cran: gplots | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0176334

shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics
Cited by: 97
Author(s): Bohdan B. Khomtchouk, John L. Hennessy, Claes Wahlestedt
Software Mentions: 7
Published: over 9 years ago

10.1371/journal.pgen.1008265

Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain
Cited by: 23
Author(s): Aldrin B. Lugena, Ying Zhang, Jérôme S. Menet, Christine Merlin
Software Mentions: 7
Published: over 7 years ago

10.3389/fgene.2015.00287

Design, measurement and processing of region-specific DNA methylation assays: the mass spectrometry-based method EpiTYPER
Cited by: 56
Author(s): H. Eka D. Suchiman, Roderick C. Slieker, Dennis Kremer, P. Eline Slagboom, Bastiaan T. Heijmans, Elmar W. Tobi
Software Mentions: 7
Published: about 11 years ago

10.3389/fmicb.2020.00669

Patterns in Microbial Assemblages Exported From the Meltwater of Arctic and Sub-Arctic Glaciers
Cited by: 20
Author(s): Tyler J. Kohler, Petra Vinšová, Lukáš Falteisek, Jakub D. Žárský, Jacob C. Yde, Jade E. Hatton, Jon R. Hawkings, Guillaume Lamarche-Gagnon, Eran Hood, Karen A. Cameron, Marek Stibal
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0048365

Molecular and Immunological Characterization of Gluten Proteins Isolated from Oat Cultivars That Differ in Toxicity for Celiac Disease
Cited by: 67
Author(s): Ana Real, Isabel Comino, Laura de Lorenzo, Francisco Merchán, Javier Gil-Humanes, María J. Giménez, Miguel Ángel López-Casado, Ma Isabel Torres, Ángel Cebolla, Carolina Sousa, Francisco Barro, Fernando Pistón
Software Mentions: 7
Published: almost 14 years ago

10.1002/ece3.3234

The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen Pseudogymnoascus destructans
Cited by: 21
Author(s): Christina M. Davy, Michael E. Donaldson, Craig K. R. Willis, Barry J. Saville, L. McGuire, Heather W. Mayberry, Alana Wilcox, Gudrun Wibbelt, Vikram Misra, Trent K. Bollinger, Christopher J. Kyle
Software Mentions: 7
Published: about 9 years ago

10.1038/s41598-019-44491-x

The LL-100 panel: 100 cell lines for blood cancer studies
Cited by: 67
Author(s): Hilmar Quentmeier, Claudia Pommerenke, Wilhelm G. Dirks, Sonja Eberth, Max Koeppel, Roderick A.F. MacLeod, Stefan Nagel, Klaus G. Steube, Cord C. Uphoff, Hans G. Drexler
Software Mentions: 7
Published: over 7 years ago

10.3390/md15080252

Fatty Acid Profile Is Modulated by Dietary Resveratrol in Rainbow Trout (Oncorhynchus mykiss)
Cited by: 23
Author(s): Claudia Torno, Stefanie Staats, Sonia de Pascual‐Teresa, Gerald Rimbach, Carsten Schulz
Software Mentions: 7
Published: about 9 years ago

10.15252/msb.20177881

High‐resolution definition of humoral immune response correlates of effective immunity against <scp>HIV</scp>
Cited by: 33
Author(s): Galit Alter, Karen G. Dowell, Eric N. Brown, Todd J. Suscovich, Anastassia Mikhailova, Alison E. Mahan, Bruce D. Walker, Falk Nimmerjahn, Chris Bailey‐Kellogg, Margaret E. Ackerman
Software Mentions: 7
Published: over 8 years ago

10.3389/fmicb.2019.02621

Influence of Various Processing Parameters on the Microbial Community Dynamics, Metabolomic Profiles, and Cup Quality During Wet Coffee Processing
Cited by: 31
Author(s): Sophia Jiyuan Zhang, Florac De Bruyn, Vasileios Pothakos, Gonzalo F Contreras, Z. Y. Cai, Cyril Moccand, Stefan Weckx, Luc De Vuyst
Software Mentions: 7
Published: almost 7 years ago

10.15252/msb.20209652

A substrate‐based ontology for human solute carriers
Cited by: 24
Author(s): Eva Meixner, Ulrich Goldmann, Vitaly Sedlyarov, Stefania Scorzoni, Manuele Rebsamen, Enrico Gottardi, Giulio Superti‐Furga
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-017-13397-x

The effect of insecticide synergist treatment on genome-wide gene expression in a polyphagous pest
Cited by: 28
Author(s): Simon Snoeck, Robert Greenhalgh, Luc Tirry, Richard M. Clark, Thomas Van Leeuwen, Wannes Dermauw
Software Mentions: 7
Published: about 9 years ago

10.3390/molecules24162977

VOC Profiles of Saliva in Assessment of Halitosis and Submandibular Abscesses Using HS-SPME-GC/MS Technique
Cited by: 32
Author(s): Fernanda Monedeiro, Maciej Milanowski, Ileana-Andreea Raţiu, Hubert Zmysłowski, Tomasz Ligor, Bogusław Buszewski
Software Mentions: 7
Published: about 7 years ago

10.1371/journal.pone.0007225

MicroRNAs Show Mutually Exclusive Expression Patterns in the Brain of Adult Male Rats
Cited by: 94
Author(s): Line Olsen, Mikkel Klausen, Lone Helboe, Finn Cilius Nielsen, Thomas Werge
Software Mentions: 7
Published: about 17 years ago

10.1371/journal.pone.0076051

Alterations in miRNA Levels in the Dentate Gyrus in Epileptic Rats
Cited by: 79
Author(s): Anna Bot, Konrad J. Dębski, Katarzyna Łukasiuk
Software Mentions: 7
Published: about 13 years ago

10.1186/s12864-018-5145-4

Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices
Cited by: 21
Author(s): Emilien Peltier, Vikas Sharma, Maria Martí Raga, Miguel Roncoroni, Margaux Bernard, Vladimir Jiranek, Yves Gibon, Philippe Marullo
Software Mentions: 7
Published: almost 8 years ago

10.1371/journal.pone.0209231

Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents
Cited by: 11
Author(s): Christopher Cheleuitte-Nieves, Christopher A. Gulvik, John R. McQuiston, Ben W. Humrighouse, Melissa Bell, Aaron Villarma, Vincent A. Fischetti, Lars F. Westblade, Neil S Lipman
Software Mentions: 7
Published: almost 8 years ago

10.3389/fmicb.2019.02359

Annual Protist Community Dynamics in a Freshwater Ecosystem Undergoing Contrasted Climatic Conditions: The Saint-Charles River (Canada)
Cited by: 21
Author(s): Perrine Cruaud, Adrien Vigneron, Marie‐Stéphanie Fradette, Caetano C. Dorea, Alexander I. Culley, Manuel J. Rodriguez, Steve J. Charette
Software Mentions: 7
Published: about 7 years ago

10.1371/journal.pone.0132866

swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing
Cited by: 43
Author(s): Zhen Wang, Xianfeng Li, Yi Jiang, Qianzhi Shao, Qi Liu, Bingyu Chen, Dongsheng Huang
Software Mentions: 7
Published: over 11 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: almost 9 years ago

10.1371/journal.pone.0210197

Screening dietary biochanin A, daidzein, equol and genistein for their potential to increase DHA biosynthesis in rainbow trout (Oncorhynchus mykiss)
Cited by: 6
Author(s): Anna Fickler, Stefanie Staats, Gerald Rimbach, Carsten Schulz
Software Mentions: 7
Published: almost 8 years ago

10.7554/eLife.51413

Endothelial heterogeneity across distinct vascular beds during homeostasis and inflammation
Cited by: 190
Author(s): Ankit Jambusaria, Zhigang Hong, Lianghui Zhang, Shubhi Srivastava, Arundhati Jana, Péter T. Tóth, Yang Dai, Asrar B. Malik, Jalees Rehman
Software Mentions: 7
Published: almost 7 years ago

10.3390/microorganisms9020315

TAL Effector Repertoires of Strains of Xanthomonas phaseoli pv. manihotis in Commercial Cassava Crops Reveal High Diversity at the Country Scale
Cited by: 6
Author(s): Carlos A Zárate-Chaves, Daniela Osorio-Rodríguez, Ruben E. Mora, Álvaro L. Pérez‐Quintero, Alexis Dereeper, Silvia Restrepo, Camilo López, Boris Szurek, Adriana Bernal
Software Mentions: 7
Published: over 5 years ago

10.1186/s13046-019-1505-4

A pre-existing population of ZEB2+ quiescent cells with stemness and mesenchymal features dictate chemoresistance in colorectal cancer
Cited by: 54
Author(s): Federica Francescangeli, Paola Contavalli, Maria Laura De Angelis, Silvia Careccia, Michele Signore, Tobias Haas, Federico Salaris, Marta Baiocchi, Alessandra Boe, Alessandro Giuliani, Olga Tcheremenskaia, Alfredo Pagliuca, Ombretta Guardiola, Gabriella Minchiotti, Lidia Colace, Antonio Ciardi, Vito D’Andrea, Filippo La Torre, Jan Paul Medema, Ruggero De Maria, Ann Zeuner
Software Mentions: 7
Published: almost 7 years ago

10.1038/s41598-021-96967-4

Parasites and diet as main drivers of the Malagasy gut microbiome richness and function
Cited by: 3
Author(s): Stanislas Mondot, Philippe Poirier, Ahmed Abou-Bacar, Valentin Greigert, Julie Brunet, Céline Nourrisson, Milijaona Randrianarivelojosia, Jean-Louis Razafindrakoto, Eugène Morel, Rivo Rakotomalala, Marion Leclerc, Karine Le Roux, Céline Monot, Patricia Lepage, Ermanno Candolfi
Software Mentions: 7
Published: about 5 years ago

10.1186/s12864-019-6308-7

Human gene expression variability and its dependence on methylation and aging
Cited by: 23
Author(s): Nasser Bashkeel, Theodore J. Perkins, Mads Kærn, Jonathan M. Lee
Software Mentions: 7
Published: almost 7 years ago

10.15252/msb.20178041

Molecular transitions in early progenitors during human cord blood hematopoiesis
Cited by: 120
Author(s): Shiwei Zheng, Efthymia Papalexi, Andrew Butler, William Stephenson, Rahul Satija
Software Mentions: 7
Published: over 8 years ago

10.7554/eLife.29312

Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis
Cited by: 35
Author(s): Isabelle Bergiers, Tallulah Andrews, Özge Vargel Bölükbaşı, Andreas Buneß, Ewa Janosz, Natalia López-Anguita, Kerstin Ganter, Kinga Kosim, Cemre Celen, Gülce Itır Perçin, Paul Collier, Bianka Baying, Vladimı́r Beneš, Martin Hemberg, Christophe Lancrin
Software Mentions: 7
Published: over 8 years ago

10.3389/fmicb.2020.00765

Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes
Cited by: 10
Author(s): Paula Luize Camargos Fonseca, Fernanda Badotti, Ruth B De-Paula, Daniel S. Araújo, Dener Eduardo Bortolini, Luiz-Eduardo Del-Bem, Vasco Azevedo, Bertram Brenig, Eric Roberto Guimarães Rocha Aguiar, Aristóteles Goés-Neto
Software Mentions: 7
Published: over 6 years ago

10.1186/1471-2164-11-349

Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3
Cited by: 70
Author(s): RM Schmid, Patrick Baum, Carina Ittrich, Katrin Fundel‐Clemens, Wolfgang Huber, Benedikt Brors, Roland Eils, Andreas Weith, Detlev Mennerich, Karsten Quast
Software Mentions: 7
Published: over 16 years ago

10.1186/s12864-018-4805-8

Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq
Cited by: 14
Author(s): Karel Sedlář, Pavlína Koščová, Maryna Vasylkivska, Barbora Branská, Jan Kolek, Kristyna Kupkova, Petra Patáková, Ivo Provazník
Software Mentions: 7
Published: over 8 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: about 9 years ago

10.3389/fmicb.2018.02528

Bacterial Diversity and the Geochemical Landscape in the Southwestern Gulf of Mexico
Cited by: 32
Author(s): Elizabeth Ernestina Godoy-Lozano, Alejandra Escobar‐Zepeda, Luciana Raggi, Enrique Merino, Rosa Marı́a Gutiérrez-Rı́os, Katy Juarez, Lorenzo Segovia, Alexei F. Licea-Navarro, Adolfo Gracía, Alejandro Sánchez-Flores, Liliana Pardo-López
Software Mentions: 7
Published: about 8 years ago

10.1371/journal.pbio.3000301

Proteome-wide analysis of chaperone-mediated autophagy targeting motifs
Cited by: 125
Author(s): Philipp Kirchner, Mathieu Bourdenx, Julio Madrigal‐Matute, Simoni Tiano, Antonio Díaz, Boris Bartholdy, Britta Will, Ana María Cuervo
Software Mentions: 7
Published: over 7 years ago

10.1038/s41598-017-15712-y

Genome-wide analyses of long noncoding RNA expression profiles in lung adenocarcinoma
Cited by: 20
Author(s): Peng Zhang, Jun Wang, Bin Shan, Fulai Yuan, Bin Li, Yeping Dong, Wei Peng, Weisong Shi, Yuanda Cheng, Yang Gao, Chunfang Zhang, Chaojun Duan
Software Mentions: 7
Published: almost 9 years ago

10.3389/fimmu.2018.01444

Elucidating T Cell Activation-Dependent Mechanisms for Bifurcation of Regulatory and Effector T Cell Differentiation by Multidimensional and Single-Cell Analysis
Cited by: 10
Author(s): Alla Bradley, Takeji Hashimoto, M. Ono
Software Mentions: 7
Published: over 8 years ago

10.18632/aging.101356

A hypothesis-driven approach identifies CDK4 and CDK6 inhibitors as candidate drugs for treatments of adrenocortical carcinomas
Cited by: 22
Author(s): Djihad Hadjadj, Su-Jung Kim, Thomas Denecker, Laura Ben Driss, Jean‐Charles Cadoret, Chrystelle Maric, Giuseppe Baldacci, Fabien Fauchereau
Software Mentions: 7
Published: almost 9 years ago

10.1038/s41598-017-10853-6

The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages
Cited by: 39
Author(s): Elton J. R. Vasconcelos, Luis DaSilva, David S. Pires, Guilherme M. Lavezzo, Adriana S. A. Pereira, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 7
Published: about 9 years ago

10.1016/j.csbj.2021.04.056

A computational analysis of transcriptional profiles from CD8(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression
Cited by: 3
Author(s): Sergey Ivanov, Dmitry Filimonov, O. Tarasova
Software Mentions: 7
Published: almost 6 years ago

10.1038/s42003-020-01416-z

Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota
Cited by: 37
Author(s): Sachiko Ishida, Koichi Kato, Masami Tanaka, Toshitaka Odamaki, Rieko Kubo, Eri Mitsuyama, Jin‐zhong Xiao, Rui Yamaguchi, Satoshi Uematsu, Seiya Imoto, Satoru Miyano
Software Mentions: 7
Published: almost 6 years ago

10.1186/s40168-017-0280-8

Human presence impacts fungal diversity of inflated lunar/Mars analog habitat
Cited by: 23
Author(s): Adriana Blachowicz, Teresa Mayer, Mina Bashir, Thomas R. Pieber, Pablo de León, Kasthuri Venkateswaran
Software Mentions: 7
Published: over 9 years ago

10.1111/jcmm.15472

Transcriptomic landscape profiling of metformin‐treated healthy mice: Implication for potential hypertension risk when prophylactically used
Cited by: 4
Author(s): Yuhuan Meng, Rui Xiang, Han Yan, Yiran Zhou, Yuntao Hu, Jichun Yang, Yuan Zhou, Qinghua Cui
Software Mentions: 7
Published: over 6 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: about 5 years ago

10.1002/jcsm.12665

Myogenesis modelled by human pluripotent stem cells: a multi‐omic study of Duchenne myopathy early onset
Cited by: 28
Author(s): Virginie Mournetas, Emmanuelle Massouridès, Jean-Baptiste Dupont, Étienne Kornobis, Hélène Polveche, Margot Jarrige, Alan R L Dorval, Maxime R. F. Gosselin, Antigoni Manousopoulou, Spiros D. Garbis, Dariusz C. Górecki, Christian Pinset
Software Mentions: 7
Published: over 5 years ago

10.1186/s40168-016-0167-0

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation
Cited by: 28
Author(s): Teresa Mayer, Adriana Blachowicz, Alexander J. Probst, Parag Vaishampayan, Aleksandra Checinska, Tiffany M. Swarmer, Pablo de León, Kasthuri Venkateswaran
Software Mentions: 7
Published: over 10 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: over 7 years ago

10.3390/jcm8112024

Monitoring of Bactericidal Effects of Silver Nanoparticles Based on Protein Signatures and VOC Emissions from Escherichia coli and Selected Salivary Bacteria
Cited by: 11
Author(s): Monedeiro, Pomastowski, Milanowski, Ligor, Buszewski
Software Mentions: 7
Published: almost 7 years ago

10.1186/s12864-017-3662-1

Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals
Cited by: 18
Author(s): Masahiro Uesaka, Kiyokazu Agata, Takao Oishi, Kinichi Nakashima, Takuya Imamura
Software Mentions: 7
Published: over 9 years ago

10.1186/s40168-015-0116-3

Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities
Cited by: 151
Author(s): Aleksandra Checinska, Alexander J. Probst, Parag Vaishampayan, James R. White, Deepika Kumar, В. П. Степанов, George E. Fox, R. Henrik Nilsson, Duane L. Pierson, Jay L. Perry, Kasthuri Venkateswaran
Software Mentions: 7
Published: about 11 years ago

10.1186/s12864-017-4167-7

SaVanT: a web-based tool for the sample-level visualization of molecular signatures in gene expression profiles
Cited by: 30
Author(s): David Lopez, Dennis Montoya, Michael Ambrose, Larry Lam, Leah Briscoe, Claire Adams, Robert L. Modlin, Matteo Pellegrini
Software Mentions: 7
Published: about 9 years ago

10.7717/peerj.7044

Skin bacterial communities of neotropical treefrogs vary with local environmental conditions at the time of sampling
Cited by: 19
Author(s): Angie Estrada, Myra C. Hughey, Daniel Medina, Eria A. Rebollar, Jenifer B. Walke, Reid N. Harris, Lisa K. Belden
Software Mentions: 7
Published: over 7 years ago

10.3390/cells10092215

Autophagy-Associated IL-15 Production Is Involved in the Pathogenesis of Leprosy Type 1 Reaction
Cited by: 0
Author(s): Bruno Jorge de Andrade Silva, Tamiris Lameira Bittencourt, Thyago Leal-Calvo, Mayara Abud Mendes, Rhana Berto da Silva Prata, Mayara Garcia de Mattos Barbosa, Priscila Ribeiro Andrade, Suzana Côrte-Real, Gilberto Marcelo Sperandio da Silva, Milton Ozório Moraes, Euzenir Nunes Sarno, Roberta Olmo Pinheiro
Software Mentions: 7
Published: about 5 years ago

10.1155/2018/3149495

Development of Regional Disparities in Alzheimer’s Disease Mortality in the Slovak Republic from 1996 to 2015
Cited by: 2
Author(s): Beata Gavurová, Viliam Kováč, D Jarcusková
Software Mentions: 7
Published: about 8 years ago

10.1186/s40168-017-0374-3

Dietary energy drives the dynamic response of bovine rumen viral communities
Cited by: 63
Author(s): Christopher L. Anderson, Matthew B. Sullivan, Samodha C. Fernando
Software Mentions: 7
Published: almost 9 years ago

10.1371/journal.pone.0250496

Optimizing the P balance: How do modern maize hybrids react to different starter fertilizers?
Cited by: 7
Author(s): Thea Mi Weiß, Willmar L. Leiser, Alice-Jacqueline Reineke, Dongdong Li, Wenxin Liu, Volker Hahn, Tobias Würschum
Software Mentions: 7
Published: over 5 years ago

10.1155/2021/2628824

A Potential ceRNA Network for Neurological Damage in Preterm Infants
Cited by: 7
Author(s): Hui‐Zi Jin, Xinlan Liang, Zhenyu Cai
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2019.00281

Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean
Cited by: 36
Author(s): Jackie Zorz, Ciara Willis, A. Comeau, Morgan G. I. Langille, Catherine L. Johnson, William K. W. Li, Julie LaRoche
Software Mentions: 7
Published: over 7 years ago

10.1111/1751-7915.13301

Desulfitobacteriumcontributes to the microbial transformation of 2,4,5-T by methanogenic enrichment cultures from a Vietnamese active landfill
Cited by: 12
Author(s): Ute Lechner, Dominique Türkowsky, Thi Thu Hang Dinh, Hassan Al-Fathi, Stefan Schwoch, Stefan Franke, Michelle-Sophie Gerlach, Mandy Koch, Martin von Bergen, Nico Jehmlich, Thi Cam Ha Dang
Software Mentions: 7
Published: about 8 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: over 5 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

10.1371/journal.pone.0124600

MLViS: A Web Tool for Machine Learning-Based Virtual Screening in Early-Phase of Drug Discovery and Development
Cited by: 36
Author(s): Selçuk Korkmaz, Gökmen Zararsız, Dinçer Göksülük
Software Mentions: 7
Published: over 11 years ago

10.3390/biomedicines9050454

mRNA Profiles of Porcine Parathyroid Glands Following Variable Phosphorus Supplies throughout Fetal and Postnatal Life
Cited by: 8
Author(s): Michael Oster, Henry Reyer, Christian Gerlinger, Nares Trakooljul, Puntita Siengdee, Jonas Keiler, Siriluck Ponsuksili, Petra Wolf, Klaus Wimmers
Software Mentions: 7
Published: over 5 years ago

10.1007/s00401-021-02263-w

Distinct amyloid-β and tau-associated microglia profiles in Alzheimer’s disease
Cited by: 143
Author(s): Emma Gerrits, Nieske Brouwer, Susanne M. Kooistra, Maya E. Woodbury, Yannick Vermeiren, Mirjam Lambourne, Jan Mulder, Markus P. Kummer, Thomas Möller, Knut Biber, Wilfred F. A. den Dunnen, Peter Paul De Deyn, Bart J. L. Eggen, Erik Boddeke
Software Mentions: 7
Published: over 5 years ago

10.1080/19490976.2020.1794466

Alterations of gut microbiota composition in neonates conceived by assisted reproductive technology and its relation to infant growth
Cited by: 6
Author(s): Qun Lü, Yuan Lin, Ting Chen, Hong Lv, Feiyang Diao, Cong Liu, Meijuan Peng, Xiufeng Ling, Hong Li, Yun Wang, Yongyue Wei, Jiangbo Du, Guangfu Jin, Yankai Xia, Hongxia Ma, Xingyin Liu, Hongbing Shen, Zhibin Hu
Software Mentions: 7
Published: about 6 years ago

10.15252/msb.20177974

Systematic characterization of pan‐cancer mutation clusters
Cited by: 31
Author(s): Marija Buljan, Peter Blattmann, Ruedi Aebersold, Michael Boutros
Software Mentions: 6
Published: over 8 years ago

10.1038/gim.2015.156

VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data
Cited by: 58
Author(s): Trevor J. Pugh, Sami S. Amr, Mark J. Bowser, Sivakumar Gowrisankar, Elizabeth Hynes, Lisa Mahanta, Heidi L. Rehm, Birgit Funke, Matthew S. Lebo
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pone.0052884

Wrangling Phosphoproteomic Data to Elucidate Cancer Signaling Pathways
Cited by: 17
Author(s): Mark L. Grimes, Wan-Jui Lee, Laurens van der Maaten, Paul Shannon
Software Mentions: 6
Published: almost 14 years ago

10.1002/1878-0261.12161

Comparative genomics reveals that loss of lunatic fringe (LFNG) promotes melanoma metastasis
Cited by: 19
Author(s): Martín Del Castillo Velasco-Herrera, Louise van der Weyden, Jérémie Nsengimana, Anneliese O. Speak, Marcela Sjöberg, D. Timothy Bishop, Göran Jönsson, Julia Newton-Bishop, David J. Adams
Software Mentions: 6
Published: almost 9 years ago

10.7717/peerj.8371

The effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the transcriptome of aryl hydrocarbon receptor (AhR) knock-down porcine granulosa cells
Cited by: 4
Author(s): Monika Ruszkowska, Agnieszka Sadowska, Anna Nynca, Karina Orlowska, Sylwia Świgońska, Tomasz Molcan, Łukasz Paukszto, J Jastrzebski, Renata E. Ciereszko
Software Mentions: 6
Published: almost 7 years ago

10.3389/fmicb.2017.01563

Role of Age-Related Shifts in Rumen Bacteria and Methanogens in Methane Production in Cattle
Cited by: 28
Author(s): Chong Liu, Qinghui Meng, Yongxing Chen, Mengsi Xu, Min Shen, Rui Gao, Shangquan Gan
Software Mentions: 6
Published: about 9 years ago

10.1371/journal.pone.0204542

NOJAH: NOt Just Another Heatmap for genome-wide cluster analysis
Cited by: 9
Author(s): Manali Rupji, Bhakti Dwivedi, Jeanne Kowalski
Software Mentions: 6
Published: over 7 years ago

10.7717/peerj.2452

Canopy position has a profound effect on soybean seed composition
Cited by: 27
Author(s): Steven C. Huber, Kunzhi Li, Randall L. Nelson, Alexander Ulanov, Catherine M. DeMuro, Ivan Baxter
Software Mentions: 6
Published: about 10 years ago

10.26508/lsa.202000974

GATA transcription factors, SOX17 and TFAP2C, drive the human germ-cell specification program
Cited by: 30
Author(s): Yôji Kojima, Chika Yamashiro, Yusuke Murase, Yukihiro Yabuta, Ikuhiro Okamoto, Chizuru Iwatani, Hideaki Tsuchiya, Masataka Nakaya, Tomoyuki Tsukiyama, Tomonori Nakamura, Takuya Yamamoto, Mitinori Saitou
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0180322

Affected pathways and transcriptional regulators in gene expression response to an ultra-marathon trail: Global and independent activity approaches
Cited by: 6
Author(s): María Maqueda, Emma Roca, Daniel Brotons, José Manuel Nieto Soria, Alexandre Perera
Software Mentions: 6
Published: about 9 years ago

10.26508/lsa.202000976

Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection
Cited by: 5
Author(s): Nikhil Ram-Mohan, Simone A. Thair, Ulrike M. Litzenburger, Steven Cogill, Nadya Andini, Xi Yang, Howard Y. Chang, Samuel Yang
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2016.02064

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System
Cited by: 177
Author(s): Manoeli Lupatini, G.W. Korthals, Mattias de Hollander, Thierry Janssens, Eiko E. Kuramae
Software Mentions: 6
Published: almost 10 years ago

10.1186/s12864-019-5933-5

Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thaliana
Cited by: 13
Author(s): Sony Kumari, Sneha Yadav, Debadutta Patra, Sharmila Singh, Ananda K. Sarkar, Kishore C. S. Panigrahi
Software Mentions: 6
Published: over 7 years ago

10.1186/s12864-019-6034-1

De novo profiling of RNA viruses in Anopheles malaria vector mosquitoes from forest ecological zones in Senegal and Cambodia
Cited by: 19
Author(s): Eugeni Belda, Ferdinand Nanfack-Minkeu, Karin Eiglmeier, Guillaume Carissimo, Inge Holm, Mawlouth Diallo, Diawo Diallo, Amélie Vantaux, Saorin Kim, Igor V. Sharakhov, Kenneth D. Vernick
Software Mentions: 6
Published: about 7 years ago

10.3389/fmicb.2020.01036

Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants
Cited by: 29
Author(s): Qian Zhang, Jacquelinne J. Acuña, Nitza G. Inostroza, Paola Durán, Marı́a de la Luz Mora, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-020-6684-z

Transcriptomic analysis of marine endophytic fungi extract identifies highly enriched anti-fungal fractions targeting cancer pathways in HepG2 cell lines
Cited by: 7
Author(s): Ethel J. S. Blessie, Wasco Wruck, Benaiah Annertey Abbey, Audrey Ncube, Nina Graffmann, Vincent Amarh, Patrick Kobina Arthur, James Adjaye
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0242675

Diversity of bacteria populations associated with different thallus regions of the brown alga Laminaria digitata
Cited by: 20
Author(s): Maureen W. Ihua, Jamie A. FitzGerald, Freddy Guihéneuf, Stephen A. Jackson, Marcus J. Claesson, Dagmar B. Stengel, Alan D. W. Dobson
Software Mentions: 6
Published: almost 6 years ago

10.1186/1471-2164-15-1028

Visualisation of the T cell differentiation programme by Canonical Correspondence Analysis of transcriptomes
Cited by: 17
Author(s): M. Ono, Reiko Tanaka, Manabu Kano
Software Mentions: 6
Published: almost 13 years ago

10.1007/s12275-020-9536-2

STATR: A simple analysis pipeline of Ribo-Seq in bacteria
Cited by: 7
Author(s): Donghui Choe, Bernhard Ø. Palsson, Byung-Kwan Cho
Software Mentions: 6
Published: almost 7 years ago

10.1007/s00239-021-10012-6

Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires
Cited by: 8
Author(s): Thomas D. Lewin, Amy H. Royall, Peter W.H. Holland
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0106084

Patterns of MiRNA Expression in Arctic Charr Development
Cited by: 24
Author(s): Kalina H. Kapralova, Sigríður Rut Franzdóttir, Hákon Jónsson, Sigurður S. Snorrason, Zophonı́as O. Jónsson
Software Mentions: 6
Published: about 12 years ago

10.1002/jev2.12022

Microglial derived extracellular vesicles activate autophagy and mediate multi‐target signaling to maintain cellular homeostasis
Cited by: 22
Author(s): Bram Van den Broek, Isabel Pintelon, Ibrahim Hamad, Sofie Kessels, Mansour Haidar, Niels Hellings, Jerome J. A. Hendriks, Markus Kleinewietfeld, Bert Brône, Vincent Timmerman, Jean‐Pierre Timmermans, Veerle Somers, Luc Michiels, Joy Irobi
Software Mentions: 6
Published: almost 6 years ago

10.1186/1471-2164-10-270

Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events
Cited by: 110
Author(s): Sônia Sousa Melo Cavalcanti de Albuquerque, Céline Carret, Ana Rita Grosso, Alice S. Tarun, Xinxia Peng, Stefan H. I. Kappe, Miguel Prudêncio, Maria M. Mota
Software Mentions: 6
Published: over 17 years ago

10.1038/s41396-020-00844-3

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles
Cited by: 45
Author(s): Annelein Meisner, L. Basten Snoek, Joseph Nesme, Elizabeth Dent, Samuel Jacquiod, Aimée T. Classen, Anders Priemé
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41396-021-00931-z

Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline
Cited by: 8
Author(s): Grégoire Michoud, David Kamanda Ngugi, Alan Barozzi, Giuseppe Merlino, María Ll. Calleja, António Delgado Huertas, Xosé Anxelu G. Morán, Daniele Daffonchio
Software Mentions: 6
Published: over 5 years ago

10.1038/leu.2015.172

Genome-scale definition of the transcriptional programme associated with compromised PU.1 activity in acute myeloid leukaemia
Cited by: 15
Author(s): Jonathan Sive, Silvia Basilico, Rebecca Hannah, Sarah Kinston, Fernando J. Calero-Nieto, Berthold Göttgens
Software Mentions: 6
Published: over 11 years ago

10.1186/s12864-019-6076-4

Transcriptome analysis of the effect of C-C chemokine receptor 5 deficiency on cell response to Toxoplasma gondii in brain cells
Cited by: 7
Author(s): Kaoru Kobayashi, Kousuke Umeda, Fumie Ihara, Sadao Tanaka, Junya Yamagishi, Yutaka Suzuki, Yoshifumi Nishikawa
Software Mentions: 6
Published: about 7 years ago

10.1186/s13229-020-00346-1

Identification of amygdala-expressed genes associated with autism spectrum disorder
Cited by: 19
Author(s): María Jesús Presentación Herrero, Dmitry Velmeshev, David Hernandez‐Pineda, Saarthak Sethi, Shawn F. Sorrells, Payal Banerjee, Catherine Sullivan, Abha R. Gupta, Arnold R. Kriegstein, Joshua G. Corbin
Software Mentions: 6
Published: over 6 years ago

10.1186/1471-2164-15-353

Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
Cited by: 49
Author(s): Richard Landstorfer, Svenja Simon, Steffen Schober, Daniel A. Keim, Siegfried Scherer, Klaus Neuhaus
Software Mentions: 6
Published: over 12 years ago

10.1093/bib/bbw102

A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles
Cited by: 1
Author(s): Felicia Ng, David Ruau, Lorenz Wernisch, Berthold Göttgens
Software Mentions: 6
Published: about 10 years ago

10.1186/s12863-021-00991-2

The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells
Cited by: 4
Author(s): Ritu Mann-Nüttel, Shafaqat Ali, Patrick Petzsch, Karl Köhrer, Judith Alferink, Stefanie Scheu
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2018.01888

Infection-Induced Changes Within the Endocytic Recycling Compartment Suggest a Roadmap of Human Cytomegalovirus Egress
Cited by: 16
Author(s): William L. Close, James Glassbrook, Stephen J. Gurczynski, Philip E. Pellett
Software Mentions: 6
Published: about 8 years ago

10.3389/fmicb.2015.01038

Turbulence-driven shifts in holobionts and planktonic microbial assemblages in St. Peter and St. Paul Archipelago, Mid-Atlantic Ridge, Brazil
Cited by: 10
Author(s): Ana Paula B. Moreira, Pedro Milet Meirelles, Eidy de Oliveira Santos, Gilberto M. Amado‐Filho, Ronaldo B. Francini‐Filho, Cristiane C. Thompson, Fabiano L. Thompson
Software Mentions: 6
Published: about 11 years ago

10.1371/journal.pcbi.1005351

ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour
Cited by: 3
Author(s): Stephanie Evans, Kieran Alden, Lourdes Cucurull‐Sanchez, Christopher Larminie, Mark Coles, Marika C. Kullberg, Jon Timmis
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pbio.3000741

Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei
Cited by: 32
Author(s): Eva Doleželová, Michaela Kunzová, Mario Dejung, Michal Levin, Brian Panicucci, Clément Regnault, Christian J. Janzen, Michael P. Barrett, Falk Butter, Alena Zı́ková
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pcbi.1003671

Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions
Cited by: 41
Author(s): Shira Rockowitz, Wen-Hui Lien, Erika Pedrosa, Gang Wei, Mingyan Lin, Keji Zhao, Herbert M. Lachman, Elaine Fuchs, Deyou Zheng
Software Mentions: 6
Published: over 12 years ago

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Papers Mentioning gplots 2,122