Difference between revisions of "ISA"
Line 123: Line 123:
 
<pubmed>
 
<pubmed>
 
18464786
 
18464786
 +
[[Media:PPA.pdf|18464786]]
 
</pubmed>
 
</pubmed>
 
  [[Media:PPA.pdf|PDF]]
 
  [[Media:PPA.pdf|PDF]]

Revision as of 10:32, 1 February 2016



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

Malankar GS, Shelar DS, Butcher RJ, Manjare ST
Development of diselenide-based fluorogenic system for the selective and sensitive detection of the Hg(II) in aqueous media.
Dalton Trans: 2025 Jan 31;
[PubMed:39886849] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Truong T, Boukhris M, Tuffreau-Martin AS, Molho A, Chiaroni PM, Zamora P, De Pommereau A, Rostain L, Mangiameli A, Cianci A, Aboyans V, Teiger E, Boukantar M, Gallet R
Ultra-Low Contrast IVUS-Guided PCI in Patients With Severe Chronic Kidney Disease: An Observational Prospective Study.
Circ Cardiovasc Interv: 2025 Jan 31;e014854
[PubMed:39886761] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Goyal S, Sakhi P, Kalidindi S, Nema D, Pakhare AP
Knowledge, Attitudes, Perceptions, and Practices Related to Artificial Intelligence in Radiology Among Indian Radiologists and Residents: A Multicenter Nationwide Study.
Cureus: 2024 Dec, 16(12);e76667
[PubMed:39886734] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Attia D, Levi-Kalisman Y, Bitton R, Yerushalmi-Rozen R
Gum Arabic induced assembly of cellulose nanocrystals in aqueous media.
Nanoscale Adv: 2025 Jan 22;
[PubMed:39886611] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Wu CC, Okano K, Religia P, Soma Y, Takahashi M, Izumi Y, Bamba T, Honda K
Combination of Two-Stage Continuous Feeding and Optimized Synthetic Medium Increases Lipid Production in Lipomyces starkeyi.
Eng Life Sci: 2025 Jan, 25(1);e70003
[PubMed:39886606] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Wang N, Chang M, Liu S, Chen B
Study on the changes and influencing factors of depression in Chinese women with cancer: an analysis based on CHARLS panel data.
Front Public Health: 2024, 12;1485196
[PubMed:39886394] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Robert C, Tan WY, Ling LH, Hilal S
Association of arterial structure and function with incident cardiovascular diseases and cognitive decline.
Alzheimers Dement (Amst): 2025 Jan-Mar, 17(1);e70069
[PubMed:39886319] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Cook SC, Barnes GD, Berlacher K, Capers Q 4th, Fradley MG, Reardon LC, Rzeszut A, Sulistio M, Echols M
Experiences of Lesbian, Gay, Bisexual, Transgender, and Queer Cardiology Physicians and Fellows in Training.
JACC Adv: 2025 Feb, 4(2);101545
[PubMed:39886307] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Wyche S, Olson J, Karanu M, Omondi E, Olonyo M
Limitations of Using Mobile Phones for Managing Type 1 Diabetes (T1D) Among Youth in Low and Middle-Income Countries: Implications for mHealth.
Proc ACM Hum Comput Interact: 2024 Nov, 8(CSCW2);
[PubMed:39886256] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Afaq M, Vashisht K, Al-Dhoon A, Abraham D, Atanasov AG, Matin M, Arshad Z, Kashyap R, Nawaz FA
Impact of #PCOSweightloss: A global X hashtag analysis study of weight loss narratives in the PCOS community.
Digit Health: 2025 Jan-Dec, 11;20552076251314100
[PubMed:39886094] [WorldCat.org: ISSN ESSN ] [DOI] ( )

van Wijk M, Tran HH, Vu BNT, Tacoli C, Nguyen TCT, Pham QD, Nguyen THT, Nguyen TT, Nguyen HAT, Trinh TS, Pham TD, Tran HKT, Vu DTV, Dang DA, Tran TD, Nguyen DT, van Doorn HR, Kesteman T, Lewycka S
Prevalence and determinants of faecal carriage of carbapenem- and third-generation cephalosporin-resistant Enterobacterales: a cross-sectional household survey in northern Vietnam.
Lancet Reg Health West Pac: 2025 Jan, 54;101281
[PubMed:39886041] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Thorpe S, Malone N, Vigil K, Duroseau B, Iyiewuare P, Palomino K
Minority stressors and psychological correlates of sexual distress among Black queer and heterosexual women.
Sex Relation Ther: 2024, 39(4);1423-1440
[PubMed:39885902] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Dashti F, Abdulsalam HM
The influence of social media applications on learning English as a second language.
Heliyon: 2025 Jan 30, 11(2);e41874
[PubMed:39885874] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Kaur A, Bagherifard M, Anderson AB, Tariq N, Syrgiannis Z, Spanopoulos I
A perylene-based fluorescent probe for highly efficient SDS detection.
Anal Methods: 2025 Jan 31;
[PubMed:39885785] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Yu H, Balestra SRG, Gao ZR, Camblor MA
An overloaded pure silica zeolite ISV synthesized using a phosphonium cation.
Dalton Trans: 2025 Jan 31;
[PubMed:39885758] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Wang SQ, Yao ZC, Shi ZQ, Liu X, Tang T, Pan HR, Zheng L, Zhang Q, Su D, Zhuang Z, Zhao L, An Q, Hu JS
Pd(1)Ni(2) Trimer Sites Drive Efficient and Durable Hydrogen Oxidation in Alkaline Media.
J Am Chem Soc: 2025 Jan 30;
[PubMed:39885727] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Caparrós FJ, Gomes PA, García-Algar M, Rivero M, Grand S, Borràs M, Sagales J, Gómez-de Pedro S
Versatile methodology for the synthesis of stable magnetic SERS-encoded clusters for sensing applications.
Nanoscale: 2025 Jan 31;
[PubMed:39885725] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Thater G, Frerichs I, Büttner S, Schoenberg SO, Froelich M, Ayx I
Reduction of Streak Artifacts in the Superior Vena Cava for Better Visualization of Mediastinal Structures Through Virtual Monoenergetic Reconstructions Using a Photon-counting Detector Computed Tomography.
J Thorac Imaging: 2025 Jan 31;
[PubMed:39885700] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Bruaset GT, Johansen JD, Grimholt TK
The tip of an iceberg? Adult children's experiences with parental suicidal behaviour in childhood.
Int J Qual Stud Health Well-being: 2025 Dec, 20(1);2459299
[PubMed:39885697] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Eaton E, Martorell CT, Sawyer J, Schreibman TS, Felzien GS, Meza Jimenez J, Anderson Chadha C, Carter J, Napolitan C, Simone L, Molloy L, Douglas B
Impacts of a multipronged initiative with community HIV clinics to support retention and re-engagement in HIV care.
HIV Res Clin Pract: 2025 Dec, 26(1);2455814
[PubMed:39885691] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Tang H, Zhan Z, Liu X, Huang X
Propionylation of Fis K32 in Salmonella enterica serovar Typhi: a key modification affecting pathogenicity.
Future Microbiol: 2025 Jan 30;1-9
[PubMed:39885648] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Noda K, Atale N, Austin T, Geller DA, Gerlach J, Sanchez PG
Hepatic conditioning results in better lung endothelial cell preservation under hypoxic environment in vitro.
Int J Artif Organs: 2025 Jan 30;3913988251315092
[PubMed:39885637] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Agwu P, Mbachu C, Onwujekwe O
Enhancing the role of mass media in the translation of evidence from health policy and systems research in Nigeria.
Health Res Policy Syst: 2025 Jan 30, 23(1);16
[PubMed:39885524] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Alasfour M, Lajami Z, Algashami A
Perceived impact of physiotherapy-related debates on the social platform "X" on physiotherapists' professional development and knowledge acquisition: a cross-sectional study.
BMC Med Educ: 2025 Jan 30, 25(1);155
[PubMed:39885504] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Abdelaziz MN, Hefnawy A, Azzam H, Reisha O, Hamdy O
Knowledge and attitude among Egyptian medical students regarding the role of human papillomavirus vaccine in prevention of oropharyngeal cancer: a questionnaire-based observational study.
Sci Rep: 2025 Jan 30, 15(1);3767
[PubMed:39885233] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Subbiahanadar Chelladurai K, Selvan Christyraj JD, Rajagopalan K, Selvan Christyraj JRS
Advancing ex vivo functional whole-organ prostate gland model for regeneration and drug screening.
Sci Rep: 2025 Jan 30, 15(1);3758
[PubMed:39885212] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Romagnani P, Agarwal R, Chan JCN, Levin A, Kalyesubula R, Karam S, Nangaku M, Rodríguez-Iturbe B, Anders HJ
Chronic kidney disease.
Nat Rev Dis Primers: 2025 Jan 30, 11(1);8
[PubMed:39885176] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Najahi A, Delgado-Aguilar M, Putaux JL, Boufi S
High-Yield Cellulose Nanocrystals from Bleached Eucalyptus Fibers via Maleic Acid Hydrothermal Treatment and High-Pressure Homogenization.
Biomacromolecules: 2025 Jan 30;
[PubMed:39885169] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Yu Y, Wei Q, Tang S, Xiao F, Cai H, Li J
Sexually Explicit Media Exposure, Sexual Violence Victimization, and Sexual Risk Behaviors Among HIV-Positive Men Who Have Sex with Men with New Drug Abuse in Jinan, China.
Arch Sex Behav: 2025 Jan 30;
[PubMed:39885047] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Fernández-Salas A, Romero-Pérez JB, Alonso-Díaz MÁ
Does the use of engorged adult ticks of Rhipicephalus microplus as substrate modifies the acaricidal behavior of Metarhizium anisopliae?
Exp Appl Acarol: 2025 Jan 30, 94(2);34
[PubMed:39885013] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Mekonen EG, Ali MS, Workneh BS
Zero vegetable or fruit consumption and its associated factors among children aged 6 to 23 months in Kenya: a multilevel analysis of a large population-based survey.
Eur J Pediatr: 2025 Jan 30, 184(2);164
[PubMed:39884982] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Vieira L, Kang C, Martins M, Grilo A
Potential benefits of social media in educating healthcare professionals and students on medical imaging with ionizing radiation: A scoping review.
Radiography (Lond): 2025 Jan 30;
[PubMed:39884928] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Vassey J, Kennedy CJ, Chang HH, Unger JB
Generative AI in a new era of computer model-informed tobacco research: a short report.
Tob Control: 2025 Jan 30;
[PubMed:39884867] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Yu LQ, Do EK, Minter T, Koris K, Khatib B, Jacobs MA, Graham AL, Hair EC
Cessation and knowledge-building messaging are associated with e-cigarette cessation intentions among youth and young adults in the USA.
Tob Control: 2025 Jan 30;
[PubMed:39884866] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Kaja SM, Miller KK, Adler SJ, Hooper L
Helping Teens Move + Thrive: Adolescents' Preferences for Online Exercise Videos.
Health Promot Pract: 2025 Jan 30;15248399251314423
[PubMed:39884734] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Willis E, Wang Y, Goudarzvand S, Lee Y
What's on the agenda? Examining public health communication about opioids.
J Health Psychol: 2025 Jan 30;13591053241312043
[PubMed:39884726] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Tanguay C, Barbeau K, Lavigne G, Carbonneau N
Examining How Sociocultural Appearance Pressures Relate to Positive and Negative Facets of Body Image and Eating Behaviors in Adolescents: An Exploratory Person-Centered Approach.
Appetite: 2025 Jan 28;107890
[PubMed:39884512] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Freeman J, Sanders IMJG, Harmanus C, Clark EV, Berry AM, Smits WK
Antimicrobial susceptibility testing of Clostridioides difficile: a dual-site study of three different media and three therapeutic antimicrobials.
Clin Microbiol Infect: 2025 Jan 28;
[PubMed:39884503] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hebbar SD, Trivedi DR
Discriminative ion detection of Hg(2+) and Cu(2+) and selective recognition of PO(4)(3-) ions: Real time monitoring in food and water samples and molecular keypad lock integration.
Spectrochim Acta A Mol Biomol Spectrosc: 2025 Jan 21, 331;125706
[PubMed:39884209] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Murakami T, Saito N, Matsukami H, Takaoka M, Fujimori T
Destruction of perfluorooctanoic acid (PFOA) and perfluorooctadecanoic acid (PFOcDA) by incineration: Analysis of the by-products and their characteristics.
Chemosphere: 2025 Jan 29, 373;144165
[PubMed:39884143] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Steyn S, Slabbert M
Self-Guided Smartphone App (Vimbo) for the Reduction of Symptoms of Depression and Anxiety in South African Adults: Pilot Quantitative Single-Arm Study.
JMIR Form Res: 2025 Jan 30, 9;e54216
[PubMed:39883938] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Arifi D, Resch B, Santillana M, Guan WW, Knoblauch S, Lautenbach S, Jaenisch T, Morales I, Havas C
Geosocial Media's Early Warning Capabilities Across US County-Level Political Clusters: Observational Study.
JMIR Infodemiology: 2025 Jan 30, 5;e58539
[PubMed:39883923] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Elhassan SE, Sajid MR, Syed AM, Fathima SA, Khan BS, Tamim H
Assessing Familiarity, Usage Patterns, and Attitudes of Medical Students Toward ChatGPT and Other Chat-Based AI Apps in Medical Education: Cross-Sectional Questionnaire Study.
JMIR Med Educ: 2025 Jan 30, 11;e63065
[PubMed:39883912] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Ghorbani M, Roxburgh NPC, Tran MP, Blinco JP, Kempe K
Nitroxide-Containing Poly(2-oxazoline)s Show Dual-Stimuli-Responsive Behavior and Radical-Trapping Activity.
Biomacromolecules: 2025 Jan 30;
[PubMed:39883722] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Um S, Sopheab H
Breast and cervical cancer screening among women at reproductive age in Cambodia: A secondary analysis of Cambodia Demographic and Health Survey 2022.
PLoS One: 2025, 20(1);e0295881
[PubMed:39883702] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Sela A, Neter O, Lohr V, Cihelka P, Wang F, Zwilling M, Phillip Sabou J, Ulman M
Signals of propaganda-Detecting and estimating political influences in information spread in social networks.
PLoS One: 2025, 20(1);e0309688
[PubMed:39883667] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Mok KC, Liu M, Wang X
The physical activity and sedentary behavior among pregnant women in Macao: A cross-sectional study.
PLoS One: 2025, 20(1);e0318352
[PubMed:39883663] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Abdo E, Ismail MA, Al Hadidi S, Al-Mrahleh M, Saleh T, Zihlif M, Ababneh NA
Effect of cytotoxic CD8+ T-cells secretory proteins on hypoxic pancreatic cancer cells.
PLoS One: 2025, 20(1);e0311615
[PubMed:39883638] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Schwartz R, Borland T, Shahid M, Kuzmich K, Chaiton M
Long-term engagement in smoking cessation campaign: A mixed methods randomized trial.
PLoS One: 2025, 20(1);e0318160
[PubMed:39883629] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Maharjan S, Isaksson JM, Krupova M, Rämä T, Hansen KØ, Hammer Andersen J, Hansen EH
Metabolomics-Guided Discovery of Bipolarolides H-O, New Ophiobolin-Type Sesterterpenes with Antibacterial Activity from the Marine-Derived Fungus Uzbekistanica storfjordensis sp. nov.
J Nat Prod: 2025 Jan 30;
[PubMed:39883606] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Harper KC, Ronot M, Wells ML, Luna A, Ba-Ssalamah A, Wang J, Welle CL, Silva AC, Fidler J, Venkatesh SK
Hypointense Findings on Hepatobiliary Phase MR Images.
Radiographics: 2025 Feb, 45(2);e240090
[PubMed:39883575] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Volpi CR, Chama J, Blanco N, Adebiyi R, Mohanty K, Doroh A, Aigoro JA, Katu C, Ononaku U, Maigida J, Aka A, Shutt A, Dakum P, Charurat M, Adebajo S, Nowak RG
'Does human papillomavirus (HPV) cause cancer?' - A cross-sectional study of HPV awareness among sexual minority men in Nigeria.
Sex Health: 2025 Jan, 22;
[PubMed:39883557] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Trevena W, Zhong X, Alvarado M, Semenov A, Oktay A, Devlin D, Gohil AY, Chittimouju SH
Using Large Language Models to Detect and Understand Drug Discontinuation Events in Web-Based Forums: Development and Validation Study.
J Med Internet Res: 2025 Jan 30, 27;e54601
[PubMed:39883487] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Polyansky DE
Transient methods for understanding the properties of strongly oxidizing radicals.
Chem Commun (Camb): 2025 Jan 30;
[PubMed:39883424] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Depow GJ, Oldemburgo de Mello V, Inzlicht M
A positive empathy intervention to improve well-being on Instagram.
Emotion: 2025 Jan 30;
[PubMed:39883419] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Du J, Wang S, Zhang H, Liu T, Sun S, Yang C, Zaller N, Dai Z, Zha H, Zhao Y, Zhao Y, Hu X, Yan H, Gao P, Wang J, Sun Y, Zhang Z, Don O
Pre-exposure Prophylaxis (PrEP) Awareness and Engagement Among MSM at High Risk of HIV Infection in China: A Multi-City Cross-Sectional Survey.
AIDS Behav: 2025 Jan 30;
[PubMed:39883368] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Seo J, Singh R, Choi JH
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions.
J Chem Inf Model: 2025 Jan 30;
[PubMed:39883143] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Başgöl Ş, Küçükkaya B
The Effect of Health Fatalism and Health-Seeking Behaviors on the Frequency of Non-Medication Coping Strategy Use in Women with Urinary Incontinence in Türkiye.
Int Urogynecol J: 2025 Jan 30;
[PubMed:39883124] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

López L, Calderón D, Salinas L, Graham JP, Blount ZD, Trueba G
A plasmid with the bla (CTX-M) gene enhances the fitness of Escherichia coli strains under laboratory conditions.
Microbiology (Reading): 2025 Jan, 171(1);
[PubMed:39883084] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Bleiweis M, Stukov Y, Kugler LR, Bilgili A, Peek GJ, Jacobs JP
Berlin Heart EXCOR sVAD implantation technique for neonates and infants with functionally univentricular ductal-dependent systemic circulation.
Multimed Man Cardiothorac Surg: 2025 Jan 30, 2025;
[PubMed:39883029] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Kumar Y, Basu S, Chatterji D, Ghosh A, Jayaraman N, Maiti PK
Self-Assembly of Mycolic Acid in Water: Monolayer or Bilayer.
Langmuir: 2025 Jan 30;
[PubMed:39882987] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Christodoulou I, Gkaniatsou E, Steunou N, Kisserli A, Cohen JHM, Haouas M, Sicard C
Screening of Aluminum-Based MOFs for Effective In Situ Immobilization of Biomolecules.
Inorg Chem: 2025 Jan 30;
[PubMed:39882866] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Coyle D, Ormandy P, Fernandes da Silva N, Davies S, BISTRO trial investigators
Public and patient involvement (PPI) in the design, execution and dissemination of a trial: the BISTRO trial.
Health Technol Assess: 2025 Jan 29;1-18
[PubMed:39882698] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Joshi R, Kilinsky A
HPV vaccine hesitancy in the United States.
Curr Opin Pediatr: 2025 Jan 23;
[PubMed:39882684] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Rajagopal T, Chandrashekaran V
"Leaving no one behind": digital empathy and inclusive media literacy education for young adults on the autism spectrum.
Int J Dev Disabil: 2025, 71(1);190-202
[PubMed:39882414] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Zavala CFC, Porta OA, Martín A, Valderrama EV, Lis MDR, Pachacama WG, Soto D
Concurrent validity of a new screening test to evaluate the information processing speed.
Dement Neuropsychol: 2025, 19;e20240183
[PubMed:39882254] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Qiang Q, Zhang Z, Li X, Li C, Mao M, Ding X, Zhang J, Li S, Lai Z, Yang J, Cao P, Ye W, Wang S, Yang J
The amino acid permease SlAAP6 contributes to tomato growth and salt tolerance by mediating branched-chain amino acid transport.
Hortic Res: 2025 Jan, 12(1);uhae286
[PubMed:39882176] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Kuang Y
Cyber anti-intellectualism and science communication during the COVID-19 pandemic: a cross-sectional study.
Front Public Health: 2024, 12;1491096
[PubMed:39882127] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Yang DM, Min FL, Li Y, Ling JL, Zhong HX, Xia YC, Feng Y, Zhao LY, Li ZH, Wen LL
Interaction between nitrate and trichloroethene bioreduction in mixed anaerobic cultures.
Front Microbiol: 2024, 15;1504235
[PubMed:39881997] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Ábrahám Á, Gyulai G, Mihály J, Horváth A, Dobay O, Varga Z, Kiss É, Horváti K
Optimizing lipopeptide bioactivity: The impact of non-ionic surfactant dressing.
J Pharm Anal: 2024 Dec, 14(12);101020
[PubMed:39881961] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Tajane SB, Pawar S, Mohite ST, Patil SR
Comparative Analysis of In-House and Commercially Available Media for Determining the Antifungal Susceptibility Profile of Candida Species.
Cureus: 2024 Dec, 16(12);e76591
[PubMed:39881933] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Nkaiwuatei J, Hamza H, Akbi S, Muzondo N
Enhancing the general public knowledge of antimicrobial resistance (AMR) in Africa: a video-based Brief Educational Resource Review.
JAC Antimicrob Resist: 2025 Feb, 7(1);dlaf005
[PubMed:39881798] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Gardner S, Bezati G, Godfrey T, Baird K, Bilal U, Loudon E, Young R, MacKenzie LE
Analysis of over 1600 chemistry YouTube channels from 2005 to 2023.
R Soc Open Sci: 2025 Jan, 12(1);241599
[PubMed:39881790] [WorldCat.org: ISSN ESSN ] [DOI] ( )

van Maanen JC, Bach FC, Snuggs JW, Ito K, Wauben MHM, Le Maitre CL, Tryfonidou MA
Explorative Study of Modulatory Effects of Notochordal Cell-Derived Extracellular Vesicles on the IL-1β-Induced Catabolic Cascade in Nucleus Pulposus Cell Pellets and Explants.
JOR Spine: 2025 Mar, 8(1);e70043
[PubMed:39881783] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Spee BTM, Stap TB, Plijnaer M, Pasman G, Zeggio S, Duits A, Crone JS, Haeyen S, Pelowski M, Bloem BR, Koksma JJ
Co-creating a person-centered creative engagement intervention for Parkinson's care.
Front Psychol: 2024, 15;1469120
[PubMed:39881707] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Cubelo F
A Courageous Journey of a Foreign-Born Intensive Care Unit Nurse in Finland: A Narrative Case Study.
Policy Polit Nurs Pract: 2025 Jan 29;15271544241309312
[PubMed:39881562] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Mehta S, Wang E, McMullen E, Abdi P, Metko D, Grewal R, Vender R
A Cross-Sectional Analysis of Psoriasis Patient Experiences on YouTube and TikTok.
J Cutan Med Surg: 2025 Jan 29;12034754251316293
[PubMed:39881532] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Spiegel DY, Friesner ID, Zhang W, Zack T, Yan G, Willcox J, Prionas N, Singer L, Park C, Hong JC
Exploring the Social Media Discussion of Breast Cancer Treatment Choices: Quantitative Natural Language Processing Study.
JMIR Cancer: 2025 Jan 28, 11;e52886
[PubMed:39881478] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Zhao J, Zhang S, Gong Z, Mao W, Bao W, Li Q, Bai Y, Gao F, Feng S
NLRP3: a key regulator of skin wound healing and macrophage-fibroblast interactions in mice.
Cell Commun Signal: 2025 Jan 29, 23(1);55
[PubMed:39881348] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Almarzouki AF, Alem A, Shrourou F, Kaki S, Khushi M, Mutawakkil A, Bamabad M, Fakharani N, Alshehri M, Binibrahim M
Assessing the disconnect between student interest and education in artificial intelligence in medicine in Saudi Arabia.
BMC Med Educ: 2025 Jan 30, 25(1);150
[PubMed:39881303] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Nylén-Eriksen M, Stojiljkovic M, Lillekroken D, Lindeflaten K, Hessevaagbakke E, Flølo TN, Hovland OJ, Solberg AMS, Hansen S, Bjørnnes AK, Tørris C
Game-thinking; utilizing serious games and gamification in nursing education - a systematic review and meta-analysis.
BMC Med Educ: 2025 Jan 29, 25(1);140
[PubMed:39881301] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Özen Çınar İ, Özkaya Bozkurt E
Digital Motherhood in the Postpartum Period: A Descriptive Study.
Matern Child Health J: 2025 Jan 29;
[PubMed:39881098] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Lakatos D, Kovács B, Czigler I, Demetrovics Z, File D
Wanting and liking of Facebook functions and their correlation to problematic use.
Sci Rep: 2025 Jan 29, 15(1);3643
[PubMed:39880878] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Shah AP, Majeti KR, Ekman FK, Selvaraj S, Sharma D, Sinha R, Soupene E, Chati P, Luna SE, Charlesworth CT, McCreary T, Lesch BJ, Tran T, Chu SN, Porteus MH, Kyle Cromer M
Engineering synthetic signaling receptors to enable erythropoietin-free erythropoiesis.
Nat Commun: 2025 Jan 29, 16(1);1140
[PubMed:39880867] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Kang S, Kim J, Kim S, Chun H, Heo J, Reboul CF, Meana-Pañeda R, Van CTS, Choi H, Lee Y, Rhee J, Lee M, Kang D, Kim BH, Hyeon T, Han B, Ercius P, Lee WC, Elmlund H, Park J
Time-resolved Brownian tomography of single nanocrystals in liquid during oxidative etching.
Nat Commun: 2025 Jan 29, 16(1);1158
[PubMed:39880816] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Vega-Macaya F, Villarreal P, Peña TA, Abarca V, Cofré AA, Oporto CI, Mardones W, Nespolo RF, Cubillos FA
Experimental Evolution and Hybridization Enhance the Fermentative Capacity of Wild Saccharomyces eubayanus Strains.
FEMS Yeast Res: 2025 Jan 29;
[PubMed:39880790] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Dean S, Torbey S
When It's Not Tics: Functional Tic-Like Behaviors.
Psychiatr Clin North Am: 2025 Mar, 48(1);151-163
[PubMed:39880510] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Martinenaite E, Lecoq I, Aaboe-Jørgensen M, Ahmad SM, Perez-Penco M, Glöckner HJ, Chapellier M, Lara de la Torre L, Olsen LR, Rømer AMA, Pedersen AW, Andersen MH
Arginase-1-specific T cells target and modulate tumor-associated macrophages.
J Immunother Cancer: 2025 Jan 29, 13(1);
[PubMed:39880485] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Brown JM, Tahir S, Franco-Arellano B, LeSage A, Hughes J, Kapralos B, Lou W, Vogel E, Farkouh M, Tugault-Lafleur C, Arcand J
Efficacy of the Foodbot Factory digital curriculum-based nutrition education intervention in improving children's nutrition knowledge, attitudes and behaviours in elementary school classrooms: protocol for a cluster randomised controlled trial.
BMJ Open: 2025 Jan 28, 15(1);e092426
[PubMed:39880422] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Budhwani H, Yigit I, Bruce J, Bond CL, Johnson A
Adolescent Youth Survey on HIV Prevention and Sexual Health Education in Alabama: Protocol for a Web-Based Survey With Fraud Protection Study.
JMIR Res Protoc: 2025 Jan 29, 14;e63114
[PubMed:39880394] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Benabdderrahmane K, Stirnemann J, Ramtani S, Falentin-Daudré C
Biodegradation study in FBS media of polycaprolactone patch as a potential prenatal treatment for myelomeningocele.
J Biomater Appl: 2025 Jan 29;8853282251316894
[PubMed:39880383] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Agam N, Dolgin V, Star A, Freund O, Jean MM, Safran A, Poleg T, Zahger D, Birk OS
Mitral Valve Prolapse Caused by TLL1 Gain-of-Function Mutation.
Can J Cardiol: 2025 Jan 27;
[PubMed:39880331] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Lian C, Wei MT, Liu XJ, Li XL, Zhang XF
Comment on "The use of plastic, disposable combs for hair retraction in dermatologic surgery".
J Am Acad Dermatol: 2025 Jan 27;
[PubMed:39880173] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Nguyen MA, Williams C, Gard AL, Connor JH
Endothelial Growth Media Components Alters SARS-CoV-2 Spike-Directed Growth Kinetics.
J Virol Methods: 2025 Jan 27;115111
[PubMed:39880099] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ramírez NS, Lining D, Albertó E, Pose G
Effect on viability and yield on Pleurotus pulmonarius and Ganoderma lucidum after 3 years of cryopreservation without cryoprotectants.
Cryobiology: 2025 Jan 27;105204
[PubMed:39880070] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Bernard J, Kim JK, Morrison B, Spencer K, Rasper A, Bylund J, Grant C, Dropkin B
Website Transparency and Information Dissemination among Urology Residency Programs.
Urology: 2025 Jan 27;
[PubMed:39880046] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Alvarado Garcia A, Rahman L, J Gregoski M, Andrade I Jr
Comparison of patient testimonials of orthognathic surgery on YouTube and TikTok.
Angle Orthod: 2025 Jan 30;
[PubMed:39880020] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Akinyede O, Yustyniuk V, Ochwo S, Aworh M, Wilkins M
Preliminary exploration of ChatGPT-4 shows the potential of generative artificial intelligence for culturally tailored, multilingual antimicrobial resistance awareness messaging.
Am J Vet Res: 2025 Jan 29;1-6
[PubMed:39879655] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Thomas J, Lucht A, Segler J, Wundrack R, Miché M, Lieb R, Kuchinke L, Meinlschmidt G
An Explainable Artificial Intelligence Text Classifier for Suicidality Prediction in Youth Crisis Text Line Users: Development and Validation Study.
JMIR Public Health Surveill: 2025 Jan 29, 11;e63809
[PubMed:39879608] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Alexander KL, Naman CB, Iwasaki A, Mangoni A, Leao T, Reher R, Petras D, Kim H, Ternon E, Caro-Diaz EJE, Glukhov E, Mitrevska JA, Avalon NE, Duggan BM, Gerwick L, Gerwick WH
Fatuamide A, a Hybrid PKS/NRPS Metallophore from a Leptolyngbya sp. Marine Cyanobacterium Collected in American Samoa.
J Nat Prod: 2025 Jan 29;
[PubMed:39879528] [WorldCat.org: ISSN ESSN ] [DOI] ( a) 

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"