ISA

Revision as of 11:32, 1 February 2016 by Micha (talk | contribs)



An ISA transcription module


Large sets of data, like expression profile from many samples, require analytic tools to reduce their complexity. The Iterative Signature Algorithm (ISA) was designed to reduce the complexity of very large sets of data by decomposing it into so-called "modules". In the context of gene expression data these modules consist of subsets of genes that exhibit a coherent expression profile only over a subset of microarray experiments. Genes and arrays may be attributed to multiple modules and the level of required coherence can be varied resulting in different "resolutions" of the modular mapping. Since the ISA does not rely on the computation of correlation matrices (like many other tools), it is extremely fast even for very large datasets.

Software for Gene expression data

We developed the eisa GNU R package to facilitate the modular analysis of gene expression data. The package uses standard BioConductor data structures and includes various visualization tools as well.

Requirements, download and installation

To use eisa you will need a working GNU R installation.

As of the 23rd of April, 2010, the eisa package is an official BioConductor package.

eisa depends on a number of other R packages: isa2, Biobase, AnnotationDbi, Category, genefilter, DBI. The good news is that all these dependencies are installed automatically, and all you need to do is to start R and type in 

 source("http://bioconductor.org/biocLite.R")
 biocLite("eisa")

at your R prompt. See the eisa package page at the BioConductor website for details.

Alternatively, you can also download the package from here:

License

The eisa package is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.

Software for any tabular data

The ISA can be applied to identify coherent substructures (i.e. modules) from any rectangular matrix of data. You can use the isa2 R package for such an analysis.

Requirements

No additional R package is required to install and use isa2. But on Linux and Unix systems you will need a C compiler to install it. E.g. on Ubuntu Linux you will need to install the build-essential package.

Installation

The isa2 package is available from CRAN, the standard R package repository. You can install it on any platform that is supported by GNU R, e.g. Microsoft Windows, Mac OSX and Linux systems. To install it, start R and type in 

 install.packages("isa2")

at the prompt. On Linux and Unix-like systems, you will need a working C compiler for a successful installation.

License

The isa2 package is licensed under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.

Tutorials

The Iterative Signature Algorithm for Gene Expression Data

Shows the typical steps of modular analysis, from loading you expression data to the visualization of transcription modules.
HTML PDF Rnw R code

ISA and the biclust package

The biclust package implements several biclustering algorithms. It is possible to convert the results of biclust to transcription modules and vice-versa.
HTML PDF Rnw R code

Tissue specific expression with the Iterative Signature Algorithm

HTML PDF Rnw R code

Hierarchical module trees

A module tree is the hierarchical modular organization of a data set.
HTML PDF Rnw R code

The Iterative Signature Algorithm

Tutorial for the analysis of tabular data with the isa2 R package.
HTML PDF Rnw R code

Running ISA in parallel

Shows how to run ISA on a computer cluster or multi-processor machine, using MPI and the Rmpi and snow R packages.
HTML PDF Rnw R code

ISA internals

HTML PDF Rnw R code

Matlab package

You can download it from here. It also includes the implementation of the Ping-pong algorithm Kutalik2008NB. The "testPP.m" file explains how the algorithm is applied to a pair of toy data sets. To test the ISA functionalities, the "testISA.m" needs to be launched.

Papers

Groene N, Nickel A, Rohn AE
Insights on the Side Effects of Female Contraceptive Products From Online Drug Reviews: Natural Language Processing-Based Content Analysis.
JMIR AI: 2025 Apr 3, 4;e68809
[PubMed:40179373] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Trahair ED, Steiger D, Lowe N, Rapoport R, Kelliher C, Benvengo S, Kopil C, Chahine LM, Marras C, Mantri S
Fears and uncertainties of people with Parkinson's disease.
J Parkinsons Dis: 2025 Apr 3;1877718X251328565
[PubMed:40179210] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Heiles B, Nelissen F, Waasdorp R, Terwiel D, Park BM, Ibarra EM, Matalliotakis A, Ara T, Barturen-Larrea P, Duan M, Shapiro MG, Gazzola V, Maresca D
Nonlinear sound-sheet microscopy: Imaging opaque organs at the capillary and cellular scale.
Science: 2025 Apr 4, 388(6742);eads1325
[PubMed:40179181] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Wang Y, Li J, Shan S
A double-edged sword effect: the implications of Internet exposure for Netizens' tolerant attitudes toward people living with HIV/AIDS.
AIDS Care: 2025 Apr 3;1-17
[PubMed:40179122] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hu G, Wang Z, Xie Y, Lin Z
The existing characteristics, transport patterns, and significance of nanoparticulate pollutants in groundwater surrounding an industrial park.
PLoS One: 2025, 20(4);e0321264
[PubMed:40179085] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Yin LX, Lohse CM, Yost KJ, Tuchscherer AM, Martin EJ, Semann H, Calcano GA, Price DL, Tasche KK, Van Abel KM, Moore EJ
Patient-Reported Quality-of-Life Outcome Measure After Parotidectomy.
JAMA Otolaryngol Head Neck Surg: 2025 Apr 3;
[PubMed:40178828] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Onifade A, Katolo HW, Mookerjee S, Bhutta MF
Epidemiology of Chronic Suppurative Otitis Media: Systematic Review To Estimate Global Prevalence.
J Epidemiol Glob Health: 2025 Apr 3, 15(1);55
[PubMed:40178730] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Ravi K, Tan YS, Kamali MZM, Muniandy SV
Elucidation of Foraging Strategies of Ganoderma lucidum and Ganoderma neo-japonicum on Different Nutrients Composition Using Fractal Morphology.
Curr Microbiol: 2025 Apr 3, 82(5);229
[PubMed:40178632] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Kelly BS
Embracing graphical abstracts in European Radiology.
Eur Radiol: 2025 Apr 3;
[PubMed:40178573] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Kowitt SD, Noar SM, Duguid I, Johnson M, Lazard AJ, Thrasher JF, Goldstein AO
Identifying Promising Message Themes for Youth Who Use Multiple Tobacco Products.
J Adolesc Health: 2025 Apr 3;
[PubMed:40178461] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Bhattarai B, Christopher GF
Mechanical properties of Staphylococcus aureus and Pseudomonas aeruginosa dual-species biofilms grown in chronic wound-based models.
Soft Matter: 2025 Apr 3;
[PubMed:40178412] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Stejskal V, Vendl T, Feng S, Qin Y, Aulicky R, Li Z
The relationship between taxonomic classification and applied entomology: stored product pests as a model group.
J Insect Sci: 2025 Mar 14, 25(2);
[PubMed:40178352] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Benhadid-Brahmi Y, Amaris Hobson C, Abdelmoumene L, Jaouen E, Magnan M, Gits-Muselli M, Lescat M, Tenaillon O, Bonacorsi S, Birgy A
Evaluation of phenotypic and genotypic methods for detecting KPC variants.
Antimicrob Agents Chemother: 2025 Apr 3;e0008225
[PubMed:40178306] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Nieboga E, Schuster A, Drapala DM, Melnykova M, Gut A, Lipska W, Kwitniewski M, Migaczewski M, Czesnikiewicz-Guzik M, Kaczmarzyk T, Potempa J, Grabiec AM
Synergistic induction of PGE2 by oral pathogens and TNF promotes gingival fibroblast-driven stromal-immune cross-talk in periodontitis.
mBio: 2025 Apr 3;e0004625
[PubMed:40178270] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Akbarzadeh R
Pt/SnO(2)/Sb(2)O(4) nanoparticle catalyst embedded in multi-walled carbon nanotubes as an active material for electrochemical hydrogen storage application.
Dalton Trans: 2025 Apr 3;
[PubMed:40178238] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Taieb A
Topical Steroid Withdrawal: The Challenging Transition from Patient Self-Diagnosis on Social Media to Medical Science and Care.
Acta Derm Venereol: 2025 Apr 3, 105;adv43455
[PubMed:40178221] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Mansori S, Tendulkar A, Rostamzadeh M
Gynecologic Cancer Screening: Understanding Barriers Through Social Cognitive Theory and Health Belief Model.
Health Educ Behav: 2025 Apr 3;10901981251328590
[PubMed:40178144] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Chisholm P, Brown J, Jiranantakan T, Harrod ME, McDonald C, Cullinan U, Roberts DM
Opioid overdoses following use of cocaine and methamphetamine in New South Wales, and the public health responses.
Emerg Med Australas: 2025 Apr, 37(2);e70038
[PubMed:40178058] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Hu H, Liu S, Sun H, Sun W, Tang J, Wei L, Chen X, Chen Q, Lin Y, Tian Z, Su J
Low-Ir-Content Ir(0.10)Mn(0.90)O(2) Solid Solution for Highly Active Oxygen Evolution in Acid Media.
Small: 2025 Apr 3;e2412096
[PubMed:40178026] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Zheng P, Wu L, Lee MKH, Nelson A, Betenbaugh M, Barman I
Deep Learning-Powered Colloidal Digital SERS for Precise Monitoring of Cell Culture Media.
Nano Lett: 2025 Apr 3;
[PubMed:40177940] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

El Abass SA, Alossaimi MA, Altamimi ASA, El-Deen AK
Micellar media effect on the ultrasensitive quantitation of a diuretic medication at nano-scale levels with environmentally benign impact.
Anal Methods: 2025 Apr 3;
[PubMed:40177909] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Xu X, Wang FM, Wang LW, Tang SF
Bioenzyme Inspired Heterointerface Construction of NiFeSe/Ni(3)S(2) for Improved Overall Water Splitting.
Inorg Chem: 2025 Apr 3;
[PubMed:40177864] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Song J, Lee Y, Kim MS, Ha G, Jang W, Batjargal U, Kim Y, Kim HJ, Lee J
High throughput drug screening platform utilizing capillary and artery cell layered models based on tumor-vascular cell interactions.
Lab Chip: 2025 Apr 3;
[PubMed:40177711] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Moya S, Lamont K, Brennan ML, Ciavarino G, Costa M, Allepuz A, Tamminen LM, Correia-Gomes C, De Carvalho Ferreira H, Dogusan MM, Imperial T, De Meneghi D, Kjosevski M, Chantziaras I, Burrell A
Stakeholders' perspectives on communicating biosecurity to encourage behavior change in farmers.
Front Vet Sci: 2025, 12;1562648
[PubMed:40177679] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Blom P, Huizing PC, de Monlevad JPRC, van Kessel MAHJ, Lücker S
Obtaining complete and canonical ammonia-oxidizing bacteria through specific labeling and cell sorting.
ISME Commun: 2025 Jan, 5(1);ycae145
[PubMed:40177467] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Abdikarim H, Muse YH, Muse AH
Associated Factors of Awareness and Knowledge About HIV/AIDS Among Women of Reproductive Age in Somaliland: Insights From a Nationwide Survey.
AIDS Res Treat: 2025, 2025;3425388
[PubMed:40177413] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Scorzo AV, Kwon CY, Strawbridge RR, Jack Hoopes P, Roberts DW, Davis SC
Elucidating the effect of tumor and background region-of-interest selection on the performance metrics used to assess fluorescence imaging.
J Biomed Opt: 2025 Apr, 30(4);046004
[PubMed:40177378] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Faryabi E, Sheikhhosseini E, Yahyazadehfar M
Iron ore pellets based-Ag(2)O nanoparticles as efficient Bi-functional heterogeneous catalyst for the synthesis tetrahydrobenzo[α]xanthens in green media.
Front Chem: 2025, 13;1413080
[PubMed:40177351] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Xu T, Zhang Y, Zhou Y, Yin L, Min X, Wu S, Zhang C, Ruan L
Association of Vascular Aging Phenotypes with Adverse Clinical Outcomes in the Chinese Population: A Multicentre Study.
Clin Interv Aging: 2025, 20;403-414
[PubMed:40177341] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Hameed A, Malik D
Bridging the Gap in Smoking Cessation: Unveiling Tobacco Harm Reduction in Pakistan Through Print Media Content Analysis.
Biomed Res Int: 2025, 2025;3822509
[PubMed:40177294] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Norris KC, Salerno J, Bairey Merz CN, Kaushik V, Gelleta S, Castillo A, Nidich S, Gaylord-King C, Schneider RH
A randomized controlled trial of meditation and health education on carotid intima-media thickness and major adverse cardiovascular events in Black men and women.
Front Med (Lausanne): 2025, 12;1513699
[PubMed:40177279] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Battaglia AM, Sacco A, Giorgio E, Petriaggi L, Elzanowska J, Cruz AR, Rocha L, Pereira CE, Strano Moraes MC, Palazzo L, De Vitis C, Costa-Silva B, Biamonte F
Expulsion of iron-rich ferritin via CD63-mediated exosome drives ferroptosis resistance in ovarian cancer cells.
Front Cell Dev Biol: 2025, 13;1532097
[PubMed:40177133] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Linares-Navarro R, Sanz-Muñoz I, Onecha-Vallejo V, Fernández-Espinilla V, Eiros JM, Castrodeza-Sanz J, Prada-García C
Psychosocial impact and stigma on men who have sex with men due to monkeypox.
Front Public Health: 2025, 13;1479680
[PubMed:40177086] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Zhang K, Jin T, Chen Y, Jiang L, Xie Y, Wang J
Effects of information involvement on subjective well-being during public health emergencies: the mediating roles of emotional regulation and social support.
Front Public Health: 2025, 13;1490771
[PubMed:40177084] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Yan X, Yan J, Tan C, Fu Y, Wang S
Your fitness-sharing is a reminder for my poor body: how fitness posts exposure on social media harms female body esteem.
Front Psychol: 2025, 16;1515575
[PubMed:40177054] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Azulay-Abulafia L, Giraldelli G, Alves AL, Baka J, Tavares Rodrigues F
Can Trichoscopy Suggest the Agent in Tinea Capitis?
Skin Appendage Disord: 2025 Apr, 11(2);128-134
[PubMed:40176996] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Ingram M
Toward a politics of shame: cripping understandings of affect in disabled people's encounters with unsolicited advice.
Front Sociol: 2025, 10;1401812
[PubMed:40176959] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Quinn EK, Duffy RT, Larsen K, Dalton M, Peters CE
Anti-masking Posts on Instagram: Content Analysis During the COVID-19 Pandemic.
Saf Health Work: 2025 Mar, 16(1);27-35
[PubMed:40176930] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Papayannakos CJ, Israr M, DeVoti JA, Lam F, Arazi A, Frank DK, Kamdar DP, Pereira LM, Seetharamu N, Steinberg BM, Bonagura VR
Oropharyngeal carcinomas induce circulating monocytes to express a TAM-like pro-tumor expression profile that suppresses T-cell proliferation.
Front Immunol: 2025, 16;1539780
[PubMed:40176808] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Das B
Unveiling mechanistic insights and applications of aggregation-enhanced emission (AEE)-active polynuclear transition metal complexes.
Chem Commun (Camb): 2025 Apr 3;
[PubMed:40176728] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Javdani A, Bae J, Ivanushkin G, Dusselier M
Dual organic structure-directing agents in zeolite synthesis: cooperation or competition?
Mater Horiz: 2025 Apr 3;
[PubMed:40176721] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hao RT, Zhang L
[Research progress on exposure and health risks of perchlorate in the environment].
Zhonghua Yu Fang Yi Xue Za Zhi: 2025 Apr 6, 59(4);509-515
[PubMed:40176675] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Lemire L, Reyes SJ, Durocher Y, Voyer R, Henry O, Pham PL
N-1 semi-continuous transient perfusion in shake flask for ultra-high density seeding of CHO cell cultures in benchtop bioreactors.
Biotechnol Prog: 2025 Apr 3;e70029
[PubMed:40176554] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Liu P, Bai S, Li M, Zhou R
Test Anxiety and Trait Anxiety in Adolescence: Same or Different Structures?
J Clin Psychol: 2025 Apr 2;
[PubMed:40176481] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Erickson RLM, Meyer-Gutbrod J
It's Only a Crisis if It's Fit to Print: Examining the Relationship Between Overdose Rates, News Coverage, and the Presence of the Opioid Crisis in State Legislative Campaigns.
J Health Polit Policy Law: 2025 Apr 3;
[PubMed:40176407] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Daungsupawong H, Wiwanitkit V
The Association Between Mindfulness and Social Media Addiction Among Nurses: Comment.
Workplace Health Saf: 2025 Apr 2;21650799251333070
[PubMed:40176324] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Luo M, Duan Z, Luo W, Niu Z
The increased risk of cyberbullying and its negative impact on mental health among sexual minority college students compared to their peers.
Child Adolesc Psychiatry Ment Health: 2025 Apr 2, 19(1);36
[PubMed:40176061] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Arslan N, Esin K, Ayyıldız F
A validity and reliability study of the artificial intelligence attitude scale (AIAS-4) and its relationship with social media addiction and eating behaviors in Turkish adults.
BMC Public Health: 2025 Apr 2, 25(1);1244
[PubMed:40175951] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Roberts CE, Oseni DA, Bohle-Frankel B, Reardon CL
Get your Head in the Game!: A Review of Factors that Impact Collegiate Student-Athlete Mental Health Using a Biopsychosocial-Structural Framework.
Curr Psychiatry Rep: 2025 Apr 3;
[PubMed:40175841] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Park YW, Tao X, Fisher CB
Race and Anti-Racist Online Coping as Moderators of College Adjustment Associated with Exposure to Social Media Racism among Asian, Black, and Hispanic/Latine Students.
J Youth Adolesc: 2025 Apr 2;
[PubMed:40175836] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

DeAguero J, Howard T, Escobar GP, Dokladny K, Wagner B
Early endolysosomal dysfunction is a contributing factor to gadolinium-based contrast agent mouse renal proximal tubule epithelial cell injury.
Cell Biol Toxicol: 2025 Apr 3, 41(1);65
[PubMed:40175829] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Gao Y, He X, Deng Y, Wang X, Shen J, Xu W, Cai R, Lan X, Chen J, He Y
Human dental follicle cell-derived conditioned media enhance periodontal regeneration by regulating the osteogenic differentiation and inflammation of periodontal ligament stem cells and macrophage polarization.
Mol Cell Biochem: 2025 Apr 2;
[PubMed:40175780] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Arima J, Matsumoto T, Nagamura H, Tsukamoto R, Haga H, Shimizu K
Development of a nitrifying bacterial community for a low temperature recirculating aquaculture system.
World J Microbiol Biotechnol: 2025 Apr 3, 41(4);123
[PubMed:40175779] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Pearson H
Do smartphones and social media really harm teens' mental health?
Nature: 2025 Apr, 640(8057);26-28
[PubMed:40175759] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Gimenes M, Lambert E, Chaussoy L, Wilson MA, Quémart P
VOC-ADO: A lexical database for French-speaking adolescents.
Behav Res Methods: 2025 Apr 2, 57(5);137
[PubMed:40175669] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Khine HEE, Suriya U, Rungrotmongkol T, Chamni S, Lu Y, Bénard A, Lan B, Mukhopadhyay D, Chang D, Biankin A, Schneider-Stock R, Grützmann R, Sungthong R, Pilarsky C, Chaotham C
Jorunnamycin A induces apoptosis in pancreatic ductal adenocarcinoma cells, spheroids, and patient-derived organoids by modulating KRAS-mediated survival pathways.
Sci Rep: 2025 Apr 3, 15(1);11376
[PubMed:40175514] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Clarkson DL, Kontar EP, Chrysaphi N, Emslie AG, Jeffrey NLS, Krupar V, Vecchio A
Tracing the heliospheric magnetic field via anisotropic radio-wave scattering.
Sci Rep: 2025 Apr 2, 15(1);11335
[PubMed:40175477] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Barber LE, Smith-Ireland D, Enun B, Johnson DA
Understanding sleep health in Black American adults: A qualitative analysis of barriers, facilitators, and perspectives on sleep interventions.
Sleep Health: 2025 Apr 1;
[PubMed:40175266] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Adhikari T, Montenegro T, Jung JW, Oare C, Fonseca G, Beaulieu L, Alshreef A, Ferreira C
The use of Monte Carlo simulation techniques in brachytherapy: A comprehensive literature review.
Brachytherapy: 2025 Apr 1;
[PubMed:40175201] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Madhavan AA, Kranz PG, Brinjikji W, Mark IT, Amrhein TJ
Photon-Counting CT Myelography for the Detection of Spinal CSF Leaks.
AJNR Am J Neuroradiol: 2025 Apr 2, 46(4);846
[PubMed:40174978] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Anterasian C, Gela A, Mwambene TD, Shah JA, Ivie J, Dill-McFarland KA, Hanekom WA, Kiritsy MC, Sassetti CM, Musvosvi M, Hatherill M, Scriba TJ, Hawn TR
BCG induced innate immune response heterogeneity and susceptibility to pediatric tuberculosis.
J Immunol: 2025 Apr 2;
[PubMed:40174917] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Jiang W, Wei H, Xu Z, Kang J, Wang S, Liu D, Ren Y, Ngo HH, Guo W, Ye Y
Lighting promotes sulfate removal and improves microbial community stability in upflow anaerobic sludge bed reactors under low ratio of chemical oxygen demand to sulfate.
Bioresour Technol: 2025 Mar 31;132473
[PubMed:40174651] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Wang S, Wang H, Huang X, Wu Z, Xue H, Zhao C
A novel magnetic adsorption and capacitive deionization coupled technology for industrial saline wastewater recycling.
Water Res: 2025 Mar 26, 281;123559
[PubMed:40174564] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Suhardita K, Datuti S, Saputra R, Ramadhani E, Badriyah RUD
Strengthening suicide prevention policies in South Korea: Bridging the gap for adolescent mental health.
Asian J Psychiatr: 2025 Mar 29, 107;104472
[PubMed:40174518] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Dehaghani MST, Esfandiari Z, Khodadadi M
Application of L-leucine-based natural deep eutectic solvent and ferroferric oxide magnetic nanoparticles modified with silica and zeolitic imidazolate framework-8 (Fe(3)O(4)@SiO(2)@ZIF-8) for extracting organophosphorus pesticides from cucumber.
Food Chem: 2025 Mar 22, 481;143939
[PubMed:40174382] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Strong C, Joson P, Chu IY, Chuang TT, Wu HJ, Li CW, Huang P, Bourne A, Ku SW
Prioritization and barriers of mpox vaccination uptake among gay, bisexual and other men who have sex with men in Taiwan: 2023 HEART survey.
Vaccine: 2025 Apr 1, 53;127059
[PubMed:40174374] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Lei X, Liu B, Di C, Wei Z, Deng P, Chen Z
Molecular interactions of surfactants with other chemicals in chemical flooding processes: A comprehensive review on molecular dynamics simulation studies.
Adv Colloid Interface Sci: 2025 Mar 27, 341;103498
[PubMed:40174373] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Sackett JD, Tonucci GP, Rowe AR
Interfacial extracellular electron uptake is linked to nitrate respiration in the marine heterotroph, Thalassospira xiamenensis SN3.
Bioelectrochemistry: 2025 Mar 26, 165;108976
[PubMed:40174290] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Shahid M, Khalid S, ALOthman ZA, Al-Kahtani AA, Bibi I, Naz R, Natasha N, Niazi NK, Iqbal J, Han C, Shah NS, Murtaza B
Trace element removal from wastewater by agricultural biowastes: A data analysis on removal efficacy and optimized conditions.
Sci Total Environ: 2025 Apr 1, 975;179235
[PubMed:40174245] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Zarrillo TA, Stoner KA, Ascher JS
Biodiversity of Bees (Hymenoptera: Apoidea: Anthophila) in Connecticut (USA).
Zootaxa: 2025 Feb 12, 5586(1);1-138
[PubMed:40174048] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Wight L, Tenove C, Hirani S, Tworek H
Mental Health and Coping Strategies of Health Communicators Who Faced Online Abuse During the COVID-19 Pandemic: Mixed Methods Study.
JMIR Infodemiology: 2025 Apr 2, 5;e68483
[PubMed:40173443] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Fijany AJ, Holan CA, Bishay AE, Boctor MJ, Montorfano L, Mubang RN, Vijayasekaran A, Martinez-Jorge J, Harless CA, Thayer WP, Connor LM, Lineaweaver WC, Slater ED
Beyond the Posts: Analyzing Breast Implant Illness Discourse With Natural Language Processing and Deep Learning.
Aesthet Surg J: 2025 Apr 2;
[PubMed:40173420] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Adegboyega A, Wiggins A, Wuni A, Ickes M
The Impact of a Human Papillomavirus Facebook-Based Intervention (#HPVVaxTalks) Among Young Black (African American and Sub-Saharan African Immigrants) Adults: Pilot Pre- and Poststudy.
JMIR Form Res: 2025 Apr 2, 9;e69609
[PubMed:40173371] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Xu J, Zou Y, Chen H, Wan Z, Takagi A, Wang Z, Yu J, Liu L, Lu Y, Fan Y, Rojas OJ
Magnetoresponsive Cellulose Nanofiber Hydrogels: Dynamic Structuring, Selective Light Transmission, and Information Encoding.
ACS Nano: 2025 Apr 2;
[PubMed:40173319] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Araoka T, Toyohara K, Ryosaka M, Inui C, Matsuura M, Ma C, Watahiki J, Li Z, Iwasaki M, Watanabe A, Yokokawa R, Tabata Y, Izpisua Belmonte JC, Osafune K
Human iPSC-derived nephron progenitor cells treat acute kidney injury and chronic kidney disease in mouse models.
Sci Transl Med: 2025 Apr 2, 17(792);eadt5553
[PubMed:40173262] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Cui Y, Zhang C, Jiang B, Qin Z, Liu Z, Yang Y
Evaluation of all-for-one tourism development level: Evidence from Xinjiang production and construction corps, China.
PLoS One: 2025, 20(4);e0317834
[PubMed:40173197] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Valentin O, Foster NEV, Intartaglia B, Prud'homme MA, Schönwiesner M, Nozaradan S, Lehmann A
Intact sensorimotor rhythm abilities but altered audiovisual integration in cochlear implant users.
PLoS One: 2025, 20(4);e0320815
[PubMed:40173130] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Schoeller FA, Christov-Moore L, Lynch C, Jain A, Diot T, Reggente N
Repeated exposure decreases aesthetic chills likelihood but increases intensity.
PLoS One: 2025, 20(4);e0300494
[PubMed:40173129] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Konari AS, Sammadar S, Biswas S
Barriers to Timely Care: Understanding Delayed Health-Seeking Behavior in Chronic Otitis Media Patients in India.
Ear Nose Throat J: 2025 Apr 2;1455613251331837
[PubMed:40173056] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hoffmann D, Balcaen T, Vangrunderbeeck S, Puigdevall Mata L, Maes A, Pyka G, Dumoutier L, Behets C, De Borggraeve W, Kerckhofs G
3D Histological Analysis of Soft Tissues by Contrast-Enhanced X-Ray Microfocus Computed Tomography: Screening and Staining Optimization of Contrast-Enhancing Staining Agents.
Microsc Microanal: 2025 Mar 17, 31(2);
[PubMed:40173054] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Mukhtyar CB, Ather A, Ducker G, Ecclestone T, Fordham S, Naeem H, Coath FL
A preceptorship programme to learn ultrasonography for diagnosis of giant cell arteritis.
Scand J Rheumatol: 2025 Apr 2;1-6
[PubMed:40173023] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

García-Ramón DF, Cornelio-Santiago HP, Norabuena E, Sumarriva L, Alvarez-Chancasanampa H, Vega MN, Sotelo-Méndez A, Espinoza-Espinoza LA, Pantoja-Tirado LR, Gonzales-Agama SH, Chavarría-Marquez EY, Castro-Galarza CR
Effective novel and conventional technologies for decontamination of aflatoxin B(1) in foods: a review.
Mycotoxin Res: 2025 Apr 2;
[PubMed:40172772] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Pompecki S, Balakirski G, Löser CR
[Nail cosmetics-risks and opportunities].
Dermatologie (Heidelb): 2025 Apr 2;
[PubMed:40172625] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Grigoryan IV, Antiufrieva LA, Grigoryan AP, Pigareva VA, Generalov EA, Khomutov GB, Sybachin AV
IPECnet: ML model for predicting the area of water solubility of interpolyelectrolyte complexes.
Phys Chem Chem Phys: 2025 Apr 2;
[PubMed:40172530] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Zegarra-Flores JA, Condori-Ramos AR, Coloma-Dongo FE, Llatasi EEC, Llatasi FGC, Caceres CGM, Mamani CMC, Areche FO, Paricanaza-Ticona DC, Quispe EET, Leon-Gomez R
Analysis of the innovation system in the adoption of IR-43 (NIR) and Tinajones rice varieties by farmers of the Camaná Valley.
Braz J Biol: 2025, 85;e286882
[PubMed:40172452] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Catisquini EAT, Teixeira MM, Zampronio CDP, Oliveira JRM, Mondelli MFCG, Lourençone LFM, Brito Neto RV
Effect of active middle ear implant on auditory speech perception in individuals with ear malformation.
Codas: 2025, 37(3);e20240032
[PubMed:40172373] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Flumignan VK, Sircili MP, Franzolin MR, Tavassi AMC, Germano LG, Souza AVDS, Silva NF, Fukumasu NK, Anjos RMD, Otoch JP, Artifon ELA
Comparison between biliary plastic stents with and without application of silver nanoparticles: an in-vitro study of the biofilm formation.
Acta Cir Bras: 2025, 40;e402825
[PubMed:40172368] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Baysal F, Poschner T, Längle S, Edlinger-Stanger M, Sauer J, Andreas M
Total endoscopic valve surgery with the Ram device in combined mitral and tricuspid valve disease.
Multimed Man Cardiothorac Surg: 2025 Apr 2, 2025;
[PubMed:40172328] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Hodaei M, Mandelis A, Cheung AM
Bone ultrasound fractal dimension theory and experimental analysis with application to early osteoporosis prediction in cancellous bone.
J Acoust Soc Am: 2025 Apr 1, 157(4);2440-2460
[PubMed:40172278] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Nagata JM, Lee CM, Hur JO, Baker FC
What we know about screen time and social media in early adolescence: a review of findings from the Adolescent Brain Cognitive Development Study.
Curr Opin Pediatr: 2025 Apr 2;
[PubMed:40172268] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Rimple PA, Olafsson EB, Markus BM, Wang F, Augusto L, Lourido S, Carruthers VB
Metabolic adaptability and nutrient scavenging in Toxoplasma gondii: insights from ingestion pathway-deficient mutants.
mSphere: 2025 Apr 2;e0101124
[PubMed:40172222] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Shull LM, Wolter DJ, Kunkle DE, Legg KA, Giedroc DP, Skaar EP, Hoffman LR, Reniere ML
Analysis of genetic requirements and nutrient availability for Staphylococcus aureus growth in cystic fibrosis sputum.
mBio: 2025 Apr 2;e0037425
[PubMed:40172197] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Watson RG, Hole CR
Simple growth conditions improve targeted gene deletion in Cryptococcus neoformans.
mSphere: 2025 Apr 2;e0107024
[PubMed:40172186] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Rahmatian N, Abbasi S, Abbasi N, Tavakkoli Yaraki M
A green carbon dot@silver nanoparticle hybrid: as a turn-on fluorescent probe for the detection and quantification of cholesterol and glucose.
Nanoscale: 2025 Apr 2;
[PubMed:40171805] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Said SM, Mashadi AH, Gabr MA, Elderie A, Sanad M
Modified Ross procedure with four different strategies for right ventricular outflow tract reconstruction.
Multimed Man Cardiothorac Surg: 2025 Apr 2, 2025;
[PubMed:40171624] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Quero-Jiménez PC, Hernández-Ramírez A, Gomes G, Guzmán-Mar JL, Maia-Bila D, Hinojosa-Reyes L
A bentonite/ZIF-8 derived ZnO photocatalyst for the effective elimination of a mixture of endocrine disruptors under simulated solar light: estrogenicity mitigation.
Dalton Trans: 2025 Apr 2;
[PubMed:40171614] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Chen M, Pelras T, Benninga J, Voet VSD, Folkersma R, Loos K
Glycosylated polyplex micelles from oppositely charged block copolymers.
J Mater Chem B: 2025 Apr 2;
[PubMed:40171603] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Qtait M
Time Wasters Facing Nurses During Work in Hospital Departments.
SAGE Open Nurs: 2025 Jan-Dec, 11;23779608251328278
[PubMed:40171549] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Steers MN, Strowger M, Tanygin AB, Ward RM, Nolfi DA
The Relationship Between Alcohol-Related Content on Social Media and Alcohol Outcomes in Young Adults: A Scoping Review.
Alcohol Res: 2025, 45(1);04
[PubMed:40171547] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Angelini F, Gini G
Digital stress and friendship conflict in adolescence: the role of perceived norms and features of social media.
Front Digit Health: 2025, 7;1497222
[PubMed:40171529] [WorldCat.org: ISSN ESSN ] [DOI] ( ) 

PDF

Ihmels JH, Bergmann S
Challenges and prospects in the analysis of large-scale gene expression data.
Brief Bioinform: 2004 Dec, 5(4);313-27
[PubMed:15606968] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Ihmels J, Bergmann S, Barkai N
Defining transcription modules using large-scale gene expression data.
Bioinformatics: 2004 Sep 1, 20(13);1993-2003
[PubMed:15044247] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Bergmann S, Ihmels J, Barkai N
Similarities and differences in genome-wide expression data of six organisms.
PLoS Biol: 2004 Jan, 2(1);E9
[PubMed:14737187] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Bergmann S, Ihmels J, Barkai N
Iterative signature algorithm for the analysis of large-scale gene expression data.
Phys Rev E Stat Nonlin Soft Matter Phys: 2003 Mar, 67(3 Pt 1);031902
[PubMed:12689096] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N
Revealing modular organization in the yeast transcriptional network.
Nat Genet: 2002 Aug, 31(4);370-7
[PubMed:12134151] [WorldCat.org: ISSN ESSN ] [DOI] ( o)


<biblio>

  1. Kutalik2008NB pmid=18464786 // PDF
  2. Ihmels2004 pmid=15606968 // PDF
  3. Ihmels2004a pmid=15044247 // PDF
  4. Bergmann2004 pmid=14737187 // PDF
  5. Bergmann2003 pmid=12689096 //PDF
  6. Ihmels2002 pmid=12134151 // PDF

</biblio>

Retrieved from "http://www2.unil.ch/cbg/index.php?title=ISA&oldid=4619"