. J. Chapelle, Jonah N. Choiniere
Software Mentions: 10
Published: over 3 years ago

10.1038/s41396-020-00777-x

A network approach to elucidate and prioritize microbial dark matter in microbial communities
Cited by: 71
Author(s): Tatyana Zamkovaya, Jamie S. Foster, Valérie de Crécy‐Lagard, Ana Conesa
Software Mentions: 10
Published: about 4 years ago

10.1038/s41598-019-42533-y

MeshMonk: Open-source large-scale intensive 3D phenotyping
Cited by: 78
Author(s): Julie D. White, Alejandra Ortega-Castrillón, Harold Matthews, Arslan Zaidi, Omid Ekrami, Jonatan Snyders, Yi Fan, Tony Penington, Stefan Van Dongen, Mark D. Shriver, Peter Claes
Software Mentions: 10
Published: over 5 years ago

10.1128/mBio.01105-19

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent
Cited by: 42
Author(s): Eike J. Steinig, Sebastián Duchêne, D. Ashley Robinson, Stefan Monecke, Maho Yokoyama, Maisem Laabei, Peter Slickers, Patiyan Andersson, Deborah A. Williamson, Angela Kearns, Richard V. Goering, Elizabeth Dickson, Ralf Ehricht, Margaret Ip, Matthew V. N. O’Sullivan, Geoffrey W. Coombs, Andreas Petersen, Gráinne I. Brennan, Anna C. Shore, David C. Coleman, Annalisa Pantosti, Hermı́nia de Lencastre, Henrik Westh, Nobumichi Kobayashi, Helen Heffernan, Birgit Strommenger, Franziska Layer, Stefan Weber, Hege Vangstein Aamot, Leila Skakni, Sharon J. Peacock, Derek S. Sarovich, Simon R. Harris, Julian Parkhill, Ruth C. Massey, Matthew T. G. Holden, Stephen D. Bentley, Steven Y. C. Tong
Software Mentions: 10
Published: almost 5 years ago

10.1186/s13059-021-02473-1

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
Cited by: 20
Author(s): Rachel Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal
Software Mentions: 10
Published: about 3 years ago

10.1038/s41598-020-79875-x

Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models
Cited by: 23
Author(s): Marta Relvas, Alba Regueira-Iglesias, Carlos Balsa-Castro, Filomena Salazar, José Júlio Pacheco, Cristina Cabral, Corsina Velazco de Henriques, Inmaculada Tomás
Software Mentions: 10
Published: almost 4 years ago

10.1186/s11689-021-09360-7

Modeling familial predictors of proband outcomes in neurogenetic disorders: initial application in XYY syndrome
Cited by: 3
Author(s): Kathleen Wilson, Ari M. Fish, Catherine Mankiw, Anastasia Xenophontos, Allysa Warling, Ethan T. Whitman, Liv S. Clasen, Erin Torres, Jonathan D. Blumenthal, Armin Raznahan
Software Mentions: 10
Published: over 3 years ago

10.3390/nu13061766

Multidimensional Approach to Assess Nutrition and Lifestyle in Breastfeeding Women during the First Month of Lactation
Cited by: 9
Author(s): Andrea Gila-Díaz, Nuria Díaz-Rullo Alcántara, Gloria Herranz Carrillo, Pratibha Singh, Silvia M. Arribas, David Ramiro-Cortijo
Software Mentions: 10
Published: over 3 years ago