10.3389/fpls.2018.00029

Population Genetic Structure in Glyphosate-Resistant and -Susceptible Palmer Amaranth (Amaranthus palmeri) Populations Using Genotyping-by-sequencing (GBS)
Cited by: 26
Author(s): Anita Küpper, Harish Manmathan, Darci A. Giacomini, Eric Patterson, William B. McCloskey, Todd A. Gaines
Software Mentions: 7
Published: over 8 years ago

10.1155/2021/8897313

Systematic Investigation of the Effect of Powerful Tianma Eucommia Capsule on Ischemic Stroke Using Network Pharmacology
Cited by: 4
Author(s): Pengcheng Feng, Guixia Li, Yuandong Huang, Jinhong Pei
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0189084

Charting the transcriptional landscape of cells of renin lineage following podocyte depletion
Cited by: 1
Author(s): Alastair McClelland, Julia Lichtnekert, Diana G. Eng, Jeffrey W. Pippin, Kenneth W. Gross, Sina A. Gharib, Stuart J. Shankland
Software Mentions: 7
Published: over 8 years ago

10.1371/journal.pone.0216793

Patterns of gene expression characterize T1 and T3 clear cell renal cell carcinoma subtypes
Cited by: 4
Author(s): A. Borys, Michał Seweryn, Tomasz Gołąbek, Łukasz Bełch, Agnieszka Klimkowska, Justyna Totoń‐Żurańska, Julita Machlowska, Piotr Chłosta, Krzysztof Okoń, Paweł Wołkow
Software Mentions: 7
Published: about 7 years ago

10.1038/s41598-020-78471-3

Cellular correlates of cortical thinning throughout the lifespan
Cited by: 68
Author(s): Didac Vidal‐Piñeiro, Nadine Parker, Jean Shin, Leon French, Håkon Grydeland, Andrea Parolin Jackowski, Athanasia M. Mowinckel, Yash Patel, Zdenka Pausová, Giovanni Abrahão Salum, Øystein Sørensen, Kristine B. Walhovd, Tomáš Paus, Anders M. Fjell, Alzheimer’s Disease Neuroimaging Initiative
Software Mentions: 7
Published: over 5 years ago

10.3389/fpls.2014.00708

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants
Cited by: 19
Author(s): Deblina Patra, Mario Fasold, David Langenberger, Gerhard Steger, Ivo Große, Peter F. Stadler
Software Mentions: 7
Published: over 11 years ago

10.1002/1878-0261.12348

Integrating biomarkers across omic platforms: an approach to improve stratification of patients with indolent and aggressive prostate cancer
Cited by: 38
Author(s): Keefe Murphy, Brendan Murphy, Susie Boyce, Louise Flynn, Sarah Gilgunn, Colm J. O’Rourke, Cathy Rooney, Henning Stöckmann, Anna Walsh, Stephen P. Finn, Richard O’Kennedy, John O’Leary, Stephen R. Pennington, Antoinette S. Perry, Pauline M. Rudd, Radka Saldova, Orla Sheils, Denis C. Shields, R. William G. Watson
Software Mentions: 7
Published: almost 8 years ago

10.3389/fonc.2020.01214

The Significance of the CLDN18-ARHGAP Fusion Gene in Gastric Cancer: A Systematic Review and Meta-Analysis
Cited by: 19
Author(s): Weihan Zhang, Shouyue Zhang, Qing Hou, Yun Qin, Xin-Zu Chen, Zong‐Guang Zhou, Yang Shu, Hong‐Xi Xu, Jian‐Kun Hu
Software Mentions: 7
Published: almost 6 years ago

10.3389/fimmu.2020.585168

Distinct Age-Related Epigenetic Signatures in CD4 and CD8 T Cells
Cited by: 40
Author(s): Bin Hu, Rohit R. Jadhav, Claire E. Gustafson, Sabine Le Saux, Zhongde Ye, Xuanying Li, Lu Tian, Cornelia M. Weyand, Jörg J. Goronzy
Software Mentions: 7
Published: over 5 years ago

10.3389/fneur.2019.01117

Normative Data and Minimally Detectable Change for Inner Retinal Layer Thicknesses Using a Semi-automated OCT Image Segmentation Pipeline
Cited by: 33
Author(s): Seyedamirhosein Motamedi, K. Gawlik, Noah Ayadi, Hanna Zimmermann, Susanna Asseyer, Charlotte Bereuter, Janine Mikolajczak, Friedemann Paul, Ella-Maria Kadas, Alexander U. Brandt
Software Mentions: 7
Published: over 6 years ago

10.1002/ece3.6994

Ecological and morphological determinants of evolutionary diversification in Darwin's finches and their relatives
Cited by: 14
Author(s): Ashley M. Reaney, Yanis Bouchenak‐Khelladi, Joe Tobias, Arhat Abzhanov
Software Mentions: 7
Published: over 5 years ago

10.1002/1873-3468.13278

The gut microbiome participates in transgenerational inheritance of low‐temperature responses in <i>Drosophila melanogaster</i>
Cited by: 23
Author(s): Aman Zare, Anna-Mia Johansson, Edvin Karlsson, Nicolas Delhomme, Per Stenberg
Software Mentions: 7
Published: over 7 years ago

10.1038/s41598-021-98926-5

Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey
Cited by: 22
Author(s): Masaaki Sato, Nariaki Inoue, Ryogen Nambu, Naoki Furuichi, Tsutomu Imaizumi, Masayuki Ushio
Software Mentions: 7
Published: over 4 years ago

10.1038/srep19899

Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds
Cited by: 34
Author(s): Pui Yi Yung, Letizia Lo Grasso, Abeed Fatima Mohidin, Enzo Acerbi, Jamie Hinks, Thomas Seviour, Enrico Marsili, Federico M. Lauro
Software Mentions: 7
Published: over 10 years ago

10.1038/s41598-021-95292-0

The dynamics of reading complex words: evidence from steady-state visual evoked potentials
Cited by: 1
Author(s): Elisabeth Beyersmann, Veronica Montani, Johannes C. Ziegler, Jonathan Grainger, Ivilin Stoianov
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41598-017-14366-0

Erythropoietin Signaling Regulates Key Epigenetic and Transcription Networks in Fetal Neural Progenitor Cells
Cited by: 10
Author(s): Christina Sollinger, Jacquelyn Lillis, Jeffrey Malik, Michael Getman, Christoph Pröschel, Laurie A. Steiner
Software Mentions: 7
Published: over 8 years ago

10.1371/journal.pone.0237079

A core phyllosphere microbiome exists across distant populations of a tree species indigenous to New Zealand
Cited by: 17
Author(s): Anya Sophia Noble, Stevie Noe, Michael J. Clearwater, Charles K. Lee
Software Mentions: 7
Published: almost 6 years ago

10.3389/fpls.2020.00685

Hybridization Between Yuccas From Baja California: Genomic and Environmental Patterns
Cited by: 9
Author(s): María Clara Arteaga, Rafael Bello-Bedoy, Jaime Gasca-Pineda
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0241691

Succinivibrionaceae is dominant family in fecal microbiota of Behçet’s Syndrome patients with uveitis
Cited by: 12
Author(s): Duygu Tecer, Feride Göğüş, Ayşe Kalkancı, Merve Erdoğan, Murat Hasanreisoğlu, Çağrı Ergin, Tarkan Karakan, Ramazan Kozan, Serhat Emre Coban, Kadir Serdar Diker
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2021.664542

Nutrient-Poor Breeding Substrates of Ambrosia Beetles Are Enriched With Biologically Important Elements
Cited by: 10
Author(s): Maximilian Lehenberger, Nina Foh, Axel Göttlein, Diana L. Six, Peter H. W. Biedermann
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2020.536978

Repetitive Sampling and Control Threshold Improve 16S rRNA Gene Sequencing Results From Produced Waters Associated With Hydraulically Fractured Shale
Cited by: 2
Author(s): Jennifer L. Shelton, Elliott P. Barnhart, Leslie F. Ruppert, Aaron M. Jubb, Madalyn S. Blondes, Christina A. DeVera
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-019-46118-7

Unraveling the effects of the gut microbiota composition and function on horse endurance physiology
Cited by: 24
Author(s): Sandra Plancade, Allison Clark, Catherine Philippe, Jean‐Christophe Helbling, Marie‐Pierre Moisan, Diane Esquerré, Laurence Le Moyec, Céline Robert, Éric Barrey, Núria Mach
Software Mentions: 7
Published: almost 7 years ago

10.3390/microorganisms5040068

Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea
Cited by: 16
Author(s): Bernd Wemheuer, Franziska Wemheuer, Dimitri V. Meier, Sara Billerbeck, Helge-Ansgar Giebel, Meinhard Simon, Christoph Scherber, Rolf Daniel
Software Mentions: 7
Published: over 8 years ago

10.1016/j.ccell.2020.08.016

Metabolic Imaging Detects Resistance to PI3Kα Inhibition Mediated by Persistent FOXM1 Expression in ER+ Breast Cancer
Cited by: 35
Author(s): Susana Ros, Alan J. Wright, Paula D’Santos, De‐En Hu, Robin Hesketh, Yaniv Lubling, Dimitra Georgopoulou, Giulia Lerda, Dominique‐Laurent Couturier, Pedram Razavi, Rapahel Pelossof, Ankita Batra, Elizabeth Mannion, David Y. Lewis, Alistair Martin, Richard D. Baird, Mafalda Oliveira, Leonora W. de Boo, Sabine C. Linn, Maurizio Scaltriti, Oscar M. Rueda, Alejandra Bruna, Carlos Caldas, Kevin M. Brindle
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2018.02404

Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia
Cited by: 11
Author(s): Martina Prazeres
Software Mentions: 7
Published: over 7 years ago

10.1186/1471-2105-14-145

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform
Cited by: 10
Author(s): Josh Eckels, Cory Nathe, Elizabeth Nelson, Sara G Shoemaker, Elizabeth Van Nostrand, Nicole L. Yates, Vicki C. Ashley, Linda J. Harris, Mark Bollenbeck, Youyi Fong, Georgia D. Tomaras, Britt Piehler
Software Mentions: 7
Published: about 13 years ago

10.3389/fpls.2021.639631

Local Duplication of TIR-NBS-LRR Gene Marks Clubroot Resistance in Brassica napus cv. Tosca
Cited by: 11
Author(s): Piotr M. Kopec, Katarzyna Mikołajczyk, E. Jajor, A. Perek, Joanna Nowakowska, Christian Obermeier, Harmeet Singh Chawla, M. Korbas, I. Bartkowiak-Broda, Wojciech M. Karłowski
Software Mentions: 7
Published: about 5 years ago

10.3390/genes11040400

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant
Cited by: 7
Author(s): Alexandre Rêgo, Samridhi Chaturvedi, Amy L. Springer, Alexandra M. Lish, Caroline L. Barton, Karen M. Kapheim, Frank J. Messina, Zachariah Gompert
Software Mentions: 7
Published: about 6 years ago

10.1186/s12885-017-3689-3

GRcalculator: an online tool for calculating and mining dose–response data
Cited by: 57
Author(s): Nicholas Clark, Marc Hafner, Michal Kouril, Liz Williams, Jeremy Muhlich, Marcin Pilarczyk, Mario Niepel, Peter K. Sorger, Mario Medvedovic
Software Mentions: 7
Published: over 8 years ago

10.1111/jcmm.15252

CA9 transcriptional expression determines prognosis and tumour grade in tongue squamous cell carcinoma patients
Cited by: 9
Author(s): Chenyu Guan, Dai-qiao Ouyang, Yongjie Qiao, Kan Li, Guanghui Zheng, Xiaomei Lao, Sien Zhang, Guiqing Liao, Yujie Liang
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pcbi.1006042

The Pathway Coexpression Network: Revealing pathway relationships
Cited by: 40
Author(s): Yered Pita-Juárez, Gabriel Altschuler, Sokratis Kariotis, Wenbin Wei, Katjuša Koler, Claire Green, Rudolph E. Tanzi, Winston Hide
Software Mentions: 7
Published: over 8 years ago

10.3389/fcimb.2020.00131

Dysbiosis in Peripheral Blood Mononuclear Cell Virome Associated With Systemic Lupus Erythematosus
Cited by: 4
Author(s): Gangqiang Guo, Lele Ye, Xinyu Shi, Kejing Yan, Jingjing Huang, Kangming Lin, Dong Xing, Sisi Ye, Yuqing Wu, Baoqing Li, Chaosheng Chen, Xiangyang Xue, Huidi Zhang
Software Mentions: 7
Published: about 6 years ago

10.1186/s12864-021-07441-4

A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks
Cited by: 2
Author(s): Pedro Gabriel Nachtigall, Luiz Augusto Bovolenta, James G. Patton, Bastian Fromm, Ney Lemke, Danillo Pinhal
Software Mentions: 7
Published: over 5 years ago

10.2807/1560-7917.ES.2017.22.4.30452

Widespread activity of multiple lineages of Usutu virus, western Europe, 2016
Cited by: 105
Author(s): Dániel Cadar, Renke Lühken, Henk P. van der Jeugd, Mutien-Marie Garigliany, Ute Ziegler, Markus Keller, Jennifer Lahoreau, Lars Lachmann, Norbert Becker, Marja Kik, Bas B. Oude Munnink, Stefan Bosch, Egbert Tannich, Annick Lindén, Volker Schmidt, Marion Koopmans, Jolianne M. Rijks, Daniël Desmecht, Martin H. Groschup, Chantal Reusken, Jonas Schmidt‐Chanasit
Software Mentions: 7
Published: over 9 years ago

10.1128/mSystems.00063-20

Genomic Analysis of Bovine Staphylococcus aureus Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis
Cited by: 31
Author(s): Sohail Naushad, Diego Nobrega, Syed Ali Raza Naqvi, Herman W. Barkema, Jeroen De Buck
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pgen.1005930

Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects
Cited by: 36
Author(s): Erica Hildebrand, Sue Biggins
Software Mentions: 7
Published: over 10 years ago

10.3390/genes12081179

Dysregulation of Synaptic Signaling Genes Is Involved in Biology of Uterine Leiomyoma
Cited by: 2
Author(s): Jovan Krsteski, Mario Gorenjak, Igor But, Maja Pakiž, Uroš Potočnik
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12864-017-4304-3

Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence
Cited by: 71
Author(s): Hana Hall, Patrick S Medina, Daphne A. Cooper, Spencer E. Escobedo, Jeremiah Rounds, Kaelan J. Brennan, Christopher Vincent, Pedro Miura, R. W. Doerge, Vikki M. Weake
Software Mentions: 7
Published: over 8 years ago

10.1186/s13000-021-01118-y

Identification of immune-infiltrating cell-related biomarkers in hepatocellular carcinoma based on gene co-expression network analysis
Cited by: 6
Author(s): Yinghui Hou, Guizhi Zhang
Software Mentions: 7
Published: almost 5 years ago

10.3390/cancers13164087

Prognostic Value of Procalcitonin, C-Reactive Protein, and Lactate Levels in Emergency Evaluation of Cancer Patients with Suspected Infection
Cited by: 5
Author(s): Patrick Chaftari, Aiham Qdaisat, Anne-Marie Chaftari, Julian Maamari, Ziyi Li, Florea Lupu, Issam Raad, Ray Hachem, George A. Calin, Sai Ching Jim Yeung
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12864-021-07509-1

Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasis
Cited by: 7
Author(s): Yang Dong, Morgan Newman, Stephen Pederson, Karissa Barthelson, Nhi Hin, Michael Lardelli
Software Mentions: 7
Published: over 5 years ago

10.3390/cancers13174476

Combining APR-246 and HDAC-Inhibitors: A Novel Targeted Treatment Option for Neuroblastoma
Cited by: 8
Author(s): Michael Müller, Lisa Rösch, Sara Najafi, Charlotte Gatzweiler, Johannes Ridinger, Xenia F Gerloff, David Jones, Jochen Baßler, Sina Kreth, Sabine Stainczyk, Karen Frese, Benjamin Meder, Frank Westermann, Till Milde, Heike Peterziel, Olaf Witt, Ina Oehme
Software Mentions: 7
Published: almost 5 years ago

10.1002/ece3.4397

Effect of plant root symbionts on performance of native woody species in competition with an invasive grass in multispecies microcosms
Cited by: 6
Author(s): Christina Birnbaum, Tim K. Morald, Mark Tibbett, Richard G. Bennett, Rachel J. Standish
Software Mentions: 7
Published: almost 8 years ago

10.1128/mBio.00258-20

Critical Relevance of Stochastic Effects on Low-Bacterial-Biomass 16S rRNA Gene Analysis
Cited by: 27
Author(s): John R. Erb-Downward, Nicole R. Falkowski, Jennifer D’Souza, Lisa McCloskey, Roderick A. McDonald, Christopher Brown, Kerby Shedden, Robert P. Dickson, Christine M. Freeman, Kathleen A. Stringer, Betsy Foxman, Gary B. Huffnagle, Jeffrey L. Curtis, Sara D. Adar
Software Mentions: 7
Published: about 6 years ago

10.1038/s41598-020-71805-1

Northstar enables automatic classification of known and novel cell types from tumor samples
Cited by: 8
Author(s): Fabio Zanini, Bojk A. Berghuis, Robert C. Jones, Benedetta Nicolis di Robilant, Rachel Yuan Nong, Jeffrey A. Norton, Michael F. Clarke, Stephen R. Quake
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-020-75723-0

Veteran trees are a source of natural enemies
Cited by: 9
Author(s): Ross Wetherbee, Tone Birkemoe, Anne Sverdrup‐Thygeson
Software Mentions: 7
Published: over 5 years ago

10.1093/bib/bbz126

Systematic evaluation of differential splicing tools for RNA-seq studies
Cited by: 99
Author(s): Arfa Mehmood, Asta Laiho, Mikko S Venäläinen, Aidan McGlinchey, Ning Wang, Laura L. Elo
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-020-64110-4

The Intersection between Spliff Usage, Tobacco Smoking, and Having the First Joint after Waking
Cited by: 0
Author(s): Navin Kumar, Cheneal Puljević, Jason Ferris, Adam Winstock, Monica J. Barratt
Software Mentions: 7
Published: about 6 years ago

10.1038/s41598-020-77578-x

Empty mesoporous silica particles significantly delay disease progression and extend survival in a mouse model of ALS
Cited by: 7
Author(s): Marcel F. Leyton-Jaimes, Patrik Ivert, Jan Hoeber, Yilin Han, Adam Feiler, Chunfang Zhou, Stanislava Pankratova, Varda Shoshan‐Barmatz, Adrian Israelson, Elena N. Kozlova
Software Mentions: 7
Published: over 5 years ago

10.3389/fpls.2021.661361

Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks
Cited by: 2
Author(s): Laura Serrano-Ron, Javier Cabrera, Pablo Pérez-García, Miguel A. Moreno-Risueño
Software Mentions: 7
Published: about 5 years ago

10.1186/s13059-021-02321-2

Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach
Cited by: 23
Author(s): Oriana Genolet, Anna A. Monaco, Ilona Dunkel, Michael Boettcher, Edda G. Schulz
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0232646

Two-step mixed model approach to analyzing differential alternative RNA splicing
Cited by: 0
Author(s): Li Luo, Huining Kang, Xichen Li, Scott A. Ness, Christine A. Stidley
Software Mentions: 7
Published: over 5 years ago

10.3389/fvets.2020.580523

The Influence of Predictability and Controllability on Stress Responses to the Aversive Component of a Virtual Fence
Cited by: 16
Author(s): Tellisa Kearton, Danila Marini, Frances Cowley, Sue Belson, Hamideh Keshavarzi, Bonnie T. Mayes, Lee C
Software Mentions: 7
Published: over 5 years ago

10.3389/fvets.2020.00214

Cultural “Blind Spots,” Social Influence and the Welfare of Working Donkeys in Brick Kilns in Northern India
Cited by: 16
Author(s): Tamlin Watson, Laura M Kubasiewicz, Natasha Chamberlain, Caroline Nye, Zoe Raw, Faith Burden
Software Mentions: 7
Published: about 6 years ago

10.1002/gepi.22205

Imputed gene associations identify replicable <i>trans</i>‐acting genes enriched in transcription pathways and complex traits
Cited by: 13
Author(s): Heather E. Wheeler, Sally Ploch, Alvaro N. Barbeira, Rodrigo Bonazzola, Angela Andaleon, Alireza Fotuhi Siahpirani, Ashis Saha, Alexis Battle, Sushmita Roy, Hae Kyung Im
Software Mentions: 7
Published: about 7 years ago

10.1111/1365-2656.12178

Building integral projection models: a user's guide
Cited by: 113
Author(s): Mark Rees, Dylan Z. Childs, Stephen P. Ellner
Software Mentions: 7
Published: over 12 years ago

10.1038/s41422-020-00412-6

Single-cell transcriptomic atlas of primate cardiopulmonary aging
Cited by: 76
Author(s): Shuai Ma, Shuhui Sun, Jiaming Li, Yanling Fan, Jing Qu, Liang Sun, Si Wang, Yiyuan Zhang, Shanshan Yang, Zunpeng Liu, Zeming Wu, Sheng Zhang, Qiaoran Wang, Ai Zheng, Shuguang Duo, Yang Yu, Juan Carlos Izpisúa Belmonte, Piu Chan, Qi Zhou, Moshi Song, Weiqi Zhang, Guang Hui Liu
Software Mentions: 7
Published: almost 6 years ago

10.7717/peerj.8945

Choosing what is left: the spatial structure of a wild herbivore population within a livestock-dominated landscape
Cited by: 10
Author(s): Maria de Los Milagros Antun, Ricardo Baldi
Software Mentions: 7
Published: about 6 years ago

10.3390/cancers12030690

Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo
Cited by: 17
Author(s): Nicholas R. Hum, Aimy Sebastian, Sean F. Gilmore, Wei He, Kelly A. Martin, Aubree Hinckley, Karen Dubbin, Monica L. Moya, Elizabeth K. Wheeler, Matthew A. Coleman, Gabriela G. Loots
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-020-79296-w

Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon
Cited by: 6
Author(s): Andrea M. Makkay, Artemis S. Louyakis, Nikhil Ram-Mohan, Uri Gophna, J. Peter Gogarten, R. Thane Papke
Software Mentions: 7
Published: over 5 years ago

10.3389/fcell.2021.726716

Identification of an Immune-Related Long Noncoding RNA Pairs Model to Predict Survival and Immune Features in Gastric Cancer
Cited by: 8
Author(s): Shenglei Song, Shuhao Liu, Zhewei Wei, Xinghan Jin, Deli Mao, Yulong He, Bo Li, Changhua Zhang
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12859-019-2599-6

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
Cited by: 189
Author(s): Tianyu Wang, Boyang Li, Craig E. Nelson, Sheida Nabavi
Software Mentions: 7
Published: over 7 years ago

10.3390/microorganisms8101592

Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes
Cited by: 12
Author(s): Andrés Sánchez-Quinto, Daniel Cerqueda‐García, Luisa I. Falcón, Osiris Gaona, Santiago Martínez-Correa, Javier Nieto, Isaac González‐Santoyo
Software Mentions: 7
Published: over 5 years ago

10.3389/fpsyg.2020.599094

Co-occurrence Patterns of Character Strengths and Measured Core Virtues in German-Speaking Adults
Cited by: 6
Author(s): Willibald Ruch, Sonja Heintz, Lisa Wagner
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.51529

Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stability
Cited by: 48
Author(s): Tamsin J Samuels, Aino I Järvelin, David Ish‐Horowicz, Ilan Davis
Software Mentions: 7
Published: over 6 years ago

10.3389/fphar.2021.688528

Explore the Usefulness of Concurrent Chemotherapy in Stage II Nasopharyngeal Carcinoma: A Retrospective Study
Cited by: 3
Author(s): Peijing Li, YuLin Lai, Fang He, Yuan-Yuan Chen, Zhuo‐Sheng Gu, Wei Luo, Qun Zhang
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41388-021-01876-5

The FLI portion of EWS/FLI contributes a transcriptional regulatory function that is distinct and separable from its DNA-binding function in Ewing sarcoma
Cited by: 12
Author(s): Megann A. Boone, Cenny Taslim, Julie Crow, Julia Selich‐Anderson, Andrea K. Byrum, Iftekhar A. Showpnil, Benjamin D. Sunkel, Meng Wang, Benjamin Z. Stanton, Emily R. Theisen, Stephen L. Lessnick
Software Mentions: 7
Published: about 5 years ago

10.3390/ijerph16214257

Spatiotemporal Patterns of Cholera Hospitalization in Vellore, India
Cited by: 4
Author(s): Aishwarya Venkat, Tania M. Alarcon Falconi, Melissa Cruz, Meghan A. Hartwick, Shalini Anandan, Naveen Kumar, Honorine D. Ward, Balaji Veeraraghavan, Elena N. Naumova
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-019-50485-6

Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors
Cited by: 28
Author(s): Sumona P. Dhara, Andrea Rau, Michael J. Flister, Nicole M. Recka, Michael D. Laiosa, Paul L. Auer, Ava J. Udvadia
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0234848

Assessment of varying changes of vegetation and the response to climatic factors using GIMMS NDVI3g on the Tibetan Plateau
Cited by: 12
Author(s): Yuke Zhou, Jiangwen Fan, Xiaoying Wang
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0237893

The response of culturally important plants to experimental warming and clipping in Pakistan Himalayas
Cited by: 2
Author(s): Saira Karimi, Muhammad Ali Nawaz, Saadia Naseem, Ahmed Akrem, Hussain Ali, Olivier Dangles, Zahid Ali
Software Mentions: 7
Published: about 5 years ago

10.1186/s42523-021-00130-3

Differential effects of elevated nest temperature and parasitism on the gut microbiota of wild avian hosts
Cited by: 5
Author(s): Melissa R. Ingala, Lauren Albert, Alyssa Addesso, Mackenzie J. Watkins, Sarah A. Knutie
Software Mentions: 7
Published: over 4 years ago

10.1186/s40168-018-0595-0

Skin and gut microbiomes of a wild mammal respond to different environmental cues
Cited by: 38
Author(s): Anton Lavrinienko, Eugene Tukalenko, Tapio Mappes, Phillip C. Watts
Software Mentions: 7
Published: over 7 years ago

10.1080/19490976.2020.1840764

Dynamics of the bacterial gut microbiota during controlled human infection with <i>Necator americanus</i> larvae
Cited by: 6
Author(s): Quinten R Ducarmon, Marie-Astrid Hoogerwerf, Jacqueline J. Janse, A. R. Geelen, J. Koopman, Romy D. Zwittink, Jelle J. Goeman, Ed J. Kuijper, Meta Roestenberg
Software Mentions: 7
Published: over 5 years ago

10.1186/s12870-020-02808-3

Integrated Transcriptomic and Metabolomic analysis reveals a transcriptional regulation network for the biosynthesis of carotenoids and flavonoids in ‘Cara cara’ navel Orange
Cited by: 18
Author(s): Haipeng Zhang, Jiajing Chen, Zhaoxin Peng, Meiyan Shi, Xiao Liu, Wen Huang, Youwu Jiang, Yunjiang Cheng, Juan Xu, Hongyan Zhang
Software Mentions: 7
Published: over 5 years ago

10.3390/bios3030238

A Comparison of Methods for RNA-Seq Differential Expression Analysis and a New Empirical Bayes Approach
Cited by: 20
Author(s): Sergiusz Wesołowski, Marc R. Birtwistle, Grzegorz A. Rempała
Software Mentions: 7
Published: about 13 years ago

10.1186/s13742-015-0077-2

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future
Cited by: 83
Author(s): Georgios A. Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Θεοδόσιος Θεοδοσίου, Anton J. Enright, Ioannis Iliopoulos
Software Mentions: 7
Published: almost 11 years ago

10.1371/journal.pone.0222822

Range of motion and between-measurement variation of spinal kinematics in sound horses at trot on the straight line and on the lunge
Cited by: 8
Author(s): A. M. Hardeman, Anna Byström, L. Roepstorff, J. H. Swagemakers, P. R. van Weeren, F. M. Serra Bragança
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.62800

Mapping immune variation and var gene switching in naive hosts infected with Plasmodium falciparum
Cited by: 18
Author(s): Kathryn H. Milne, Alasdair Ivens, Adam J. Reid, Magda E. Lotkowska, Áine O’Toole, Geetha Sankaranarayanan, Diana Muñoz Sandoval, Wiebke Nahrendorf, Clément Regnault, Nick J. Edwards, Sarah E. Silk, Ruth Payne, Angela M. Minassian, Navin Venkatraman, Mandy Sanders, Adrian V. S. Hill, Michael P. Barrett, Matthew Berriman, Simon J. Draper, J. Alexandra Rowe, Philip J. Spence
Software Mentions: 7
Published: over 5 years ago

10.3390/cancers13163929

Maturation State-Specific Alternative Splicing in FLT3-ITD and NPM1 Mutated AML
Cited by: 4
Author(s): Anna Wojtuszkiewicz, Inge van der Werf, Stephan Hütter, Wencke Walter, Constance Baer, Wolfgang Kern, Jeroen Janssen, Gert J. Ossenkoppele, Claudia Haferlach, Jacqueline Cloos, Torsten Haferlach
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12885-021-08462-8

Construction and comprehensive analysis of a ceRNA network to reveal potential prognostic biomarkers for lung adenocarcinoma
Cited by: 12
Author(s): Lei Gao, Ling Zhang
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13148-020-00837-1

Differential CpG DNA methylation in peripheral naïve CD4+ T-cells in early rheumatoid arthritis patients
Cited by: 21
Author(s): Rujiraporn Pitaksalee, AN Burska, Shoaib Ajaib, Joshua Hugh Rogers, Rekha Parmar, K. Mydlova, Xuanxiao Xie, Alastair Droop, Jagtar Singh Nijjar, P Chambers, Paul Emery, Richard Hodgett, Iain B. McInnes, Frédérique Ponchel
Software Mentions: 7
Published: about 6 years ago

10.1186/s13063-021-05130-x

Systematic review of available software for multi-arm multi-stage and platform clinical trial design
Cited by: 18
Author(s): Elias Laurin Meyer, Peter Mesenbrink, Tobias Mielke, Tom Parke, Daniel D. Evans, Franz König
Software Mentions: 7
Published: over 5 years ago

10.3389/fonc.2021.657094

LINC01977 Promotes Breast Cancer Progression and Chemoresistance to Doxorubicin by Targeting miR-212-3p/GOLM1 Axis
Cited by: 12
Author(s): Zheng Li, Yaming Li, Xiaolong Wang, Yiran Liang, Dan Luo, Dianwen Han, Chen Li, Tong Chen, Hanwen Zhang, Ying Liu, Zekun Wang, Bing Chen, Limin Wang, Wenjing Zhao, Qifeng Yang
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-021-92036-y

Capitalizing on transcriptome profiling to optimize and identify targets for promoting early murine folliculogenesis in vitro
Cited by: 6
Author(s): Andrea Jones, Beatriz Peñalver Bernabé, Vasantha Padmanabhan, Jun Li, Ariella Shikanov
Software Mentions: 7
Published: about 5 years ago

10.1093/g3journal/jkab025

Nested association mapping reveals the genetic architecture of spike emergence and anthesis timing in intermediate wheatgrass
Cited by: 10
Author(s): Kayla R. Altendorf, Steven R. Larson, Lee R. DeHaan, Jared Crain, Jeffrey L. Neyhart, Kevin M. Dorn, James A. Anderson
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0243672

Characterisation and chemometric evaluation of 17 elements in ten seaweed species from Greenland
Cited by: 11
Author(s): Katharina Kreissig, Lisbeth Truelstrup Hansen, Pernille Erland Jensen, Susse Wegeberg, Ole Geertz‐Hansen, Jens Jørgen Sloth
Software Mentions: 7
Published: over 5 years ago

10.1186/s13148-021-01145-y

Childhood-onset dystonia-causing KMT2B variants result in a distinctive genomic hypermethylation profile
Cited by: 17
Author(s): Andrea Ciolfi, Aidin Foroutan, Alessandro Capuano, Lucia Pedace, Lorena Travaglini, Simone Pizzi, Marco Andreani, Evelina Miele, Federica Invernizzi, Chiara Reale, Celeste Panteghini, Maria Iascone, Marcello Niceta, Ralitza H. Gavrilova, Laura Schultz‐Rogers, Emanuele Agolini, Maria Francesca Bedeschi, Paolo Prontera, Matteo Garibaldi, Serena Galosi, Vincenzo Leuzzi, Paola Soliveri, Rory J. Olson, Giovanna Zorzi, Barbara Garavaglia, Marco Tartaglia, Bekim Sadiković
Software Mentions: 7
Published: almost 5 years ago

10.3389/fmicb.2021.569791

Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem
Cited by: 15
Author(s): Yaqi You, Ken Aho, Kathleen A. Lohse, Stacy G. Schwabedissen, Rhesa N. Ledbetter, Timothy S. Magnuson
Software Mentions: 7
Published: about 5 years ago

10.1186/s13148-019-0658-5

Gene domain-specific DNA methylation episignatures highlight distinct molecular entities of ADNP syndrome
Cited by: 65
Author(s): Eric G. Bend, Erfan Aref‐Eshghi, David B. Everman, R. Curtis Rogers, Sara Cathey, Eloise J. Prijoles, Michael J. Lyons, Heather L. Davis, Katie Clarkson, Karen W. Gripp, Dong Liu, Elizabeth Bhoj, Elaine H. Zackai, Paul R. Mark, Hákon Hákonarson, Laurie A. Demmer, Michael A. Levy, Jennifer Kerkhof, Alan Stuart, David I. Rodenhiser, Michael J. Friez, Roger E. Stevenson, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 7
Published: about 7 years ago

10.1186/s40168-020-00869-y

Topography of the respiratory tract bacterial microbiota in cattle
Cited by: 36
Author(s): Christopher McMullen, Trevor W. Alexander, Renaud Léguillette, Matthew L. Workentine, Edouard Timsit
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0128391

Optimizing the Protection of Cattle against Escherichia coli O157:H7 Colonization through Immunization with Different Combinations of H7 Flagellin, Tir, Intimin-531 or EspA
Cited by: 27
Author(s): Tom N. McNeilly, Mairi C. Mitchell, Alexander Corbishley, Mintu Nath, Hannah Simmonds, Sean P. McAteer, Aditya Mahajan, J. C. Low, David George Emslie Smith, John F. Huntley, David L. Gally
Software Mentions: 7
Published: about 11 years ago

10.1371/journal.pgen.1008375

DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories
Cited by: 29
Author(s): Sheila Lutz, Christian Brion, Margaret Kliebhan, Frank W. Albert
Software Mentions: 7
Published: over 6 years ago

10.1093/gigascience/giy167

SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis
Cited by: 2
Author(s): Samuel Blanck, Guillemette Marot
Software Mentions: 7
Published: over 7 years ago

10.1093/bioinformatics/btz031

ensembldb: an R package to create and use Ensembl-based annotation resources
Cited by: 76
Author(s): Johannes Michael Rainer, Laurent Gatto, Christian X. Weichenberger
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pone.0200729

The murine female intestinal microbiota does not shift throughout the estrous cycle
Cited by: 18
Author(s): Jessica G. Wallace, Ryan Potts, Jake C. Szamosi, Michael G. Surette, Deborah M. Sloboda
Software Mentions: 7
Published: almost 8 years ago

10.1371/journal.pone.0233899

Recapitulation of prostate tissue cell type-specific transcriptomes by an in vivo primary prostate tissue xenograft model
Cited by: 2
Author(s): Nelson T. Gross, Jianmin Wang, Michael V. Fiandalo, Eduardo Cortes Gomez, Anica Watts, Alejandro Godoy, Gary J. Smith, Yue Wu
Software Mentions: 7
Published: about 6 years ago

10.3390/pharmacy9010027

Sentiment Analysis of Online Reviews for Selective Serotonin Reuptake Inhibitors and Serotonin–Norepinephrine Reuptake Inhibitors
Cited by: 3
Author(s): Chad T. Compagner, Corey A. Lester, Michael P. Dorsch
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1009331

A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle
Cited by: 20
Author(s): Young Lim Lee, Hitoshi Takeda, Gabriel Costa Monteiro Moreira, Latifa Karim, Erik Mullaart, Wouter Coppieters, Ruth Appeltant, R.F. Veerkamp, Martien A. M. Groenen, Michel Georges, Mirte Bosse, Tom Druet, A.C. Bouwman, Carole Charlier
Software Mentions: 7
Published: almost 5 years ago

10.7717/peerj.2888

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization
Cited by: 67
Author(s): Xun Zhu, Travers Ching, Xinghua Pan, Sherman M. Weissman, Lana X. Garmire
Software Mentions: 7
Published: over 9 years ago