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Revision as of 11:32, 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

Smith SL, Parashar R, Nanda S, Shiffman J, Shroff ZC, Shawar YR, Hamunakwadi DL
Shifting patterns and competing explanations for infectious disease priority in global health agenda setting arenas.
Health Policy Plan: 2024 May 16;
[PubMed:38753344] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Chen D, Parsa R, Hope A, Hannon B, Mak E, Eng L, Liu FF, Fallah-Rad N, Heesters AM, Raman S
Physician and Artificial Intelligence Chatbot Responses to Cancer Questions From Social Media.
JAMA Oncol: 2024 May 16;
[PubMed:38753317] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Horrocks L, Holloway D, Rymer J, Bruce D
Quality improvement project - Reducing the inadvertent prescribing of unopposed estrogen in primary care Dr Liz Horrocks Banstead PCN.
Post Reprod Health: 2024 May 16;20533691241240552
[PubMed:38753305] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

McAlpine D, MacKay M, Grant LE, Papadopoulos A, McWhirter JE
Modernizing public health communication competencies in Canada: A survey of the Canadian public health workforce.
Can J Public Health: 2024 May 16;
[PubMed:38753267] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Giroux CM, Kim S, Thomas A
How the knowledge shared using social media is taken up into health professions education practice: A qualitative descriptive study.
Adv Health Sci Educ Theory Pract: 2024 May 16;
[PubMed:38753203] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Yoshida K, Nagayama Y, Funama Y, Ishiuchi S, Motohara T, Masuda T, Nakaura T, Ishiko T, Hirai T, Beppu T
Low tube voltage and deep-learning reconstruction for reducing radiation and contrast medium doses in thin-slice abdominal CT: a prospective clinical trial.
Eur Radiol: 2024 May 16;
[PubMed:38753193] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Chen Y, Meng Y, Zhang J, Xie Y, Guo H, He M, Shi X, Mei Y, Sheng X, Xie D
Leakage Proof, Flame-Retardant, and Electromagnetic Shield Wood Morphology Genetic Composite Phase Change Materials for Solar Thermal Energy Harvesting.
Nanomicro Lett: 2024 May 16, 16(1);196
[PubMed:38753068] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

İzgördü ÖK, Gurbanov R, Darcan C
Understanding the transition to viable but non-culturable state in Escherichia coli W3110: a comprehensive analysis of potential spectrochemical biomarkers.
World J Microbiol Biotechnol: 2024 May 16, 40(7);203
[PubMed:38753033] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Srinivasan N, Chandran R, Narayanan J, Sasikumar DK, Raju V
Half-turned truncal switch operation for dextro-transposition of the great arteries with ventricular septal defect and left ventricular outflow tract obstruction and an abnormal coronary pattern.
Multimed Man Cardiothorac Surg: 2024 May 16, 2024;
[PubMed:38752879] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

He K, Kou G, Cai H, Tian G, Xu Z, Yang Z
Effects of Contact Surface Shape on Dynamic Lifetime and Strength of Molecular Bond Clusters under Displacement- and Force-Controlled Loading Conditions.
Langmuir: 2024 May 16;
[PubMed:38752855] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Li X, Wang Y, Cui J, Shi Y, Cai Y
Occurrence and Fate of Per- and Polyfluoroalkyl Substances (PFAS) in Atmosphere: Size-Dependent Gas-Particle Partitioning, Precipitation Scavenging, and Amplification.
Environ Sci Technol: 2024 May 16;
[PubMed:38752583] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Tieu L, Qiu JL, Puvipalan V, Pasternak R
EXPRESS: Experimental evidence for a semantic typology of emoji: Inferences of co-, pro-, and post-text emoji.
Q J Exp Psychol (Hove): 2024 May 16;17470218241255786
[PubMed:38752511] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Gao J, Proffitt DR, Marecki JC, Protacio RU, Wahls WP, Byrd AK, Raney KD
Two residues in the DNA binding site of Pif1 helicase are essential for nuclear functions but dispensable for mitochondrial respiratory growth.
Nucleic Acids Res: 2024 May 16;
[PubMed:38752483] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Chowdhury MZI, Mubin N, Mohib T, Chowdhury N, Chowdhury TF, Laskar AMH, Sultana S, Raihan M, Turin TC
Cancer screening research in Bangladesh: Insights from a scoping review.
Glob Public Health: 2024 Jan, 19(1);2351186
[PubMed:38752425] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Salzer R, Hrastelj N, Smith A
European Employment Survey for Chemists (ESEC3) Careers of Chemistry Graduates in Europe.
Chemistry: 2024 May 16;e202401223
[PubMed:38752275] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Shen X, Jia G
[Research progress in the treatment of distal humeral metaphyseal-diaphyseal junction fracture in children].
Zhongguo Xiu Fu Chong Jian Wai Ke Za Zhi: 2024 May 15, 38(5);613-617
[PubMed:38752250] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Kawsar M, Sahadat Hossain M, Tabassum S, Bahadur NM, Ahmed S
Different solvents and organic modifiers for the control of crystallographic parameters in nano-crystallite hydroxyapatite for amplification of photocatalytic activity.
Nanoscale Adv: 2024 May 14, 6(10);2682-2700
[PubMed:38752133] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Padmapriya D, Shanthi C
Hydrolysates with emulsifying properties prepared from protein wastes using microbial protease.
Food Sci Biotechnol: 2024 Jun, 33(8);1847-1857
[PubMed:38752117] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Alkarak S, Badheeb AM, Al-Dowais A, Alhabes H, Almahwiti K, Aman AA, Alhajlan MA, Seada I, Alshamrani SA, Alhussein B
Factors Affecting Breast Cancer Screening Behavior Among Women in Saudi Arabia: A Retrospective Cross-Sectional Study.
Cureus: 2024 Apr, 16(4);e58324
[PubMed:38752053] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Pavuluri KS, Pathi D, Dash SK, Das P, Panda SS
Microalbuminuria as a Predictor of Early Neurological Deterioration and Poor Functional Outcomes in Acute Ischemic Stroke.
Cureus: 2024 Apr, 16(4);e58311
[PubMed:38752035] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Clark HM, Stokes AE, Edwards JL, Payton RR, Schrick FN, Campagna SR, Sarumi Q, Hessock EA, Roberts SR, Azaridolatabad N, Moorey SE
Impact of preovulatory follicle maturity on oocyte metabolism and embryo development.
PNAS Nexus: 2024 May, 3(5);pgae181
[PubMed:38752021] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Ariolli A, Canè M, Di Fede M, Tavarini S, Taddei AR, Buno KP, Delany I, Rossi Paccani S, Pezzicoli A
Modeling airway persistent infection of Moraxella catarrhalis and nontypeable Haemophilus influenzae by using human in vitro models.
Front Cell Infect Microbiol: 2024, 14;1397940
[PubMed:38751999] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Kanthabalan A, Emmanuel A, Alexander C, Bhatt N, Chan V, Kalejaiye O, Narahari K, Kasivisvanathan V, Shabbir M
An international survey of contemporary practices towards fertility assessment and preservation in patients undergoing radical inguinal orchidectomy for testicular cancer.
BJUI Compass: 2024 May, 5(5);445-453
[PubMed:38751948] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Razzaque MA, Haroon RM
Nurses on Social Media: Global Challenges and Pakistani Context.
J Pak Med Assoc: 2024 Apr, 74(4);620
[PubMed:38751250] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Torres-Terán I, Venczel M, Klein S
Prediction of subcutaneous drug absorption - Development of novel simulated interstitial fluid media for predictive subcutaneous in vitro assays.
Int J Pharm: 2024 May 13;124227
[PubMed:38750979] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Melo GB, Nakayama LF, Cardoso VS, Andrade Dos Santos L, Malerbi FK
Synchronous Diagnosis of Diabetic Retinopathy by a Handheld Retinal Camera, Artificial Intelligence, and Simultaneous Specialist Confirmation.
Ophthalmol Retina: 2024 May 13;
[PubMed:38750937] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ghosh S, Wu X, Chen Y, Hu J
Application of UV LEDs to inactivate antibiotic resistant bacteria: Kinetics, efficiencies, and reactivations.
Sci Total Environ: 2024 May 13;173075
[PubMed:38750759] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Mitra S, Saran RK, Srivastava S, Rensing C
Pesticides in the environment: Degradation routes, pesticide transformation products and ecotoxicological considerations.
Sci Total Environ: 2024 May 13;173026
[PubMed:38750741] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Wiemer SJ, Mediratta JK, Triana RR, Card J, Rallis D, Rieck KL, Holmes E, Krishnan DG
What Is the Incidence of Anesthesia-Related Adverse Events in Oral and Maxillofacial Surgery Offices? A Review of 61,237 Sedation Cases From a Large Private Practice Consortium.
J Oral Maxillofac Surg: 2024 Apr 25;
[PubMed:38750658] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hagaggi NSA, Rady EAE
The potential of Bacillus species isolated from Cinnamomum camphora for biofuel production.
Microb Cell Fact: 2024 May 15, 23(1);139
[PubMed:38750603] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Abazid RM, Pati N, Elrayes M, Chandy M, Hassanin M, Mathew A, De S, Bagur R, Tzemos N
Role of myocardial strain imaging in diagnosing inducible myocardial ischemia with treadmill contrast-enhanced stress echocardiography.
BMC Cardiovasc Disord: 2024 May 16, 24(1);254
[PubMed:38750460] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Rabe M, Gröne OR, von Bernstorff C, Knorr M
The effects of language proficiency and awareness of time limit in animated vs. text-based situational judgment tests.
BMC Med Educ: 2024 May 15, 24(1);540
[PubMed:38750433] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Liu C, Zheng F, Zhang X, Pan J, Ding W, Tian X
Selective venous sampling for secondary hypertension.
Hypertens Res: 2024 May 15;
[PubMed:38750220] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hailu BA
Trend and principal components of HIV/AIDS among adults in SSA.
Sci Rep: 2024 May 15, 14(1);11098
[PubMed:38750039] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Wraae CAD, Opstrup N, Kyvik KO, Brixen K, Wien C
The use and application of Lean Management methods to research processes-a scoping review protocol.
BMJ Open: 2024 May 15, 14(5);e074207
[PubMed:38749681] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Zdeňková K, Jirešová J, Lokajová E, Klenivskyi M, Julák J, Marin MAL, Tichá P, Domonkos M, Demo P, Scholtz V
Modeling the growth of Aspergillus brasiliensis affected by a non-thermal plasma.
J Appl Microbiol: 2024 May 15;
[PubMed:38749678] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Vassey J, Vogel EA, Unger JB
US adolescents' response to nicotine warning labels in influencer e-cigarette marketing social media posts: a survey-based randomised between-subject experiment.
Tob Control: 2024 May 15;
[PubMed:38749676] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Alhemyari MH, Satarasi P, Joseph J, Bagga B
Nocardia keratitis after small incision lenticule extraction (SMILE).
BMJ Case Rep: 2024 May 15, 17(5);
[PubMed:38749526] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Cole HA, Grimm LJ, Omofoye TS, Cooke EA, Heitkamp DE, Mills MK, Wang M, Maxfield CM, Chapman T
Women in leadership matters: Achieving diversity in radiology residency recruitment.
Clin Imaging: 2024 Apr 12, 111;110144
[PubMed:38749319] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Liu X, Chen M, Wang D, Du F, Xu N, Sun W, Han Z
Cr(VI) removal during cotransport of nano-iron-particles combined with iron sulfides in groundwater: Effects of D. vulgaris and S. putrefaciens.
J Hazard Mater: 2024 May 13, 472;134583
[PubMed:38749250] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Vavassori M, Donzelli G
Impact of COVID-19 restrictive measures during lockdown period on eating disorders: An umbrella review.
Nutrition: 2024 Apr 6, 124;112463
[PubMed:38749229] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Zhang W, Zhang S, Guo P, Chen H, Zhou Y, Yu F
Efficient and durable oxygen reduction in alkaline media by doping heteroatomic boron into Fe(SA)-NC catalyst.
J Colloid Interface Sci: 2024 May 12, 669;896-901
[PubMed:38749228] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Shang M, Zhou B, Qiu H, Gong Y, Xin L, Xiao W, Xu G, Dai C, Zhang H, Wu Z, Wang L
Self-supported Ru-Fe-O(x) nanospheres as efficient electrocatalyst to boost overall water-splitting in acid and alkaline media.
J Colloid Interface Sci: 2024 May 9, 669;856-863
[PubMed:38749224] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, Hunter JE, Berry-Kravis E, Hipp H, Todd PK
FMR1 Disorders.

1993;

[PubMed:20301558] ( )

Ozaki Y, Tierney A, Pfordresher PQ, McBride JM, Benetos E, Proutskova P, Chiba G, Liu F, Jacoby N, Purdy SC, Opondo P, Fitch WT, Hegde S, Rocamora M, Thorne R, Nweke F, Sadaphal DP, Sadaphal PM, Hadavi S, Fujii S, Choo S, Naruse M, Ehara U, Sy L, Parselelo ML, Anglada-Tort M, Hansen NC, Haiduk F, Færøvik U, Magalhães V, Krzyżanowski W, Shcherbakova O, Hereld D, Barbosa BS, Varella MAC, van Tongeren M, Dessiatnitchenko P, Zar SZ, El Kahla I, Muslu O, Troy J, Lomsadze T, Kurdova D, Tsope C, Fredriksson D, Arabadjiev A, Sarbah JP, Arhine A, Meachair TÓ, Silva-Zurita J, Soto-Silva I, Millalonco NEM, Ambrazevičius R, Loui P, Ravignani A, Jadoul Y, Larrouy-Maestri P, Bruder C, Teyxokawa TP, Kuikuro U, Natsitsabui R, Sagarzazu NB, Raviv L, Zeng M, Varnosfaderani SD, Gómez-Cañón JS, Kolff K, der Nederlanden CVB, Chhatwal M, David RM, Setiawan IPG, Lekakul G, Borsan VN, Nguqu N, Savage PE
Globally, songs and instrumental melodies are slower and higher and use more stable pitches than speech: A Registered Report.
Sci Adv: 2024 May 17, 10(20);eadm9797
[PubMed:38748798] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Dalli LL, Prvulj Z, Mihailidou AS, Freak-Poli R, Chapman N, Purvis T, Kim J, Kilkenny MF
Improving #Hypertension Awareness: Utility of Social Media to Communicate About High Blood Pressure.
Hypertension: 2024 Jun, 81(6);e71-e73
[PubMed:38748764] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Abbott P, Shanks R, Stanley I, D'Ambruoso L
A protocol for a critical realist systematic synthesis of interventions to promote pupils' wellbeing by improving the school climate in low- and middle-income countries.
PLoS One: 2024, 19(5);e0286489
[PubMed:38748720] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Brown MC, Araújo-Soares V, Skinner R, Brown J, Glaser AW, Hanratty H, McCabe MG, Amariutei AE, Mauri S, Sharp L
Protocol for the 'Supporting Young Cancer Survivors who Smoke' study (PRISM): Informing the development of a smoking cessation intervention for childhood, adolescent and young adult cancer survivors in England.
PLoS One: 2024, 19(5);e0299321
[PubMed:38748708] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Mostofinejad A, Romero DA, Brinson D, Marin-Araujo AE, Bazylak A, Waddell TK, Haykal S, Karoubi G, Amon CH
In silico model development and optimization of in vitro lung cell population growth.
PLoS One: 2024, 19(5);e0300902
[PubMed:38748626] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Xie Y, Yang F, Huang J, He Y, Zhou Y, Qian Y, Cai W, Zhou J
Declining Chinese attitudes toward the United States amid COVID-19.
Proc Natl Acad Sci U S A: 2024 May 21, 121(21);e2322920121
[PubMed:38748587] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Sowers TD, Blackmon MD, Wilkin RT, Rovero M, Bone SE, Jerden ML, Nelson CM, Bradham KD
Lead Speciation, Bioaccessibility, and Sources for a Contaminated Subset of House Dust and Soils Collected from Similar United States Residences.
Environ Sci Technol: 2024 May 15;
[PubMed:38748567] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Zhang H, Lin F, Zheng T, Gao J, Wang Z, Zhang K, Zhang X, Xu C, Zhao F, Xie H, Li Q, Cao K, Gu Y, Mao N
Artificial intelligence-based classification of breast lesion from contrast enhanced mammography: a multicenter study.
Int J Surg: 2024 May 1, 110(5);2593-2603
[PubMed:38748500] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Liu X, Hu Q, Wang J, Wu X, Hu D
Difference in Rumor Dissemination and Debunking Before and After the Relaxation of COVID-19 Prevention and Control Measures in China: Infodemiology Study.
J Med Internet Res: 2024 May 15, 26;e48564
[PubMed:38748460] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Bonny SQ, Zhou X, Khan MF, Rahman MM, Xin Y, Vankadari N, Tikhomirova A, Homman-Ludiye J, Roujeinikova A
Functional and biochemical characterisation of remote homologues of type IV pili proteins PilN and PilO in Helicobacter pylori.
IUBMB Life: 2024 May 15;
[PubMed:38748402] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Pollio EW, Wang J, Randle E, Pollio DE, North CS
A qualitative narrative study of rescue and recovery workers responding to the terrorist bombing of Oklahoma City's Murrah Building.
J Occup Environ Med: 2024 May 15;
[PubMed:38748398] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Vagios S, Sun B, Yeh J, Sacha CR
International attitudes towards medical and planned oocyte cryopreservation.
J Assist Reprod Genet: 2024 May 15;
[PubMed:38748360] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Rose L, Novice M, Kobayashi S, Minta A, Novice T, Sicco KL, Dulmage B
Characterization of the role of Facebook groups for patients who use scalp cooling therapy: a survey study.
Support Care Cancer: 2024 May 15, 32(6);351
[PubMed:38748328] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Struckmeier AK, Buchbender M, Agaimy A, Kesting M
Diagnostic accuracy of contrast-enhanced computed tomography in assessing bone invasion in patients with oral squamous cell carcinoma.
Clin Oral Investig: 2024 May 15, 28(6);314
[PubMed:38748270] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Stiti M, Kornienko V, Kristensson E, Castanet G, Berrocal E
Instantaneous thermometry imaging using two-photon laser-induced fluorescence.
Opt Lett: 2024 May 15, 49(10);2569-2572
[PubMed:38748107] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Ng YL, Lin Z
Between Technological Utopia and Dystopia: Online Expression of Compulsory Use of Surveillance Technology.
Sci Eng Ethics: 2024 May 15, 30(3);19
[PubMed:38748085] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Yadav M, Singh A, Singh Y
Statistical theory of fluids confined in quenched disordered porous media.
J Chem Phys: 2024 May 7, 160(17);
[PubMed:38748032] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Okazaki S
A new dynamic Monte Carlo method satisfying n-particle diffusion equation with position-dependent diffusion coefficient, free energy, and intermolecular interactions.
J Chem Phys: 2024 May 7, 160(17);
[PubMed:38748011] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Denninger L, Brunst H, van Wilderen LJGW, Horz M, Masood HMA, McNitt CD, Burghardt I, Popik VV, Bredenbeck J
Switch the click: Ultrafast photochemistry of photoDIBO-OH tracked by time-resolved IR spectroscopy.
J Chem Phys: 2024 May 7, 160(17);
[PubMed:38747992] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Frey Esgård V, Lindman I, Braend AM, Fossum GH, Lundberg T, Moberg A, Nordeman L, Papachristodoulou C, Sundvall PD
Diagnostic methods and written advice for acute otitis media in primary health care.
Scand J Prim Health Care: 2024 May 15;1-6
[PubMed:38747888] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Al-Kenani HQM, Shaheed OM
Evaluation of some immunological markers in co-infection of COVID-19 with thrush candidiasis.
Rev Assoc Med Bras (1992): 2024, 70(4);e20230845
[PubMed:38747876] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Lelis CF, Prietsch SOM, Cesar JA
Unplanned pregnancy in the extreme South of Brazil: prevalence, trends, and associated factors.
Cien Saude Colet: 2024 May, 29(5);e11122023
[PubMed:38747772] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Dias LKS, Sanhueza-Sanzana C, Pinheiro Júnior FML, Martins AF, Correia FGS, de Aguiar IWO, Ferreira NC, Stolow J, Rutherford G, Teixeira MG, Pires Neto RDJ, de Almeida RLF, Coelho ICB, Frota CC, Kendall C, Kerr LRFS
Use of insect repellent as personal protection among women of childbearing age in an arbovirus endemic area in Northeastern Brazil.
Rev Bras Epidemiol: 2024, 27;e240025
[PubMed:38747743] [WorldCat.org: ISSN ESSN ] [DOI] ( )

El-Khoury JR, Mady C
Breast cancer awareness messages: investigating response among Lebanese women.
Health Promot Int: 2024 Jun 1, 39(3);
[PubMed:38747514] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Epe-Jungeblodt F, Pauli P, Schwab F, Andreatta M
Trauma history and course of therapy in a naturalistic cognitive behavior therapy outpatient sample: An archive data study.
J Clin Psychol: 2024 May 15;
[PubMed:38747513] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Warburton WA, Mohi S, Sweller N, Tarabay C, Spencer L, Olsen K
Violent and prosocial music: Evidence for the impact of lyrics and musical tone on aggressive thoughts, feelings, and behaviors.
Aggress Behav: 2024 May, 50(3);e22148
[PubMed:38747497] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Quiroga NI, Grando LE, Oller XM, Paglialunga PL, Montes ÁG, Sanchez-Lorente D
Malignant pleural mesothelioma: Description of pleural decortication and hyperthermic chemotherapy technique in multimodal therapy.
Multimed Man Cardiothorac Surg: 2024 May 15, 2024;
[PubMed:38747474] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Wang HY, Slater GW
Field-driven polyelectrolyte-polymer collisions in nanochannels.
J Chem Phys: 2024 May 21, 160(19);
[PubMed:38747436] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Arshad A, Usman M, Majeed Khan H, Rahman Z, Manzoor M, Gul B
Effect of COVID-19 vaccination on menstrual cycle irregularities among females: A cross-sectional study in Pakistan.
Pak J Pharm Sci: 2024 Jan, 37(1(Special));215-222
[PubMed:38747272] [WorldCat.org: ISSN ESSN ] ( p)

Kornacki C, Rodriguez J, Rodriguez J, Calac AJ, Calac D, Lee J, Moore R, Brucks L, Jacques I, Yang M, Almodovar V, Berber SS
Reducing Commercial Tobacco Sales to Youth On and Around California Tribal Reservations with a Reward and Reminder Retail Intervention.
Nicotine Tob Res: 2024 May 15;
[PubMed:38747187] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Luan Z, Wang F, Tian Y
Enhanced Near-infrared Phosphorescent Emission Modulated by Clipping of Metallotweezers in Aqueous Media.
Chemistry: 2024 May 15;e202401022
[PubMed:38747055] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Lo Destro C
Unraveling the impact of self-esteem on the utilization of Instagram filters: the mediating role of fear of negative evaluation.
Front Psychol: 2024, 15;1302662
[PubMed:38746921] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Ali AM, Elshabrawy SM, Kamoun EA
Evaluation of the mechanical properties and degradation behavior of chitosan-PVA-graphene oxide nanocomposite scaffolds in vitro.
J Taibah Univ Med Sci: 2024 Jun, 19(3);585-597
[PubMed:38746912] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Mushtaq S, Lee KC, Park JA, Kim JY
Efficient Radiolabeling of Proteins and Antibodies via Maleamate-Cysteine Bioconjugation.
ACS Med Chem Lett: 2024 May 9, 15(5);691-695
[PubMed:38746876] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Fahey OB, Carr DJ, Ocean EM, Nittas V, Kane CP, Monti PM, Wray TB
Black social media influencers engage higher percentages of Black gay and bisexual men in online outreach for HIV prevention research relative to paid ads.
Digit Health: 2024 Jan-Dec, 10;20552076241253758
[PubMed:38746875] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Ben-Zeev D, Beaulieu A, Guler J, Larsen A, Bawaneh A
Readiness for mHealth interventions in Jordan: Refugee camp and urban community survey.
Internet Interv: 2024 Jun, 36;100746
[PubMed:38746872] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Da Silva T, Momen R, Al Kaabi N, Masrur M, Holdsworth S, Prevost K, Logan S, Santa Mina D, Mucsi I, Bhat M, Alba AC, Reid WD, Ferreira M, Mathur S, Janaudis-Ferreira T, Wickerson L, Rozenberg D
Online resources as a source of information for exercise and physical activity in solid organ transplant recipients.
Front Sports Act Living: 2024, 6;1353663
[PubMed:38746829] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Harrison LM, Brisard BM, Cashwell KD, Mulkey AL, Schmidt CA
"A Low-Cost Microfluidics System for Light Microscopy Experiments".
bioRxiv: 2024 Apr 30;
[PubMed:38746427] [DOI] ( e)

Gentile JE, Heiss C, Corridon TL, Mortberg MA, Fruhwürth S, Guzman K, Grötschel L, Chan K, Herring NC, Janicki T, Nhass R, Sarathy JM, Erickson B, Kunz R, Erickson A, Braun C, Henry KT, Bry L, Arnold SE, Minikel EV, Zetterberg H, Vallabh SM
Evidence that minocycline treatment confounds the interpretation of neurofilament as a biomarker.
medRxiv: 2024 May 2;
[PubMed:38746398] [DOI] ( e)

Lenneman CM, Rose EM, Strawska BA, Tyszkiewicz NA, Dean-Christie K, Katz E, Roche JM, de Morree A, Roche R, Tulapurkar ME, Roche JA
Extruded alginate tubes with myogenic potential.
bioRxiv: 2024 May 3;
[PubMed:38746385] [DOI] ( e)

Barry M, Trivedi A, Miyazawa B, Vivona L, Shimmin D, Pathipati P, Keane C, Cuschieri J, Pati S
Regulation of Vascular Endothelial Integrity by Mesenchymal Stem Cell Extracellular Vesicles after Hemorrhagic Shock and Trauma.
Res Sq: 2024 May 2;
[PubMed:38746312] [DOI] ( e)

Qiu Y, Chen A, Yu R, Llevenes P, Seen M, Ko NY, Monti S, Denis GV
Insulin Resistance Increases TNBC Aggressiveness and Brain Metastasis via Adipocyte-derived Exosomes.
bioRxiv: 2024 May 2;
[PubMed:38746141] [DOI] ( e)

Chein J, Martinez S, Barone A
Can human intelligence safeguard against artificial intelligence? Exploring individual differences in the discernment of human from AI texts.
Res Sq: 2024 Apr 29;
[PubMed:38746113] [DOI] ( e)

Hunter H, Searle A
Postextinction Geographies: Audiovisual Afterlives of the Bucardo and the Ivory-Billed Woodpecker.
Ann Am Assoc Geogr: 2024, 114(4);770-791
[PubMed:38746042] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Hughes AM, Flint SW, Clare K, Kousoulis AA, Rothwell ER, Bould H, Howe LD
Demographic, socioeconomic and life-course risk factors for internalized weight stigma in adulthood: evidence from an English birth cohort study.
Lancet Reg Health Eur: 2024 May, 40;100895
[PubMed:38745988] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Nieuwland A, O'Mara JR, Mackenbach JD
Exploring public health researchers' approaches, barriers, and needs regarding dissemination: A mixed-methods exploration.
J Clin Transl Sci: 2024, 8(1);e81
[PubMed:38745881] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Laghmiche L, Dupire G, Franck D
A New Spectrum of Self-Injuries: TikTok-Linked Lesions.
Cureus: 2024 Apr, 16(4);e58226
[PubMed:38745811] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Domingo-Espiñeira J, Varaona A, Montero M, Lara-Abelenda FJ, Gutierrez-Rojas L, Fernández Del Campo EA, Rodriguez-Jimenez R, Pinto da Costa M, Ortega MA, Alvarez-Mon M, Alvarez-Mon MA
Public perception of psychiatry, psychology and mental health professionals: a 15-year analysis.
Front Psychiatry: 2024, 15;1369579
[PubMed:38745783] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Kim JK, Tawk K, Kim JM, Djalilian HR, Abouzari M
Google Trends Analysis of Otologic Symptom Searches Following COVID-19.
Iran J Otorhinolaryngol: 2024 May, 36(3);475-482
[PubMed:38745683] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Cham B, Weaver SR, Jones CK, Popova L, Jacques N
Prevalence and associated factors of shisha smoking among students in Senegal: Global Youth Tobacco Survey 2020.
Tob Induc Dis: 2024, 22;
[PubMed:38745595] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Uotila I, Siiskonen H, Haimakainen S, Harvima I
Tobacco smoking is associated with cutaneous squamous cell carcinoma but not with basal cell carcinoma or melanoma in adult subjects at risk of skin cancer: A cross-sectional study.
Tob Induc Dis: 2024, 22;
[PubMed:38745594] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Uysal Y, Doğaroğlu ZG, Makas MN, Çaylali Z
Boosting Water Retention in Agriculture: Vine Biochar-Doped Hydrogels' Swelling and Germination Effects.
Glob Chall: 2024 May, 8(5);2300254
[PubMed:38745560] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Gao C, Mei H, Mao X
The impact of social media intervention based on functional motivation on repeat blood donation behavior: A prospective randomized controlled trial study.
Transfusion: 2024 May 15;
[PubMed:38745532] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ju I, Chavda BP, Song H
Media Influence on Bystander Intervention for Health Protective Norms: The Integrative Model of Behavioral Prediction Perspective.
J Health Commun: 2024 May 15;1-10
[PubMed:38745474] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Thanawala SU, Klein A, Raval K, Amaro JIF, Beveridge CA, Muir AB, Falk GW, Gonzalez-Hernandez G, Lynch KL
Exploring X: barriers to care for eosinophilic esophagitis.
Dis Esophagus: 2024 May 14;
[PubMed:38745432] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Zhang X, Teng X, Zhang J, Lai Q, Cai J
Enhancing pathological complete response prediction in breast cancer: the role of dynamic characterization of DCE-MRI and its association with tumor heterogeneity.
Breast Cancer Res: 2024 May 14, 26(1);77
[PubMed:38745321] [WorldCat.org: ISSN ESSN ] [DOI] ( e) 

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>

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