cran: statmod | Projects | Ecosyste.ms: Papers

10.1186/1751-0473-8-1

MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data
Cited by: 11
Author(s): Guy Brock, Partha Mukhopadhyay, Vasyl Pihur, Cynthia L. Webb, Robert M. Greene, M. Michele Pisano
Software Mentions: 24
Published: almost 12 years ago

10.12688/f1000research.18456.1

A step-by-step guide to analyzing CAGE data using R/Bioconductor
Cited by: 10
Author(s): Malte Thodberg, Albin Sandelin
Software Mentions: 20
Published: over 5 years ago

10.3390/genes12030413

Spt4 Promotes Pol I Processivity and Transcription Elongation
Cited by: 5
Author(s): Abigail K. Huffines, Yvonne J. K. Edwards, David A. Schneider
Software Mentions: 18
Published: over 3 years ago

10.1371/journal.pone.0151935

Novel and Lost Forests in the Upper Midwestern United States, from New Estimates of Settlement-Era Composition, Stem Density, and Biomass
Cited by: 48
Author(s): Simon Goring, David J. Mladenoff, Charles V. Cogbill, Sydne Record, Christopher J. Paciorek, Stephen T. Jackson, Michael C. Dietze, Andria Dawson, Jaclyn Hatala Matthes, J. S. McLachlan, John W. Williams
Software Mentions: 17
Published: almost 8 years ago

10.1371/journal.pcbi.1009317

Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome
Cited by: 11
Author(s): Ilario De Toma, Cesar Sierra, Mara Dierssen
Software Mentions: 14
Published: about 3 years ago

10.1016/j.molcel.2020.04.008

Single-Cell Analyses Reveal Megakaryocyte-Biased Hematopoiesis in Myelofibrosis and Identify Mutant Clone-Specific Targets
Cited by: 101
Author(s): Bethan Psaila, Guanlin Wang, Alba Rodríguez-Meira, Rong Li, Elisabeth F. Heuston, Lauren C. Murphy, Daniel Yee, Ian S. Hitchcock, Nikolaos Sousos, Jennifer O’Sullivan, Stacie M. Anderson, Yotis A. Senis, Olga K. Weinberg, Monica L. Calicchio, Deena Iskander, Daniel Royston, Dragana Milojković, Irene Roberts, David M. Bodine, Supat Thongjuea, Adam J. Mead
Software Mentions: 9
Published: over 4 years ago

10.1038/s41380-020-0844-z

Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids
Cited by: 66
Author(s): Tomoyo Sawada, Thomas E. Chater, Yohei Sasagawa, Mika Yoshimura, Noriko Fujimori-Tonou, Kaori Tanaka, Kynon J.M. Benjamin, Apuã C.M. Paquola, Jennifer A. Erwin, Yukiko Goda, Itoshi Nikaido, Takeshi Kato
Software Mentions: 8
Published: over 4 years ago

10.1155/2020/2635486

Prognostic Factors in Patients with Rhabdomyosarcoma Using Competing-Risks Analysis: A Study of Cases in the SEER Database
Cited by: 7
Author(s): Didi Han, Chengzhuo Li, Xiang Li, Qiao Huang, Fengshuo Xu, Shuai Zheng, Hui Wang, Jun Lyu
Software Mentions: 7
Published: about 4 years ago

10.1038/s41598-021-81451-w

Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19
Cited by: 33
Author(s): Ilario De Toma, Mara Dierssen
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12967-017-1195-7

Her2 assessment using quantitative reverse transcriptase polymerase chain reaction reliably identifies Her2 overexpression without amplification in breast cancer cases
Cited by: 13
Author(s): Gabriele Zoppoli, Anna Garuti, Gabriella Cirmena, Ludovica Verdun di Cantogno, C. Botta, M. Gallo, Domenico Ferraioli, Enrico Carminati, Paola Baccini, Monica Curto, Piero Fregatti, Edoardo Isnaldi, Michela Lia, Roberto Murialdo, Daniele Friedman, Anna Sapino, Alberto Ballestrero
Software Mentions: 7
Published: over 7 years ago

10.1186/1471-2164-12-619

A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation
Cited by: 102
Author(s): Monica F. Poelchau, Julie A. Reynolds, David L. Denlinger, Christine G. Elsik, Peter Armbruster
Software Mentions: 6
Published: almost 13 years ago

10.3389/fcell.2021.669354

Transcriptomic Signature of Human Embryonic Thyroid Reveals Transition From Differentiation to Functional Maturation
Cited by: 7
Author(s): Geert Dom, Petr Dmitriev, Marie-Alexandra Lambot, Guy Van Vliet, Daniel Glinoer, Frédérick Libert, Anne Lefort, Jacques Emile Dumont, Carine Maenhaut
Software Mentions: 5
Published: over 3 years ago

10.1016/j.cels.2018.06.011

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data
Cited by: 63
Author(s): Nils Eling, Alison F. Richard, Sylvia Richardson, John C. Marioni, Catalina A. Vallejos
Software Mentions: 5
Published: about 6 years ago

10.7554/eLife.45374

Gender variations in citation distributions in medicine are very small and due to self-citation and journal prestige
Cited by: 43
Author(s): Jens Peter Andersen, Jesper W. Schneider, Reshma Jagsi, Mathias Wullum Nielsen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0134168

Comparative Proteomics of Activated THP-1 Cells Infected with Mycobacterium tuberculosis Identifies Putative Clearance Biomarkers for Tuberculosis Treatment
Cited by: 19
Author(s): Benjawan Kaewseekhao, Vivek Naranbhai, Sittiruk Roytrakul, Wises Namwat, Atchara Paemanee, Viraphong Lulitanond, Angkana Chaiprasert, Kiatichai Faksri
Software Mentions: 4
Published: over 9 years ago

10.1002/ece3.3785

Host species, and not environment, predicts variation in blood parasite prevalence, distribution, and diversity along a humidity gradient in northern South America
Cited by: 39
Author(s): Paulo C. Pulgarín‐R, Juan Pablo Gómez, Scott K. Robinson, Robert E. Ricklefs, Carlos Daniel Cadena
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2016.01078

Region 4 of Rhizobium etli Primary Sigma Factor (SigA) Confers Transcriptional Laxity in Escherichia coli
Cited by: 1
Author(s): Orlando Santillán, Miguel A. Ramı́rez-Romero, Luis Lozano, Alberto Checa, Sergio Encarnación, Guillermo Dávila
Software Mentions: 4
Published: over 8 years ago

10.1186/s13024-018-0254-8

Identification and therapeutic modulation of a pro-inflammatory subset of disease-associated-microglia in Alzheimer’s disease
Cited by: 227
Author(s): Srikant Rangaraju, Eric B. Dammer, Syed Ali Raza, Priyadharshini Rathakrishnan, Hailian Xiao, Tianwen Gao, Duc M. Duong, Michael W. Pennington, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey
Software Mentions: 4
Published: over 6 years ago

10.1186/s12920-017-0295-9

RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking
Cited by: 46
Author(s): Margaret M. Parker, Robert Chase, Andrew Lamb, Alejandro Reyes, Aabida Saferali, Jeong H. Yun, Blanca E. Himes, Edwin K. Silverman, Craig P. Hersh, Peter J. Castaldi
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-52243-0

Floodplain land cover affects biomass distribution of fish functional diversity in the Amazon River
Cited by: 29
Author(s): Caroline C. Arantes, Kirk O. Winemiller, Alex Asher, Leandro Castello, Laura L. Hess, Miguel Petrere, Carlos Edwar de Carvalho Freitas
Software Mentions: 3
Published: about 5 years ago

10.1002/ece3.2734

Water, land, fire, and forest: Multi-scale determinants of rainforests in the Australian monsoon tropics
Cited by: 15
Author(s): Stefania Ondei, Lynda D. Prior, Grant J. Williamson, Tom Vigilante, David M. J. S. Bowman
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12967-019-1785-7

DRAP: a toolbox for drug response analysis and visualization tailored for preclinical drug testing on patient-derived xenograft models
Cited by: 11
Author(s): Quanxue Li, Wentao Dai, Jixiang Liu, Yixue Li, Yuanyuan Li
Software Mentions: 3
Published: almost 6 years ago

10.1128/mSystems.00161-20

Commensal Oral Rothia mucilaginosa Produces Enterobactin, a Metal-Chelating Siderophore
Cited by: 26
Author(s): Carla Uranga, Pablo Arroyo, Brendan M. Duggan, William H. Gerwick, Anna Edlund
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-016-0937-9

In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians
Cited by: 76
Author(s): Alyssa M. Molinaro, Bret J. Pearson
Software Mentions: 3
Published: over 8 years ago

10.1002/emmm.201302558

Triple negative breast cancer initiating cell subsets differ in functional and molecular characteristics and in γ‐secretase inhibitor drug responses
Cited by: 58
Author(s): Diana J. Azzam, Dekuang Zhao, Junjun Sun, Andy J. Minn, Prathibha Ranganathan, Katherine Drews-Elger, Xiaoqing Han, Manuel Picón-Ruiz, Candace A. Gilbert, Seth A. Wander, Anthony J. Capobianco, Dorraya El-Ashry, Joyce M. Slingerland
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pbio.1002364

An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway
Cited by: 35
Author(s): Kevin A. Robertson, Wei Yuan Hsieh, Thorsten Forster, Mathieu Blanc, Hongjin Lu, Peter J. Crick, Eylan Yutuc, Steven Watterson, Kimberly Martin, Samantha J. Griffiths, Anton J. Enright, Mami Yamamoto, Madapura M. Pradeepa, Kimberly A Lennox, Mark A. Behlke, Simon Talbot, Jürgen Haas, Lars Dölken, William J. Griffiths, Yuqin Wang, Ana Angulo, Peter Ghazal
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1003006

New Partners in Regulation of Gene Expression: The Enhancer of Trithorax and Polycomb Corto Interacts with Methylated Ribosomal Protein L12 Via Its Chromodomain
Cited by: 18
Author(s): Anne Coléno-Costes, Suk Min Jang, Augustin de Vanssay, Julien Rougeot, Tahar Bouceba, Neel B. Randsholt, Jean‐Michel Gibert, Stéphane Le Crom, Emmanuèle Mouchel‐Vielh, Sébastien Bloyer, Frédérique Peronnet
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0163025

Forced Trefoil Factor Family Peptide 3 (TFF3) Expression Reduces Growth, Viability, and Tumorigenicity of Human Retinoblastoma Cell Lines
Cited by: 12
Author(s): Jan Große-Kreul, Maike Busch, Claudia Winter, Stefanie Pikos, Harald Stephan, Nicole Dünker
Software Mentions: 2
Published: about 8 years ago

10.1186/s13059-015-0851-6

3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process
Cited by: 18
Author(s): Mohamed Nadhir Djekidel, Zhengyu Liang, Qi Wang, Zhirui Hu, Guipeng Li, Chen Yang, Michael Q. Zhang
Software Mentions: 2
Published: almost 9 years ago

10.1038/srep37197

A novel ENU-induced ankyrin-1 mutation impairs parasite invasion and increases erythrocyte clearance during malaria infection in mice
Cited by: 8
Author(s): Huiyan Huang, Denis C. Bauer, Patrick M. Lelliott, Andreas Greth, Brendan J. McMorran, Simon J. Foote, Gaétan Burgio
Software Mentions: 2
Published: about 8 years ago

10.1289/ehp.1509820

Effects of Developmental Activation of the Aryl Hydrocarbon Receptor by 2,3,7,8-Tetrachlorodibenzo- p -dioxin on Long-term Self-renewal of Murine Hematopoietic Stem Cells
Cited by: 17
Author(s): Michael D. Laiosa, Everett Tate, Lori S. Ahrenhoerster, Yuhong Chen, Demin Wang
Software Mentions: 1
Published: over 8 years ago

10.1038/cddis.2016.102

CD95 maintains stem cell-like and non-classical EMT programs in primary human glioblastoma cells
Cited by: 49
Author(s): Moritz Drachsler, Susanne Kleber, Álvaro Mateos, Katrin Volk, Nadine Mohr, S Chen, Branko Cirovic, Jochen Tüttenberg, Christian Gieffers, Jaromir Sykora, Christian Rainer Wirtz, Wolf Mueller, Michael Synowitz, Ana Martin‐Villalba
Software Mentions: 1
Published: over 8 years ago

10.3390/cancers11111635

SLUG Directs the Precursor State of Human Brain Tumor Stem Cells
Cited by: 13
Author(s): Charles Chesnelong, Xiaoguang Hao, Orsolya Cseh, Alice Yijun Wang, H. Artee Luchman, Samuel Weiss
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0172209

Potential effect of spliceosome inhibition in small cell lung cancer irrespective of the MYC status
Cited by: 12
Author(s): Kenichi Suda, Leslie Rozeboom, Hui Yu, Kim Ellison, Christopher J. Rivard, Tetsuya Mitsudomi, Fred R. Hirsch
Software Mentions: 1
Published: almost 8 years ago

10.1534/g3.117.300079

Ankyrin-1 Gene Exhibits Allelic Heterogeneity in Conferring Protection Against Malaria
Cited by: 3
Author(s): Huiyan Huang, Denis C. Bauer, Patrick M. Lelliott, Matthew W. A. Dixon, Leann Tilley, Brendan J. McMorran, Simon J. Foote, Gaëtan Burgio
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0168770

Identification of Post-Transcriptional Modulators of Breast Cancer Transcription Factor Activity Using MINDy
Cited by: 3
Author(s): Thomas M. Campbell, Mauro A. A. Castro, Bruce A.J. Ponder, Kerstin B. Meyer
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-10-638

Transcriptional adaptations following exercise in Thoroughbred horse skeletal muscle highlights molecular mechanisms that lead to muscle hypertrophy
Cited by: 49
Author(s): Beatrice A. McGivney, Suzanne S. Eivers, David E. MacHugh, James N. MacLeod, Grace M. O’Gorman, Stephen D. E. Park, Lisa Katz, E. W. Hill
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0051671

FGFR2 Promotes Breast Tumorigenicity through Maintenance of Breast Tumor-Initiating Cells
Cited by: 51
Author(s): Sungeun Kim, Anna Dubrovska, Richard J. Salamone, John R. Walker, Kathryn B. Grandinetti, Ghislain M. C. Bonamy, Anthony P. Orth, Jimmy Elliott, Diana Graus Porta, Carlos Garcı́a-Echeverrı́a, Venkateshwar A. Reddy
Software Mentions: 1
Published: almost 12 years ago

10.1038/srep22965

The nematode Caenorhabditis elegans as a tool to predict chemical activity on mammalian development and identify mechanisms influencing toxicological outcome
Cited by: 48
Author(s): Philippa H. Harlow, Simon J. Perry, Stephanie Widdison, S. A. Daniels, Eddie Bondo, Clemens Lamberth, Richard A. Currie, Anthony J. Flemming
Software Mentions: 1
Published: over 8 years ago

10.3390/ani11030715

A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders
Cited by: 9
Author(s): Amanda Botelho Alvarenga, Hinayah Rojas de Oliveira, Shiyi Chen, Stephen Miller, Jeremy N. Marchant‐Forde, Laís Grigoletto, Luiz F. Brito
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-017-11287-w

Neuropilin-1 is upregulated by Wnt/β-catenin signaling and is important for mammary stem cells
Cited by: 22
Author(s): Wei Liu, Ting Wu, Xiao Dong, Yi Arial Zeng
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0184905

A prolonged chronological lifespan is an unexpected benefit of the [PSI+] prion in yeast
Cited by: 13
Author(s): Kai Wang, Ronald Melki, Mehdi Kabani
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0057312

The TBC1D15 Oncoprotein Controls Stem Cell Self-Renewal through Destabilization of the Numb-p53 Complex
Cited by: 21
Author(s): Douglas E. Feldman, Chialin Chen, Vasu Punj, Keigo Machida
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0007163

Sustained Oscillations of NF-κB Produce Distinct Genome Scanning and Gene Expression Profiles
Cited by: 103
Author(s): Myong-Hee Sung, Luigi Salvatore, Rossana De Lorenzi, Anindya Indrawan, Manolis Pasparakis, Gordon L. Hager, Marco E. Bianchi, A Agresti
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pgen.1003048

Transcription Factor Oct1 Is a Somatic and Cancer Stem Cell Determinant
Cited by: 69
Author(s): Jessica Maddox, Arvind Shakya, Samuel South, Dawne N. Shelton, Jared N. Andersen, Stephanie Chidester, Jinsuk Kang, Keith M. Gligorich, David A. Jones, Gerald J. Spangrude, Bryan E. Welm, Dean Tantin
Software Mentions: 1
Published: about 12 years ago

10.1080/21505594.2020.1768338

Putative determinants of virulence in Melissococcus plutonius, the bacterial agent causing European foulbrood in honey bees
Cited by: 31
Author(s): Daniela Grossar, Verena Kilchenmann, Eva Forsgren, Jean-Daniel Charrière, Laurent Gauthier, Michel Chapuisat, Vincent Dietemann
Software Mentions: 1
Published: over 4 years ago

10.7554/eLife.07301

Registered report: Wnt activity defines colon cancer stem cells and is regulated by the microenvironment
Cited by: 10
Author(s): James Evans, Anthony Essex, Xin Hong, Nurith Amitai, Lindsey T. Brinton, Erin Griner
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms20174129

p53, miR-34a and EMP1—Newly Identified Targets of TFF3 Signaling in Y79 Retinoblastoma Cells
Cited by: 6
Author(s): Maike Busch, Stefan Klein, Jan Große-Kreul, O Scheiner, K. Metz, Harald Stephan, Nicole Dünker
Software Mentions: 1
Published: over 5 years ago

10.1186/1476-4598-10-112

Side population rather than CD133+ cells distinguishes enriched tumorigenicity in hTERT-immortalized primary prostate cancer cells
Cited by: 30
Author(s): Jianjun Zhou, Honghe Wang, Virginetta Cannon, Karen M. Wolcott, Hongbin Song, Clayton Yates
Software Mentions: 1
Published: about 13 years ago

10.18632/oncotarget.13226

Mutational activation of BRAF confers sensitivity to transforming growth factor beta inhibitors in human cancer cells
Cited by: 17
Author(s): Lindsay C. Spender, Gail Ferguson, Sijia Liu, Chao Cui, María Romina Girotti, Gary Sibbet, Ellen B. Higgs, Morven Shuttleworth, Tom Hamilton, Paul Lorigan, Michael Weller, David F. Vincent, Owen J. Sansom, Margaret C. Frame, Peter ten Dijke, Richard Marais, Gareth J. Inman
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.15392

Analysis of acquired mutations in transgenes arising in Ba/F3 transformation assays: findings and recommendations
Cited by: 11
Author(s): Kevin Watanabe-Smith, Jamila Godil, Anupriya Agarwal, Cristina E. Tognon, Brian J. Druker
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.15002

New in vivo avatars of diffuse intrinsic pontine gliomas (DIPG) from stereotactic biopsies performed at diagnosis
Cited by: 38
Author(s): Alexandre Plessier, Ludivine Ledret, Pascale Varlet, Kévin Beccaria, J. Lacombe, Sébastien Mériaux, Françoise Geffroy, Laurence Fiette, Patricia Flamant, Fabrice Chrétien, Thomas Blauwblomme, Stéphanie Puget, Jacques Grill, Marie‐Anne Debily, David Castel
Software Mentions: 1
Published: almost 8 years ago

10.1111/rssc.12235

Clustered Multistate Models with Observation Level Random Effects, Mover–Stayer Effects and Dynamic Covariates: Modelling Transition Intensities and Sojourn Times in a Study of Psoriatic Arthritis
Cited by: 6
Author(s): Sean Yiu, Vernon Farewell, Brian D. M. Tom
Software Mentions: 1
Published: over 7 years ago

10.18632/aging.202732

Lung cancer-associated mesenchymal stem cells promote tumor metastasis and tumorigenesis by induction of epithelial–mesenchymal transition and stem-like reprogram
Cited by: 11
Author(s): Chunhong Yan, Jianmei Chang, Xinmiao Song, Qi Ying, Zhenyu Ji, Ting Liu, Wenwen Yu, Feng Wei, Lili Yang, Xiubao Ren
Software Mentions: 1
Published: over 3 years ago

10.1016/j.celrep.2014.05.014

Distinct Stromal Cell Factor Combinations Can Separately Control Hematopoietic Stem Cell Survival, Proliferation, and Self-Renewal
Cited by: 45
Author(s): Stefan Wöhrer, David J.H.F. Knapp, Michael R. Copley, Claudia Benz, David G. Kent, Keegan Rowe, Sonja Babovic, Heidi Mader, Robert A.J. Oostendorp, Connie J. Eaves
Software Mentions: 1
Published: over 10 years ago

Projects: cran: statmod

Papers Mentioning statmod 55