ISA

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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

Zhao X, Sun SB
Educational Heterogeneity in the Relationship Between Internet Use and Episodic Memory Among Older Adults.
J Geriatr Psychiatry Neurol: 2025 Apr 1;8919887251330311
[PubMed:40170195] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Asghar Vahedi F, Gholizadeh L, Khajehei M
Knowledge and Awareness of Cardiovascular Risk Factors Among Women With a History of Pregnancy Complications in Australia: A World Heart Federation Cross-Sectional Study.
Aust N Z J Obstet Gynaecol: 2025 Apr 1;
[PubMed:40170108] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Zhang Y, Zheng L, Wang X, Shen X, Feng Y, Niu Y, Cai W
Understanding global mobility of dietetic talents: a survey study of overseas-educated dietetic returnees in China.
Global Health: 2025 Apr 1, 21(1);15
[PubMed:40170102] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Dekhissi A, Taik FZ, Aharrane FZ, Adnine A, Takhrifa N, Fourtassi M, Abourazzak FE
Social media as a source of information for patients with knee osteoarthritis.
BMC Musculoskelet Disord: 2025 Apr 1, 26(1);315
[PubMed:40169994] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Slettmyr A, Schandl A, Arman M, Hugelius K
Fight or flight-intensive care nurses' decisions to resign following the COVID-19 pandemic: a phenomenological hermeneutical study.
BMC Nurs: 2025 Apr 1, 24(1);360
[PubMed:40169987] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Mayo NE, Brouillette MJ, Falcone EL, Fellows LK
A patient-centered view of symptoms, functional impact, and priorities in post-COVID-19 syndrome: cross-sectional results from the Québec Action Post-COVID cohort.
BMC Infect Dis: 2025 Apr 2, 25(1);456
[PubMed:40169972] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Xu C, Wu M, Zhang X, Shen K, Guo Y, Yuan J, Zhu H
Carotid intima thickness and elasticity combined with MHR predicting the severity of coronary artery stenosis in patients with premature coronary artery disease.
BMC Cardiovasc Disord: 2025 Apr 1, 25(1);241
[PubMed:40169942] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Schinaia C
Catastrophism and catastrophic images: Ferenczi's identification with the aggressor and Ogden's autistic-contiguous position as defence mechanisms.
Am J Psychoanal: 2025 Apr 1;
[PubMed:40169868] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Al-Anazi RG, Alzaidi MSA, Eltahir MM, Alkhiri H, Alajmani SH, Darem AA, Alshahrani M, Alhebaishi N
An adaptive search mechanism with convolutional learning networks for online social media text summarization and classification model.
Sci Rep: 2025 Apr 1, 15(1);11058
[PubMed:40169845] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Yun K, Seo Y, Oh Y, Kim S, Maeng HS, Cho JG, Son YB, Son DJ, Kwon K, Kim S, Jo H, Park H
Lysyl-tRNA synthetase 1 promotes atherogenesis via autophagy-related secretion and inflammation.
Sci Rep: 2025 Apr 1, 15(1);11099
[PubMed:40169806] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Shim SR, Shin J, Hwang CM, Kim YK, Park JB, Kim JY
Tranexamic acid in ear surgery: enhancing surgical field visibility and reducing bleeding-a systematic review and meta analysis.
Sci Rep: 2025 Apr 1, 15(1);11132
[PubMed:40169708] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Sultan NA, Hamama HH, Grawish ME, El-Toukhy RI, Mahmoud SH
Impact of different capping materials extracts on proliferation and osteogenic differentiation of cultured human dental pulp stem cells.
Sci Rep: 2025 Apr 1, 15(1);11140
[PubMed:40169700] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Pazoki H, Anbia M
Kinetic and isotherm studies of cr (VI) adsorption from aqueous media by using a synthetic chitosan-allophane nanocomposite.
Sci Rep: 2025 Apr 1, 15(1);11088
[PubMed:40169671] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Chwalek P, Kuronaga M, Zhu I, Montague S, Campopiano Robinson V, Lohrmann J, Gil CAV, Susič D, Gradišek A, Schul J, Paradiso JA, Arbetman M
High-Res Acoustic and Environmental Data to Monitor Bombus dahlbomii Amid Invasive Species, Habitat Loss.
Sci Data: 2025 Apr 1, 12(1);548
[PubMed:40169623] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Evich MG, Ferreira J, Adeyemi O, Schroeder PA, Williams JC, Acrey B, Burdette D, Grieve M, Neill MP, Simmons K, Striggow BC, Cohen SB, Cyterski M, Glinski DA, Henderson WM, Kim DY, Washington JW
Mineralogical controls on PFAS and anthropogenic anions in subsurface soils and aquifers.
Nat Commun: 2025 Apr 1, 16(1);3118
[PubMed:40169557] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Pablo JN, Shires J, Castellanos J, Kapila M, Kemmelmeier LL, Berryhill ME
Changed detection: No relationship between working memory and media usage in Covid-era and contemporary young adults.
Atten Percept Psychophys: 2025 Apr 1;
[PubMed:40169525] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ip S, Angelo C, Cohen P, Tinker E, Andronicos A, Dickson M
Smoke-Free Home: Developing an Aboriginal Health Promotion and Social Marketing Campaign in Western Sydney, Australia.
Health Promot J Austr: 2025 Apr, 36(2);e949
[PubMed:40169488] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Billias N, MacEachen E
Capturing the Perspectives of "Laypeople" on Policy Effectiveness: Employers' and Precariously Employed Workers' Suggested Improvements for the Workers' Compensation System and Work Injury Processes.
J Occup Rehabil: 2025 Apr 1;
[PubMed:40169468] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Yao T, Kobayashi H, Hirai T, Tokuoka Y, Tokoro M, Asayama Y, Suzuki Y, Hatano Y, Ikeda H, Sugimura S, Yamamoto T, Yamada TG, Hosoi Y, Funahashi A, Fukunaga N, Asada Y, Kurimoto K, Yamagata K
Zinc eluted from glassware is a risk factor for embryo development in human and animal assisted reproduction†.
Biol Reprod: 2025 Apr 2;
[PubMed:40169168] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Wu Y, Kemps E, Prichard I
"Mind your figure! Watch, but don't eat": A content analysis of eating and appearance-related messages in eating videos on social media.
Body Image: 2025 Mar 31, 53;101883
[PubMed:40168938] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Han Y, Xiong G, Yang S, Luo X, Zan F, Wu X, Chen G
Role of biogas stirring in alleviating acidification and promoting methanogenesis during the anaerobic digestion of food waste: Macroscale and microscale perspectives.
Waste Manag: 2025 Mar 31, 200;114761
[PubMed:40168895] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ghosh R, Bernar J
An injection filling method for packing chromatography devices.
J Chromatogr A: 2025 Mar 26, 1749;465913
[PubMed:40168792] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Fadillah D
Unveiling the psychological impact of social media on adolescents in Indonesia: Implications for research and practice.
Asian J Psychiatr: 2025 Mar 25, 107;104463
[PubMed:40168702] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

van der Molen AJ, Laguna JJ, van de Ven AAJM, Vega F
Very rare adverse reactions to intravascular contrast media: From Kounis to sweet syndrome.
Eur J Radiol: 2025 Mar 25, 187;112066
[PubMed:40168697] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Chakraborty R, Beidelman ET, Klein M, Kobayashi LC, Eyal K, Kabudula CW, Rosenberg M
Expanded child support grant eligibility and later-life mortality among mothers in rural South Africa.
Glob Public Health: 2025 Dec, 20(1);2483870
[PubMed:40168537] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Hegelmann M, Cokoja M
Two-Phase Epoxidations with Micellar Catalysts: Insights, Limitations, and Perspectives.
Chempluschem: 2025 Apr 1;e202500122
[PubMed:40168424] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Godjo A, Donald DM, Ansaldi L, Darwish IAA, Byrne JL, Kakouli-Duarte T
Effects of hexavalent chromium on the biology of Steinernema feltiae: evaluating sublethal endpoints for ecotoxicity testing.
PLoS One: 2025, 20(4);e0320329
[PubMed:40168372] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Islek D, Sanchez T, Baral S, Brown C, Caldwell JA, Glick JL, Nestadt DF, Jones J, Lucas IL, Sarkar S, de Ruiter A, Sullivan PS, Valentine-Graves M, Winter S, Vannappagari V
Preferences and willingness for starting daily, on-demand, and long-acting injectable HIV pre-exposure prophylaxis among transfeminine persons in the US, 2022-2023.
PLoS One: 2025, 20(4);e0320961
[PubMed:40168367] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Abuhay HW, Alemu GG, Aweke MN, Alemu TG, Mengistu B, Mesfin A
Clinical breast cancer screening uptake and associated factors among reproductive age women in Kenya: further analysis of Kenyan Demographic and Health Survey 2022.
PLoS One: 2025, 20(4);e0320730
[PubMed:40168342] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Matsukubo J, Dickson S, Xiao J, Friesen EL, Solmi M, Fiedorowicz JG, Fischer B, Myran DT
Psilocybin Dispensaries and Online Health Claims in Canada.
JAMA Netw Open: 2025 Apr 1, 8(4);e252853
[PubMed:40168023] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Deng Y, Iliuk A, Tao WA, Xie Z
Phosphoproteomics of Cerebrospinal Fluid-Derived Extracellular Vesicles Applied to Primary Central Nervous System Lymphoma.
Methods Mol Biol: 2025, 2914;115-125
[PubMed:40167915] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Buscho SE, Slater N, Srinivasan S, Gupta PK
Association of Twitter author Altmetric patterns with research impact in ophthalmology.
Int Ophthalmol: 2025 Apr 1, 45(1);136
[PubMed:40167899] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Ritter C
[Digital learning methods in pharmacy].
Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz: 2025 Apr 1;
[PubMed:40167765] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Topper B, Benton A, Terry R, Pettes M, Ballato J, Kolis J, Dong L
Yb:Lu(2)O(3) single-crystal fiber: spectroscopy, amplification, and lasing.
Opt Lett: 2025 Apr 1, 50(7);2278-2281
[PubMed:40167700] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Wang W, Eisenberg Y, Chen YH, Xu C, Wise F
Efficient temporal compression of 10-μJ pulses in periodic layered Kerr media: publisher's note.
Opt Lett: 2025 Apr 1, 50(7);2158
[PubMed:40167668] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Rolin D, Mettman KM
Trending on TikTok: The Ever-Expanding/Increasingly Elastic Definition of Psychiatric Diagnoses Meets Social Media.
J Psychosoc Nurs Ment Health Serv: 2025 Apr, 63(4);3-5
[PubMed:40167458] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Slavkova KP, Kang R, Kazerouni AS, Biswas D, Belenky V, Chitalia R, Horng H, Hirano M, Xiao J, Corsetti RL, Javid SH, Spell DW, Wolff AC, Sparano JA, Khan SA, Comstock CE, Romanoff J, Gatsonis C, Lehman CD, Partridge SC, Steingrimsson J, Kontos D, Rahbar H
MRI-based Radiomic Features for Risk Stratification of Ductal Carcinoma in Situ in a Multicenter Setting (ECOG-ACRIN E4112 Trial).
Radiology: 2025 Apr, 315(1);e241628
[PubMed:40167440] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Inman R, Warris A, Bignell E
A novel pan-fungal screening platform for antifungal drug discovery: proof of principle study.
Antimicrob Agents Chemother: 2025 Apr 1;e0132824
[PubMed:40167378] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Tejedor-Tejada J, Martínez-Domínguez SJ, Hernández L, Cano-Català A, Parra P, Moreira L, Nyssen OP, Gisbert JP, Hp‐EuReg Investigators
Management of Helicobacter pylori Infection in Spain Beyond the Data Collected in the European Registry on H. pylori Management (Hp-EuReg): Results of a Nationwide Survey.
Helicobacter: 2025 Mar-Apr, 30(2);e70028
[PubMed:40167351] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Dudzinski KM, Manitzas Hill HM
Stakeholder Perspectives Regarding Captive Marine Mammals-How Can We Compromise?
Zoo Biol: 2025 Apr 1;
[PubMed:40167322] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Rahmani B, Shokrian N, Mahmoud AA, Rajkumar S, Park JB, Fanning J, Chidester JR, Lee BT
The Quality of Information About Body Dysmorphia on TikTok.
Ann Plast Surg: 2025 Apr 1, 94(4S Suppl 2);S395-S400
[PubMed:40167106] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Mashadi AH, Essa Y, Said SM
Anatomical repair for late presentation of congenitally corrected transposition of the great arteries with ventricular septal defect and left ventricular outflow tract obstruction in an 18-year-old.
Multimed Man Cardiothorac Surg: 2025 Apr 1, 2025;
[PubMed:40167036] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Muller L, Estevenon P, Tamain C, Dacheux N, Clavier N
Precipitation of morphology-controlled uranium(VI) peroxide in nitric acid media.
Dalton Trans: 2025 Apr 1;
[PubMed:40167022] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ullah A, Shah A, Chen SE, Shah A, Rodriguez-Ramos JC, Zaman R, Erbilgin N
Alliance Between Conifer Trees and Endophytic Fungi Against Insect Defoliators.
Plant Cell Environ: 2025 Apr 1;
[PubMed:40166909] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Naseem M, Tahir M, Dai J, Qu L, Nisa FU, Ahmad W, Shahbaz I, Ma Z, Khan AU, He L
Tuning the Catalytic Activity of MoS2-x-NbSx Heterostructure Nanosheets for Bifunctional Acidic Water Splitting.
Small: 2025 Apr 1;e2501464
[PubMed:40166825] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Mølhave M, Ovesen T, Madzak A
Effects of visual guidance and instrument choice on symptom recurrence following adenoidectomy: a systematic review of randomized controlled trials.
BMJ Surg Interv Health Technol: 2025, 7(1);e000370
[PubMed:40166698] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Dai HD, Kerns E, Niebur H, Deschamp A, Johnson R, Samson K, Buckley J, Woolsey S
Developing a media literacy-based e-cigarette education program via medical record systems.
Tob Prev Cessat: 2025, 11;
[PubMed:40166492] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Mita T, Katakami N, Yoshii H, Onuma T, Kaneto H, Osonoi T, Shiraiwa T, Yasuda T, Umayahara Y, Yamamoto T, Yokoyama H, Kuribayashi N, Matsumoto K, Gosho M, Shimomura I, Watada H, Collaborators on the Sitagliptin Preventive study of Intima media thickness Evaluation (SPIKE) Trial
Long-term efficacy and safety of early sitagliptin initiation in individuals with type 2 diabetes: an extension of the SPIKE study.
Diabetol Int: 2025 Apr, 16(2);272-284
[PubMed:40166439] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Hu J, Xiao W
What are the influencing factors of online learning engagement? A systematic literature review.
Front Psychol: 2025, 16;1542652
[PubMed:40166394] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Daraei OM, Singh AK, Mohapatra S, Mallick MS, Kotnala A, Shih WC
Microfluidic Nano-Plasmonic Imaging Platform for Purification- and Label-Free Single Small Extracellular Vesicle Counting.
bioRxiv: 2025 Mar 18;
[PubMed:40166220] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Mazelis I, Sun H, Kulkarni A, Torre T, Klein AM
Multi-step genomics on single cells and live cultures in sub-nanoliter capsules.
bioRxiv: 2025 Mar 17;
[PubMed:40166192] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Li X, Zhang X, Liu T, Zhang G, Chen D, Lin S
Identification of immune characteristic biomarkers and therapeutic targets in cuproptosis for rheumatoid arthritis by integrated bioinformatics analysis and single-cell RNA sequencing analysis.
Front Med (Lausanne): 2025, 12;1520400
[PubMed:40166070] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Li Y, Viswaroopan D, He W, Li J, Zuo X, Xu H, Tao C
Enhancing Relation Extraction for COVID-19 Vaccine Shot-Adverse Event Associations with Large Language Models.
Res Sq: 2025 Mar 17;
[PubMed:40166033] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Xu B, Qiu W, Gao X, Ni H, Tao X, Sun L, Lyu W
Advances in microbial degradation of skatole: A review.
Curr Res Microb Sci: 2025, 8;100378
[PubMed:40165934] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Gökkaya İ, Renda G, Ayhan F, Yazici N
Awareness of Apitherapy: a study of healthcare professionals in Türkiye.
J Pharmacopuncture: 2025 Mar 31, 28(1);35-46
[PubMed:40165878] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Köse DB, Oksa R, Savela N, Latikka R, Oksanen A
The Effect of Professional Social Media Usage on Procrastination and Work Engagement in the Face of the COVID-19 Pandemic.
Scand J Psychol: 2025 Apr 1;
[PubMed:40165754] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Anderson DJ, Troxel WM, Landvatter J, Baron KG
A randomized pilot study of a wearable device using variable complex weak magnetic fields among participants with insomnia symptoms.
J Clin Sleep Med: 2025 Apr 1;
[PubMed:40165746] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Chang CH, Cook-Patton SC, Erbaugh JT, Lu L, Masuda YJ, Molnár I, Papp D, Robinson BE
New opportunities and challenges for conservation evidence synthesis from advances in natural language processing.
Conserv Biol: 2025 Apr, 39(2);e14464
[PubMed:40165707] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Reinhart AM, Tian Y, Lilly AE
Get Vaccinated Now, But the Choice is Up to You: Framing, Psychological Reactance, and Autonomy Restoration Scripts for COVID-19 Vaccine Hesitancy.
Health Commun: 2025 Mar 31;1-12
[PubMed:40165490] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Howard MC
What is Home? Creating a Psychological-Based Framework of Home With Basic Psychological Needs Theory.
Psychol Rep: 2025 Mar 31;332941251329850
[PubMed:40165485] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Meenan R, Buller DB, Berteletti J, Henry KL, Buller MK, Cutter GR, Pagoto S, Adjei I, Chirico N
Economic Evaluation of Two Scalability Strategies for Nationwide Dissemination of an Occupational Sun Safety Intervention in a Randomized Trial.
J Occup Environ Med: 2025 Mar 14;
[PubMed:40165481] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Jones LL, Norville GA, Wunder ZI
Spontaneous Mind Wandering and Smartphone Use.
Psychol Rep: 2025 Mar 31;332941251330555
[PubMed:40165464] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Banerji A, Moore J, Waldron JL, Wolfson AR, Saff RR
Optimising Strategies for Patients With Prior Immediate Iodinated Contrast Media Reactions: Premedication or Changing Agents?
Clin Exp Allergy: 2025 Mar 31;
[PubMed:40165408] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Liang Y, Han X, Zhou T, Xiao C, Shi C, Wei X, Wu H
Diagnostic model using LI-RADS v2018 for predicting early recurrence of microvascular invasion-negative solitary hepatocellular carcinoma.
Cancer Imaging: 2025 Mar 31, 25(1);46
[PubMed:40165325] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Saleh SM, Aljamala A, Hafez D, Shqeer MA, Abukandil I, Aldiban W, Baraka A, DARS Consortium
Knowledge, attitude, practice, and barriers among physicians in the Middle East and North Africa region toward influenza vaccination for the high-risk group of patients: a cross-sectional study.
Trop Dis Travel Med Vaccines: 2025 Apr 1, 11(1);6
[PubMed:40165278] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Sheng K, Bisson DG, Saran N, Bourdages J, Coluni C, Upshaw K, Tiedemann K, Komarova SV, Ouellet JA, Haglund L
The TLR-M-CSF axis is implicated in increased bone turnover and curve progression in adolescent idiopathic scoliosis.
Arthritis Res Ther: 2025 Mar 31, 27(1);68
[PubMed:40165259] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Lukka L, Vesterinen M, Salonen A, Bergman VR, Torkki P, Palva S, Palva JM
User journey method: a case study for improving digital intervention use measurement.
BMC Health Serv Res: 2025 Apr 1, 25(1);479
[PubMed:40165237] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Latonen S, Juppo AM, Seeck H, Airaksinen M
Crisis management in Finnish hospital pharmacies during the COVID-19 pandemic.
BMC Health Serv Res: 2025 Mar 31, 25(1);474
[PubMed:40165229] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Wang W, Zhang W
Media portrayals and social stigma surrounding COVID-19 survivors: a content analysis of Chinese media coverage.
BMC Public Health: 2025 Mar 31, 25(1);1222
[PubMed:40165144] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Zhu Z, Wu K, Lu J, Dai S, Xu D, Fang W, Yu Y, Gu W
Gd-EOB-DTPA-enhanced MRI radiomics and deep learning models to predict microvascular invasion in hepatocellular carcinoma: a multicenter study.
BMC Med Imaging: 2025 Mar 31, 25(1);105
[PubMed:40165094] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Rasero J, Verstynen TD, DuPont CM, Kraynak TE, Barinas-Mitchell E, Scudder MR, Kamarck TW, Sentis AI, Leckie RL, Gianaros PJ
Stressor-Evoked Brain Activity, Cardiovascular Reactivity, and Subclinical Atherosclerosis in Midlife Adults.
J Am Heart Assoc: 2025 Mar 31;e034908
[PubMed:40165059] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hidaka H, Sakagami T, Noda Y, Shimamura A, Iwai H
Evidence Showing Three Layers of Reconstructed Tympanic Membrane After Second Regenerative Treatment.
Otol Neurotol: 2025 Mar 20;
[PubMed:40164997] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Larrow DR, Cohen MS
Endoscopic Approach for Tympanostomy Tube Insertion in Patients With Trisomy 21.
Otol Neurotol: 2025 Mar 26;
[PubMed:40164993] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Eom T, Jeong B, Kim SH, Choi SW, Oh SJ, Kong SK, Lee IW, Lee HM
Changes in the Incidence of Pediatric Otitis Media Pre- and Post-COVID-19 Pandemic in South Korea: A Study Utilizing a HIRA-Customized Cohort for the Population Aged ≤18 Years.
Otol Neurotol: 2025 Mar 19;
[PubMed:40164975] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Martínez Tolibia SE, Díaz Pacheco A, Villalobos López MÁ, Pacheco Cabañas RK, Cabrera R, Rocha J, López Y López VE
The role of AbrB from plate to bioreactor: implications of induced expression on physiological and metabolic responses in Bacillus thuringiensis.
World J Microbiol Biotechnol: 2025 Apr 1, 41(4);120
[PubMed:40164926] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Lofton-Tomenius H, Pang Y, Pallin A, Myktybekova Z, Lelham N, Riesbeck K, Vågesjö E, Roos S, Phillipson M
In Vitro Elimination of Highly Multidrug-Resistant Bacteria by the Lactic Acid Bacterial Drug Candidate ILP100.
Infect Dis Ther: 2025 Mar 31;
[PubMed:40164924] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Stoye E
Incredible close-up of colourful crab spiders - March's best science images.
Nature: 2025 Mar 31;
[PubMed:40164748] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ng LHX, Carley KM
A global comparison of social media bot and human characteristics.
Sci Rep: 2025 Mar 31, 15(1);10973
[PubMed:40164745] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Le Bras C, Mouchard A, Rault L, Cochet MF, Ménard O, Jacquet N, Chuat V, Valence F, Le Loir Y, Bellanger A, Deglaire A, Le Huërou-Luron I, Even S
New insights into the cultivability of human milk bacteria from ingestion to digestion and implications for their Immunomodulatory properties.
Sci Rep: 2025 Mar 31, 15(1);10985
[PubMed:40164734] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Ham BS
Coherence analysis of local randomness and nonlocal correlation through polarization-basis projections of entangled photon pairs.
Sci Rep: 2025 Mar 31, 15(1);10950
[PubMed:40164672] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Delshad Y, Rafipour D, Ghamari Kargar P, Maleki B, Ghani M
Carboxylic acids dendrimer functionalized magnetic nanoparticles for carbohydrates conversion to 5-hydroxymethylfurfural.
Sci Rep: 2025 Mar 31, 15(1);10969
[PubMed:40164641] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Chen W, Shi J, He Q
China's social fake news database release with brain structural, functional, and behavioural measures.
Sci Data: 2025 Mar 31, 12(1);538
[PubMed:40164637] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Tetteh HA, Blagogee T, Robbins D
Impact of AI on Access to Care a Three-Pronged Approach for Enhancing Access to Surgical Care: Lessons From Electrical Safety and the Impact of AI on Health Equity.
Am Surg: 2025 Mar 31;31348251329495
[PubMed:40164561] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Rasoulivalajoozi M, Cucuzzella C, Farhoudi M
Domains of wheelchair users' socio-emotional experiences: Design insights from a scoping review.
Disabil Health J: 2025 Mar 26;101829
[PubMed:40164524] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Mora A, García-Bernal D, Rodríguez-Lozano FJ, Ghilotti J, Lozano A, López-García S
Biocompatibility and osteogenic potential of novel tricalcium silicate-based materials in human dental pulp stem cells: Advancing vital pulp therapies.
Dent Mater: 2025 Mar 30;
[PubMed:40164523] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Xiong S, Yu Z, Lor M
Experiences of Hmong Women in the Perinatal Period.
J Obstet Gynecol Neonatal Nurs: 2025 Mar 28;
[PubMed:40164227] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Evans WD, Ichimiya M, Bingenheimer JB, Cantrell J, D'Esterre AP, Pincus O, Yu LQ, Hair EC
Design and Baseline Evaluation of Social Media Vaping Prevention Trial: Randomized Controlled Trial Study.
J Med Internet Res: 2025 Mar 31, 27;e72002
[PubMed:40164170] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Wang A, Li Q, Zheng H, Han L, Xue J, Yu L
Evaluation of surgical intervention for chronic suppurative otitis media in patients with hematologic diseases.
Acta Otolaryngol: 2025 Mar 31;1-5
[PubMed:40164142] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Çavdar D, Dölek M, Oğuz Ö
How reliable and useful are social media videos about stuttering? A comprehensive evaluation of content and credibility.
J Fluency Disord: 2025 Mar 26, 84;106116
[PubMed:40164034] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Maldonado AA, Lee EY, Shin AY, Spinner RJ
Stem cell therapy for peripheral nerve injury: illustrative cases.
J Neurosurg Case Lessons: 2025 Mar 31, 9(13);
[PubMed:40163996] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Wang J, Yang X, Hu C, Sun R, Xu G
Adsorption and separation of zirconium and hafnium from sulfate media by a conveniently synthesized (2,4,4-trimethylpentyl)(2-methylpropyl)phosphinic acid functionalized Merrifield Resin: A combined study of experiments and DFT calculations.
J Chromatogr A: 2025 Mar 23, 1749;465894
[PubMed:40163936] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Barnes LAJ, Rolfe MI, Barclay L, McCaffery K, Aslani P
Maternal health literacy and complementary medicine products: Information and recommendation sources used by pregnant and breastfeeding Australian women - results from a national online survey.
Midwifery: 2025 Mar 11, 145;104373
[PubMed:40163913] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Frenzel T, Wels T, Pietsch H, Schöckel L, Seidensticker P, Endrikat J
Recent Developments and Future Perspectives in Magnetic Resonance Imaging and Computed Tomography Contrast Media.
Invest Radiol: 2025 Apr 1;
[PubMed:40163898] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Khattak S, Al-Ansari A, Alfaraidhy M, Rajah F, Lacombe M, Kussmaul WG
Cardiology: What You May Have Missed in 2024.
Ann Intern Med: 2025 Apr 1;
[PubMed:40163883] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Huang KT, Ma Z, Yao L
Media-Induced and Psychological Factors That Foster Empathy Through Virtual Reality in Nursing Education: 2×2 Between-Subjects Experimental Study.
JMIR Med Educ: 2025 Mar 31, 11;e59083
[PubMed:40163855] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Yan Z, Liu J, Fan Y, Lu S, Xu D, Yang Y, Wang H, Mao J, Tseng HC, Chang TH, Chen Y
Ability of ChatGPT to Replace Doctors in Patient Education: Cross-Sectional Comparative Analysis of Inflammatory Bowel Disease.
J Med Internet Res: 2025 Mar 31, 27;e62857
[PubMed:40163853] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Maheux AJ, Maes C, Burnell K, Bauer DJ, Prinstein MJ, Telzer EH
Social media are many things: Addressing the components and patterns of adolescent social media use.
Ann N Y Acad Sci: 2025 Mar 31;
[PubMed:40163706] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Morena N, Htite ED, Ahisar Y, Hayman V, Rentschler CA, Meguerditchian AN
Breast Cancer Vlogs on YouTube: Descriptive and Content Analyses.
JMIR Infodemiology: 2025 Mar 31, 5;e66812
[PubMed:40163648] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Stephen DA, Nordin A, Johansson UB, Nilsson J
eHealth Literacy and Its Association With Demographic Factors, Disease-Specific Factors, and Well-Being Among Adults With Type 1 Diabetes: Cross-Sectional Survey Study.
JMIR Diabetes: 2025 Mar 31, 10;e66117
[PubMed:40163628] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Levitz P, Michot L, Malikova N, Scheel M, Weitkamp T
Probing particle dynamics in a fully opaque porous network using X-ray differential dynamic radiography (XDDR).
Soft Matter: 2025 Mar 31;
[PubMed:40163621] [WorldCat.org: ISSN ESSN ] [DOI] ( a) 

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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>

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