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

Takahashi M, Sawada Y, Aoyagi H
A forced aeration system for microbial culture of multiple shaken vessels suppresses volatilization.
Arch Microbiol: 2024 May 5, 206(6);246
[PubMed:38704767] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Clausen MC, Printz T, Nikoghosyan-Bossen G
The influence of tight tongue-ties and tongue-tie clips on speech development.
Ugeskr Laeger: 2024 Apr 29, 186(18);
[PubMed:38704717] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Erickson SJ, Yabes JG, Han Z, Roumelioti ME, Rollman BL, Weisbord SD, Steel JL, Unruh ML, Jhamb M
Associations Between Social Support and Patient-Reported Outcomes in Hemodialysis Patients: Results from the TACcare Study.
Kidney360: 2024 May 3;
[PubMed:38704664] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ni J, Ye D, Zeng W, Ma S, Wang Z, Kuang Y, Yang L
Promotion of hair growth by a conditioned medium from human umbilical cord mesenchymal stem cells cultivated in a 3D scaffold of gelatin sponge.
Eur J Med Res: 2024 May 4, 29(1);270
[PubMed:38704575] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Rolke K, Walter J, Weckbecker K, Münster E, Tillmann J
Identifying gaps in healthcare: a qualitative study of Ukrainian refugee experiences in the German system, uncovering differences, information and support needs.
BMC Health Serv Res: 2024 May 4, 24(1);585
[PubMed:38704571] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Saeidnia HR, Kozak M, Lund BD, Hassanzadeh M
Evaluation of ChatGPT's responses to information needs and information seeking of dementia patients.
Sci Rep: 2024 May 4, 14(1);10273
[PubMed:38704403] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Dalton BA, Kiefer H, Netz RR
The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media.
Nat Commun: 2024 May 4, 15(1);3761
[PubMed:38704367] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Dhalaria P, Kumar P, Verma A, Priyadarshini P, Kumar Singh A, Tripathi B, Taneja G
Exploring landscape of measles vaccination coverage: A step towards measles elimination goal in India.
Vaccine: 2024 May 3;
[PubMed:38704248] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Takagi K, Yamada M, Umeda Y
Left posterior superior mesenteric artery approach using a hanging maneuver in robotic pancreaticoduodenectomy.
J Gastrointest Surg: 2024 May, 28(5);786-788
[PubMed:38704215] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Goeteyn J, Teijink SBJ, Pesser N, van Sambeek MRHM, van Nuenen BFL, Teijink JAW
Trans-axillary thoracic outlet decompression.
Semin Vasc Surg: 2024 Mar, 37(1);66-73
[PubMed:38704186] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Mohammad A, Madhavarao CN
Comparing nitric acid treatment and microwave digestion for efficiency of metal extraction from bioprocess samples.
Anal Biochem: 2024 May 2;115555
[PubMed:38704117] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Foroughi M, Arzehgar A, Seyedhasani SN, Nadali A, Zoroufchi Benis K
Application of machine learning for antibiotic resistance in water and wastewater: A systematic review.
Chemosphere: 2024 May 2;142223
[PubMed:38704045] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Takagi K, Yasui K, Fuji T
Usefulness of Robotic-arm Hopping Technique in Robotic Left Hemihepatectomy.
J Gastrointest Surg: 2024 May 2;
[PubMed:38703988] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Li JY, Yao S, Mo Z, Miao Y, Chen Y, He W, Jin L, Tang W
Submerged plant-biochar composite system exhibits effective control over residual organic pollutants in the benthic organisms of aquaculture ponds.
Environ Pollut: 2024 May 2;124078
[PubMed:38703986] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Wu D, Chen L, Zong X, Jiang F, Wang X, Xu M, Ai F, Du W, Yin Y, Guo H
Elevated CO(2) exacerbates the risk of methylmercury exposure in consuming aquatic products: Evidence from a complex paddy wetland ecosystem.
Environ Pollut: 2024 May 2;124095
[PubMed:38703984] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Xu D, Ji Y, Du B, He B, Chen H, Sun H, Yin X
The synergistic effect of typical chiral organic acids and solution chemistry conditions on the transport of 2-arylpropionic acid chiral derivatives in porous media.
Environ Pollut: 2024 May 2;124059
[PubMed:38703979] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Yang YT
Protecting humanitarian aid workers: an urgent call.
Lancet: 2024 May 1;
[PubMed:38703780] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Su D, Wang X, Liu X, Miao J, Zhang Z, Zhang Y, Zhao L, Yu Y, Leng K, Yu Y
A comprehensive study of the colloidal properties, biocompatibility, and synergistic antioxidant actions of Antarctic krill phospholipids.
Food Chem: 2024 Apr 24, 451;139469
[PubMed:38703727] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Carroll JH, Parkin T, Cross JH, Hickson M, Williams E, Aldridge V, Collinson A
Drug-resistant epilepsy and ketogenic diet therapy - a qualitative study of families' experiences.
Seizure: 2024 Apr 26, 118;137-147
[PubMed:38703599] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ma J, Zhang T, Li J, Tian Y, Sun C
Superhydrophilic/superaerophobic CoP/CoMoO(4) multi-level hierarchitecture electrocatalyst for urea-assisted hydrogen evolution reaction in alkaline media.
J Colloid Interface Sci: 2024 May 1, 669;43-52
[PubMed:38703581] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Yan T, Lang S, Liu S, Wang S, Lin S, Cai Q, Zhao J
Strong interactions through the highly polar "Early-Late" metal-metal bonds enable single-atom catalysts good durability and superior bifunctional ORR/OER activity.
J Colloid Interface Sci: 2024 Apr 24, 669;32-42
[PubMed:38703580] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Kim E, Baek G, Jo H, Kim J, Cho A, Byun M
Nurses' media competency: A concept analysis.
Nurse Educ Today: 2024 Apr 30, 139;106232
[PubMed:38703536] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ryan CD, Griffin BT, O'Shea JP
Rationalizing Counterion Selection for the Development of Lipophilic Salts: A Case Study with Venetoclax.
Mol Pharm: 2024 May 4;
[PubMed:38703358] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Tang LK, Yobas P, Wong DNX, Pikkarainen M, Zhang R, Ho D, He HG
Personal and work-related factors associated with post-traumatic growth in nurses: A mixed studies systematic review.
J Nurs Scholarsh: 2024 May 4;
[PubMed:38703352] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Wang F, Chen L, Xu B, Ma J, Xing B, Su F, Shi C
Characterization of the migration of organic contaminants in laboratory-scale groundwater polluted by underground coal gasification.
Environ Sci Pollut Res Int: 2024 May 4;
[PubMed:38703318] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Arishi AA, Hakami IA, Mashbari HN, Hobani AH, Al-Musawa HI, Abuhadi RI, Maslouf AH, Matari MH, Albrahim HT, Algarni MA, Iskander O, Alyahyawi K
Knowledge, attitude, and perception of robotic-assisted surgery among the general population in Saudi Arabia: a cross-sectional study.
J Robot Surg: 2024 May 4, 18(1);196
[PubMed:38703278] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Ye Y, Yan X, Luo H, Kang J, Liu D, Ren Y, Ngo HH, Guo W, Cheng D, Jiang W
Comparative study of the removal of sulfate by UASB in light and dark environment.
Bioprocess Biosyst Eng: 2024 May 4;
[PubMed:38703203] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Keltsch NG, Gazanis A, Dietrich C, Wick A, Heermann R, Tremel W, Ternes TA
Development of an analytical method to quantify N-acyl-homoserine lactones in bacterial cultures, river water, and treated wastewater.
Anal Bioanal Chem: 2024 May 4;
[PubMed:38703199] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Bartlett ER, Borkowski AK, Nilles CK, Blakemore JD, Thompson WH
Entropy Drives Accelerated Ion Diffusion upon Carbon Dioxide Expansion of Electrolytes.
J Phys Chem B: 2024 May 4;
[PubMed:38703113] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Jamali SS, Somerville SV, Dief EM, Gooding JJ
Stochastic Electrochemical Measurement of a Biofouling Layer on Gold.
Anal Chem: 2024 May 3;
[PubMed:38702865] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Paulino S, Petek S, le Strat Y, Bourgougnon N, Le Blay G
Cultivable epiphytic bacteria of the Chlorophyta Ulva sp. : diversity, antibacterial and biofilm-modulating activities.
J Appl Microbiol: 2024 May 3;
[PubMed:38702839] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

De Sousa PA, Perfect L, Ye J, Samuels K, Piotrowska E, Gordon M, Mate R, Abranches E, Wishart TM, Dockrell DH, Courtney A
Hyaluronan in mesenchymal stromal cell lineage differentiation from human pluripotent stem cells: application in serum free culture.
Stem Cell Res Ther: 2024 May 3, 15(1);130
[PubMed:38702837] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Li S, Chen X, Liu L, Sun C
The relationship between social withdrawal and problematic social media use in Chinese college students: a chain mediation of alexithymia and negative body image.
BMC Psychol: 2024 May 3, 12(1);246
[PubMed:38702805] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Chu W, Zhang F, Zeng X, He F, Shang G, Guo T, Wang Q, Wu J, Li T, Zhong ZZ, Liang X, Hu J, Liu M
A GMP-compliant manufacturing method for Wharton's jelly-derived mesenchymal stromal cells.
Stem Cell Res Ther: 2024 May 3, 15(1);131
[PubMed:38702793] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Zhang X, Leng S, Liu X, Hu X, Liu Y, Li X, Feng Q, Guo W, Li N, Sheng Z, Wang S, Peng J
Ion channel Piezo1 activation aggravates the endothelial dysfunction under a high glucose environment.
Cardiovasc Diabetol: 2024 May 3, 23(1);150
[PubMed:38702777] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Burdet H, Xanthos A, Marques-Vidal P
Women are lean and men are also lean: nutrition titles in women's and men's health magazines.
BMC Public Health: 2024 May 3, 24(1);1230
[PubMed:38702675] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Lin X, Chen X, Chen Y, Xu P, Chen S
Sleep initiation patterns and sleep quality among toddlers in the southeast of China: initial study results.
BMC Pediatr: 2024 May 3, 24(1);298
[PubMed:38702673] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Yousaf T, Saleem F, Andleeb S, Ali M, Farhan Ul Haque M
Methylotrophic bacteria from rice paddy soils: mineral-nitrogen-utilizing isolates richness in bulk soil and rhizosphere.
World J Microbiol Biotechnol: 2024 May 4, 40(6);188
[PubMed:38702590] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Stoye E
Mount Etna's spectacular smoke rings and more - April's best science images.
Nature: 2024 May 3;
[PubMed:38702579] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ochoa-Viñals N, Alonso-Estrada D, Faife-Pérez E, Chen Z, Michelena-Alvarez G, Martínez-Hernández JL, García-Cruz A, Ilina A
β-Carotene production from sugarcane molasses by a newly isolated Rhodotorula toruloides L/24-26-1.
Arch Microbiol: 2024 May 3, 206(6);245
[PubMed:38702537] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Lee S, Kim J, You JS, Hyun YM, Kim JY, Lee JE
Ischemic stroke outcome after promoting CD4+CD25+ Treg cell migration through CCR4 overexpression in a tMCAO animal model.
Sci Rep: 2024 May 3, 14(1);10201
[PubMed:38702399] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Rogulska O, Vackova I, Prazak S, Turnovcova K, Kubinova S, Bacakova L, Jendelova P, Petrenko Y
Storage conditions affect the composition of the lyophilized secretome of multipotent mesenchymal stromal cells.
Sci Rep: 2024 May 3, 14(1);10243
[PubMed:38702388] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Fitzgerald MQ, Chu T, Puppo F, Blanch R, Chillón M, Subramaniam S, Muotri AR
Generation of 'semi-guided' cortical organoids with complex neural oscillations.
Nat Protoc: 2024 May 3;
[PubMed:38702386] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Grocholl J, Ferguson M, Hughes S, Trujillo S, Burall LS
Listeria monocytogenes contamination leads to survival and growth during enoki mushroom cultivation.
J Food Prot: 2024 May 1;100290
[PubMed:38701973] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Andrés EÁ, de Miguel E, de Yébenes MJG, Carmona L, Miranda CG, Ramos PC, de la Peña Lefebvre PG
Relationship between nailfold videocapillaroscopic findings and cardiovascular risk factors.
Microvasc Res: 2024 May 1;104693
[PubMed:38701966] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Xie T, Liu T, Lian B, Qian T, Chen C, Xu C, Liang P, Yang S, Wang R, Chen K, Zhang A, Zhu J
Leaching behaviour of (226)Ra from uranium tailings and adsorption behaviour in geotechnical medias.
Environ Pollut: 2024 May 1;124062
[PubMed:38701963] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Linder AC, Lusseau D
Resilience of human-nature interaction network to pandemic conditions.
Sci Total Environ: 2024 May 1;172813
[PubMed:38701924] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hassan LF, Sen R, O'Shea TM
Trehalose-based coacervates for local bioactive protein delivery to the central nervous system.
Biomaterials: 2024 Apr 27, 309;122594
[PubMed:38701641] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Garcia-Llorens J, Garcia C, Paulet P, Le-Tallec B, Dauphin G, Comte S, Catalá-Gregori P, Simon F, Sevilla-Navarro S, Sarabia J
Research Note: Validation of a new differentiation approach using the commercial ASAP(TM) media to detect the Salmonella 441/014 vaccine strain.
Poult Sci: 2024 Mar 26, 103(6);103679
[PubMed:38701627] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Custers PA, Beets GL, Bach SP, Blomqvist LK, Figueiredo N, Gollub MJ, Martling A, Melenhorst J, Ortega CD, Perez RO, Smith JJ, Lambregts DMJ, Beets-Tan RGH, Maas M
An International Expert-Based Consensus on the Definition of a Clinical Near-Complete Response After Neoadjuvant (Chemo)radiotherapy for Rectal Cancer.
Dis Colon Rectum: 2024 Jun 1, 67(6);782-795
[PubMed:38701503] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Gavassino L, Disconzi M, Noronha J
Dispersion Relations Alone Cannot Guarantee Causality.
Phys Rev Lett: 2024 Apr 19, 132(16);162301
[PubMed:38701454] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Arnone AA, Wilson AS, Soto-Pantoja DR, Cook KL
Diet modulates the gut microbiome, metabolism, and mammary gland inflammation to influence breast cancer risk.
Cancer Prev Res (Phila): 2024 May 3;
[PubMed:38701438] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hu R, Xia L, Shi C, Zhou Y, Guo X
Otitis media with effusion in preschool children with adenoid hypertrophy: Risk factors and nursing care.
Nurs Open: 2024 May, 11(5);e2165
[PubMed:38701327] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Worku KM, Araya D, Tesfa H, Birru EM, Hailu A, Aemero M
In vitro antileishmanial activities of hydro-methanolic crude extracts and solvent fractions of Clematis simensis fresen leaf, and Euphorbia abyssinica latex.
Medicine (Baltimore): 2024 May 3, 103(18);e38039
[PubMed:38701291] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Okamoto N, Seiyama A, Hori S, Takahashi S
Role of the left posterior middle temporal gyrus in shape recognition and its reconstruction during drawing: A study combining transcranial magnetic stimulation and functional near infrared spectroscopy.
PLoS One: 2024, 19(5);e0302375
[PubMed:38701103] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Muhi S, Buultjens AH, Porter JL, Marshall JL, Doerflinger M, Pidot SJ, O'Brien DP, Johnson PDR, Lavender CJ, Globan M, McCarthy J, Osowicki J, Stinear TP
Mycobacterium ulcerans challenge strain selection for a Buruli ulcer controlled human infection model.
PLoS Negl Trop Dis: 2024 May 3, 18(5);e0011979
[PubMed:38701090] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Adedokun ST, Yaya S
Prevalence of oral rehydration solution use and its determinants in the treatment of diarrhea among under-five children in sub-Saharan Africa.
PLoS One: 2024, 19(5);e0303193
[PubMed:38701083] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Teney C, Pietrantuono G, Wolfram T
What polarizes citizens? An explorative analysis of 817 attitudinal items from a non-random online panel in Germany.
PLoS One: 2024, 19(5);e0302446
[PubMed:38701079] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Keleynikov M, Cohen N, Benatov J
Maternal distress during the COVID-19 outbreak: A socio-ecological perspective.
PLoS One: 2024, 19(5);e0302266
[PubMed:38701039] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Stenner K, Edwards J, Mills L, Sherrington S, Mold F
Delegation of insulin administration: a survey of community nursing teams in England.
Br J Community Nurs: 2024 May 2, 29(5);238-244
[PubMed:38701013] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Margarita V, Carboni G, Fiori PL, Rappelli P
The presence of Trichomonas vaginalis in urogenital samples can affect the sensitivity of Mycoplasma hominis identification techniques, leading to an underestimation of bacterial infections.
New Microbiol: 2024 May, 47(1);103-106
[PubMed:38700890] [WorldCat.org: ISSN ESSN ] ( p)

Le YH, Ikawa K, Hoang HTT, Isomura H, Khong DT, Nguyen TN, Que TA, Pham DT, Tanaka K, Yamamoto Y
Abundance of Colistin-Resistance Genes in Retail Meats in Vietnam.
Foodborne Pathog Dis: 2024 May 3;
[PubMed:38700849] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Geurts SM, Vossen HGM, Van den Eijnden RJJM, Koning IM
Bidirectional Within-Family Effects of Restrictive Mediation Practices and Adolescents' Problematic Social Media Use.
J Youth Adolesc: 2024 May 3;
[PubMed:38700825] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Sato T, Ogihara Y, Kitagawa K, Ogura T, Yamada N, Dohi K
Diagnostic performance of fluoroscopic video analysis for pulmonary embolism: a prospective observational study.
Int J Cardiovasc Imaging: 2024 May 3;
[PubMed:38700820] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ali MS, Roy VC, Park JS, Haque AR, Mok JH, Zhang W, Chun BS
Protein and Polysaccharide Recovery from Shrimp Wastes by Natural Deep Eutectic Solvent Mediated Subcritical Water Hydrolysis for Biodegradable Film.
Mar Biotechnol (NY): 2024 May 3;
[PubMed:38700616] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Lima VH, Matugawa AT, Mascarin GM, Fernandes ÉKK
Complex nitrogen sources from agro-industrial byproducts: impact on production, multi-stress tolerance, virulence, and quality of Beauveria bassiana blastospores.
Microbiol Spectr: 2024 May 3;e0404023
[PubMed:38700331] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Wilson IM, Willoughby B, Tanyos A, Graham K, Walker M, Laslett AM, Ramsoomar L
A global review of the impact on women from men's alcohol drinking: the need for responding with a gendered lens.
Glob Health Action: 2024 Dec 31, 17(1);2341522
[PubMed:38700277] [WorldCat.org: ISSN ESSN ] [DOI] ( o)


A decade of amplifying your voice.
Vet Rec: 2024 May 4, 194(9);362
[PubMed:38700197] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Sohn SY, Inoue K, Bashir MT, Currier JW, Neverova NV, Ebrahimi R, Rhee CM, Lee ML, Leung AM
Thyroid Dysfunction Risk After Iodinated Contrast Media Administration: A Prospective Longitudinal Cohort Analysis.
J Clin Endocrinol Metab: 2024 May 3;
[PubMed:38700099] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Singha R, Maity P, Samanta D
Chiral Induction in a Self-Assembled Pd4 Coordination Cage with Chiral Guests.
Chemistry: 2024 May 3;e202401013
[PubMed:38700019] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ou J, Cui W, Zhao Y, Tang Y, Williams A, Wasalathanthri D, Xu J, Lee J, Borys MC, Khetan A
Use of spectroscopic process analytical technology for rapid quality evaluation during preparation of CHO cell culture media.
Biotechnol Prog: 2024 May 3;e3477
[PubMed:38699906] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Jing Z, Feng X, Li X, Zhang X, Pan C
Vaspin facilitates the proliferation and osteogenic differentiation of periodontal ligament stem cells.
J Periodontal Res: 2024 May 3;
[PubMed:38699861] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hong Y, Lee N, Kirkpatrick CE, Hu S, Lee S, Hinnant A
"Trust Me, I'm a Doctor." How TikTok Videos from Different Sources Influence Clinical Trial Participation.
Health Commun: 2024 May 3;1-12
[PubMed:38699819] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Constante Catuto MP, Tigrero-Vaca J, Villavicencio-Vasquez M, Montoya DC, Cevallos JM, Coronel-León J
Evaluation of stress tolerance and design of alternative culture media for the production of fermentation starter cultures in cacao.
Heliyon: 2024 Apr 30, 10(8);e29900
[PubMed:38699711] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Yang F, Guo Q, Ma J
A neuron model with nonlinear membranes.
Cogn Neurodyn: 2024 Apr, 18(2);673-684
[PubMed:38699608] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Chipako I, Singhal S, Hollingsworth B
Impact of sexual and reproductive health interventions among young people in sub-Saharan Africa: a scoping review.
Front Glob Womens Health: 2024, 5;1344135
[PubMed:38699461] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Feng B
Gaming with health misinformation: a social capital-based study of corrective information sharing factors in social media.
Front Public Health: 2024, 12;1351820
[PubMed:38699427] [WorldCat.org: ISSN ESSN ] [DOI] ( )

He L, Chen X, Hu J, Meng Y, Zhang Y, Chen W, Fan Y, Li T, Fang J
Score based on contrast-enhanced ultrasound predict central lymph node metastasis in papillary thyroid cancer.
Front Endocrinol (Lausanne): 2024, 15;1336787
[PubMed:38699389] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Anand S, Fusco A, Günday C, Günday-Türeli N, Donnarumma G, Danti S, Moroni L, Mota C
Tunable ciprofloxacin delivery through personalized electrospun patches for tympanic membrane perforations.
Bioact Mater: 2024 Aug, 38;109-123
[PubMed:38699239] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Gary S, Landry M, Bloom S
Spectral and Electrochemical Properties of Common Photocatalysts in Water: A Compendium for Aqueous Photoredox Catalysis.
Synlett: 2023 Oct, 34(16);1911-1914
[PubMed:38699236] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Clemons EK, Savin A, Schreieck M, Teilmann-Lock S, Trzaskowski J, Waran R
A face of one's own: The role of an online personae in a digital age and the right to control one's own online personae in the presence of digital hacking.
Electron Mark: 2024, 34(1);31
[PubMed:38699202] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Koshy P, Furian L, Nickerson P, Zaza G, Haller M, de Vries APJ, Naesens M
European Survey on Clinical Practice of Detecting and Treating T-Cell Mediated Kidney Transplant Rejection.
Transpl Int: 2024, 37;12283
[PubMed:38699173] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Heston TF
Critical Gaps in Medical Research Reporting by Online News Media.
Cureus: 2024 Apr, 16(4);e57457
[PubMed:38699087] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Shankar Havaldar K, Thoyalil M, Sathyaprasad S, Zaheer A, Belchada DK, Puthukkulangara A
A Comparative Evaluation of the Periodontal Ligament Cell Viability Using Placentrex, Propolis, and Hanks' Balanced Salt Solution: An In-Vitro Study.
Cureus: 2024 Apr, 16(4);e57454
[PubMed:38699086] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Beard JH, Raissian R, Roberts L, Partain L, Midberry J, Walker T, Trombley S, MacMillan J, Morrison CN
Systematic disparities in reporting on community firearm violence on local television news in Philadelphia, PA, USA.
Prev Med Rep: 2024 Jun, 42;102739
[PubMed:38699078] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Lin HH, Lin KH, Tsai YL, Chen RJ, Lin YC, Chen YC
Influences of Ipomoea batatas Anti-Cancer Peptide on Tomato Defense Genes.
Curr Protein Pept Sci: 2024 May 2;
[PubMed:38698748] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Kumar V, Tolosa M, Ge X, Rao G
Reinventing shake flask fermentation: The breathable flask.
Biotechnol Bioeng: 2024 May 3;
[PubMed:38698719] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Carreño-Campos C, Villegas E, Villarreal ML, Morales-Aguilar M, Govea-Alonso D, Romero-Maldonado A, Jimenez-Capdeville ME, Rosales-Mendoza S, Ortiz-Caltempa A
Statistical Experimental Designs for cLTB-Syn Vaccine Production Using Daucus carota Cell Suspension Cultures.
Planta Med: 2024 May 2;
[PubMed:38698590] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Munzer TG, Miller AL, Weeks HM, Kaciroti N, Radesky J
Greater mobile device-prompted phone pickups are associated with daily parent stress.
Acta Paediatr: 2024 May 2;
[PubMed:38698532] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Wang H, Zhang X, Zhang W, Sun H
The effects of exosomes originating from different cell sources on the differentiation of bone marrow mesenchymal stem cells into schwann cells.
J Nanobiotechnology: 2024 May 3, 22(1);220
[PubMed:38698449] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Mao T, Zhao X, Jiang K, Yang J, Xie Q, Fu J, Du B, Lei Z, Gao F
Evaluation of TikTok videos on acute pancreatitis: content quality and reliability analysis.
BMC Public Health: 2024 May 2, 24(1);1216
[PubMed:38698404] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

D'Alfonso A, De Carolis F, Serva A, Valiyeva S, Guido M, Pietroletti R
Haemorrhoidal disease in pregnancy: results from a self-assessment questionnaire administered by means of a social network.
BMC Gastroenterol: 2024 May 2, 24(1);150
[PubMed:38698334] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Purhonen R, Atanasova NS, Salokas J, Duplissy J, Loikkanen E, Maunula L
A Pilot Study of Aerosolization of Infectious Murine Norovirus in an Experimental Setup.
Food Environ Virol: 2024 May 2;
[PubMed:38698288] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Yang L, Ma XZ, Su H, Zhang J, Sheng JQ, Jin P
Safe and effective hybrid endoscopic submucosal dissection with ALL IN ONE snare in porcine gastric model (with video).
Sci Rep: 2024 May 2, 14(1);10060
[PubMed:38698246] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Mangalik S, Eichstaedt JC, Giorgi S, Mun J, Ahmed F, Gill G, V Ganesan A, Subrahmanya S, Soni N, Clouston SAP, Schwartz HA
Robust language-based mental health assessments in time and space through social media.
NPJ Digit Med: 2024 May 2, 7(1);109
[PubMed:38698174] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Patel AA, Weber PC, Levi JR
The effect of tympanostomy tubes on otoacoustic emissions.
Eur Arch Otorhinolaryngol: 2024 May 2;
[PubMed:38698162] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Lai C, Toriumi F, Yoshida M
A multilingual analysis of pro Russian misinformation on Twitter during the Russian invasion of Ukraine.
Sci Rep: 2024 May 2, 14(1);10155
[PubMed:38698157] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Shoshani A, Kor A, Bar S
The impact of social media use on psychiatric symptoms and well-being of children and adolescents in the Post-COVID-19 era: a four-year longitudinal study.
Eur Child Adolesc Psychiatry: 2024 May 2;
[PubMed:38698136] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hu J, Lai Y, Yi X
Effectiveness of social media-assisted course on learning self-efficacy.
Sci Rep: 2024 May 2, 14(1);10112
[PubMed:38698034] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Istrate R, Tulus V, Grass RN, Vanbever L, Stark WJ, Guillén-Gosálbez G
The environmental sustainability of digital content consumption.
Nat Commun: 2024 May 2, 15(1);3724
[PubMed:38697974] [WorldCat.org: ISSN ESSN ] [DOI] ( e) 

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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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