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

Cama E, Brener L, Horwitz R, Broady TR, Khoi Vu HM, Jin D, Wu KOE, Treloar C
Factors associated with hepatitis B knowledge among people of Vietnamese ethnicity in Australia.
Psychol Health Med: 2024 May 18;1-12
[PubMed:38762748] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Sharif-Nia H, She L, Allen KA, Marôco J, Kaur H, Arslan G, Gorgulu O, Osborne JW, Rahmatpour P, Khoshnavay Fomani F
Parental hesitancy toward children vaccination: a multi-country psychometric and predictive study.
BMC Public Health: 2024 May 18, 24(1);1348
[PubMed:38762744] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Kabanda R, Kiconco A, Ronald A, Beyer KMM, John SA
Correlates of intention to screen for cervical cancer among adult women in Kyotera District, Central Uganda: a community based cross-sectional study.
BMC Womens Health: 2024 May 18, 24(1);296
[PubMed:38762723] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Kostelnik EO, Howard LM, Paulson JF
Mental Health Education and Utilization Among Patients with Vestibular Disorders.
J Clin Psychol Med Settings: 2024 May 18;
[PubMed:38762705] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Mazaki J, Ishizaki T, Kuboyama Y, Udo R, Tago T, Kasahara K, Nagakawa Y
Robotic surgery for rectal cancer resection with complete intracorporeal double-stapling technique.
Tech Coloproctol: 2024 May 18, 28(1);54
[PubMed:38762703] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Fu Y, Zhong J, Tan Y, Zheng T, Liu M, Wang G
Contrast-enhanced ultrasound for differentiating benign from malignant focal solid renal lesions in pediatric patients.
Sci Rep: 2024 May 18, 14(1);11409
[PubMed:38762673] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Zurkowski CC, Yang J, Miozzi F, Vitale S, O 'Bannon EF 3rd, Jenei Z, Chariton S, Prakapenka V, Fei Y
Exploring toroidal anvil profiles for larger sample volumes above 4 Mbar.
Sci Rep: 2024 May 18, 14(1);11412
[PubMed:38762593] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Li Y, Shao L
Using an epidemiological model to explore the interplay between sharing and advertising in viral videos.
Sci Rep: 2024 May 18, 14(1);11351
[PubMed:38762591] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Lora-Ariza B, Piña A, Donado LD
Assessment of groundwater quality for human consumption and its health risks in the Middle Magdalena Valley, Colombia.
Sci Rep: 2024 May 18, 14(1);11346
[PubMed:38762566] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Johnson SL, Murray G, Kriegsfeld LJ, Manoogian ENC, Mason L, Allen JD, Berk M, Panda S, Rajgopal NA, Gibson JC, Joyner KJ, Villanueva R, Michalak EE
A randomized controlled trial to compare the effects of time-restricted eating versus Mediterranean diet on symptoms and quality of life in bipolar disorder.
BMC Psychiatry: 2024 May 18, 24(1);374
[PubMed:38762486] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Nagata JM, Weinstein S, Alsamman S, Lee CM, Dooley EE, Ganson KT, Testa A, Gooding HC, Kiss O, Baker FC, Pettee Gabriel K
Association of physical activity and screen time with cardiovascular disease risk in the Adolescent Brain Cognitive Development Study.
BMC Public Health: 2024 May 18, 24(1);1346
[PubMed:38762449] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Walker MK, Lema C, Redfern R
Potential pro-inflammatory impact of scleral lens midday fogging on human corneal epithelial cells: An in vitro study.
Cont Lens Anterior Eye: 2024 May 17;102187
[PubMed:38762441] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

GBD 2021 Risk Factors Collaborators
Global burden and strength of evidence for 88 risk factors in 204 countries and 811 subnational locations, 1990-2021: a systematic analysis for the Global Burden of Disease Study 2021.
Lancet: 2024 May 18, 403(10440);2162-2203
[PubMed:38762324] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Haykal D, Cartier H
Educational Strategies to Combat Harmful Cosmetic Dermatology Trends in Generations Alpha and Z.
Clin Dermatol: 2024 May 16;
[PubMed:38762204] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

D'Amico K, Neves RC, Grantz JM, Taechachokevivat N, Ueda A, Dorr A, Hubner A
A randomized, controlled trial examining quarter-level somatic cell count and culture-based selective dry cow therapy against blanket dry cow therapy on early-lactation production outcomes.
J Dairy Sci: 2024 May 16;
[PubMed:38762106] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Liu F, Hu N, Wang A, Ma D, Shan Y, Jiao W
Structure-dependent degradation of phthalate esters with persulfate oxidation activated by thermal in soil.
Environ Res: 2024 May 16;119167
[PubMed:38762006] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Strohbehn K, Wadensweiler PM, Richter HE, Grimes CL, Rardin CR, Rosenblatt PL, Toglia MR, Siddiqui G, Hanissian P
Effectiveness and safety of a novel, collapsible pessary for management of pelvic organ prolapse.
Am J Obstet Gynecol: 2024 May 16;
[PubMed:38761837] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Deng H, Hu H, Xiang N
Augmented Reality-Navigated Laparoscopic Left Hepatectomy For Hepatolithiasis: Identification And Preservation Of The Drainage Of Caudate Bile Ducts.
J Gastrointest Surg: 2024 May 16;
[PubMed:38761832] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Cekic S, Bediou B, Achab S, Rich M, Green CS, Bavelier D
Going beyond video game consumption when considering Internet Gaming Disorder.
Compr Psychiatry: 2024 May 10, 133;152500
[PubMed:38761770] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Li B, Mao R, Chen Z, Zhang Y, Song J, Li N, Tang B, Feng J, Guan M
The competition of heavy metals between hyporheic sediments and microplastics of driving factors in the Beiluo River Basin.
J Hazard Mater: 2024 May 11, 473;134538
[PubMed:38761759] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Cvancara K, Kaal E, Pörhölä M, Torres MB
Sibling bullying reported by emerging adults: Profiling the prevalence, roles, and forms in a cross-country investigation.
Acta Psychol (Amst): 2024 May 17, 247;104310
[PubMed:38761756] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Nikkhah M, Habibi Najafi MB, Hashemi M
A novel antifungal nanoemulsion based on reuterin-assisted synergistic essential oils: Preparation and in vitro/in vivo characterization.
Int J Food Microbiol: 2024 May 6, 418;110735
[PubMed:38761714] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

MacIvor JS, Appleby M, Miotto S, Rosenblat H, Margolis L
Plant cover and biomass change on extensive green roofs over a decade and ten lessons learned.
J Environ Manage: 2024 May 17, 360;121047
[PubMed:38761616] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ma MY, Liu Y, Yang JL, Li SY, Du M, Liu DH, Hao ZL, Guo JZ, Wu XL
Multi-metal ions co-regulated vanadium oxide cathode toward long-life aqueous zinc-ion batteries.
J Colloid Interface Sci: 2024 May 10, 670;174-181
[PubMed:38761570] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Tienda S, Vida C, Villar-Moreno R, de Vicente A, Cazorla FM
Development of a Pseudomonas-based biocontrol consortium with effective root colonization and extended beneficial side effects for plants under high-temperature stress.
Microbiol Res: 2024 May 14, 285;127761
[PubMed:38761488] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Palanisamy J, Rajagopal R, Alfarhan A
D-π-A Carbzazole Based Reactive Cyano-Substituted C = C bond Probe for Selective and Sensitive Detection of Hydrazine in Aqueous Media.
J Fluoresc: 2024 May 18;
[PubMed:38761323] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Saravanan K, Vijayaveeran A, Kathirvel P
Biodegradation of Keratin Waste by Bacillus velezensis HFS_F2 through Optimized Keratinase Production Medium.
Curr Microbiol: 2024 May 18, 81(7);179
[PubMed:38761211] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Pannu MW, Huang A, Plumlee MH
Variable PFAS removal by adsorbent media with sufficient prediction of breakthrough despite reduced contact time at pilot scale.
Water Environ Res: 2024 May, 96(5);e11035
[PubMed:38761092] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Abbasi M, Jouyban A, Ranjbar F, Soleymani J
A versatile ratiometric fluorescence nanoprobe for the determination of clonazepam in patients' plasma samples.
J Mol Recognit: 2024 May 17;e3088
[PubMed:38760976] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Caldeira V, Fonseca TAH, N'Dembo L, Araújo R, Von Rekowski CP, Sampaio PNS, Calado CRC
A new methodology for a rapid and high-throughput comparison of molecular profiles and biological activity of phytoextracts.
Biotechnol Bioeng: 2024 May 17;
[PubMed:38760962] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Correia D, Tran A, Kokole D, Neufeld M, Olsen A, Likki T, Ferreira-Borges C, Rehm J
Designing and implementing an experimental survey on knowledge and perceptions about alcohol warning labels.
Int J Methods Psychiatr Res: 2024 Jun, 33(2);e2016
[PubMed:38760902] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Marander V, Råheim M, Haukenes I, Theodorsen NM
Mothers' experiences living with diastasis recti abdominis - an interview study.
BMC Womens Health: 2024 May 17, 24(1);292
[PubMed:38760781] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Schnell PM, Zhao R, Schoenbeck S, Niles K, MacEwan SR, Fried M, Childerhose JE
How Ohio public library systems respond to opioid-related substance use: a descriptive analysis of survey results.
BMC Public Health: 2024 May 17, 24(1);1336
[PubMed:38760681] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Ng'ombe H, Bosomprah S, Phiri B, Muchimba M, Liswaniso F, Chibuye M, Luchen CC, Chibesa K, Musukuma-Chifulo K, Mwape K, Tigere S, Silwamba S, Sinkala A, Simuyandi M, Mbewe N, Kapaya F, Cunningham AF, Chilengi R, Sack D, Chisenga CC
Comparative analysis of cholera serum vibriocidal antibodies from Convalescent and vaccinated adults in Zambia.
Vaccine: 2024 May 16;
[PubMed:38760271] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Uraguchi K, Matsumoto N, Mitsuhashi T, Takao S, Makihara S, Ando M, Yorifuji T
Pediatric otitis media in Japan: A nationwide longitudinal study of the pre- and post-pneumococcal conjugate vaccine eras born in 2001 and 2010.
Vaccine: 2024 May 16;
[PubMed:38760268] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Sanderson J, Love HA
"The highest in each class was a twilight baby": scientific motherhood, twilight sleep and the eugenics movement in McClure's Magazine.
Med Humanit: 2024 May 17;
[PubMed:38760160] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Connelly DM, Hay ME, Guitar NA, Prentice K
Bridging Educational Grant in Nursing (BEGIN) students' intentions for retention in long-term, home and community care: A survey protocol.
BMJ Open: 2024 May 17, 14(5);e084744
[PubMed:38760048] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Low KJ, Watford A, Blair P, Nabney I, Powell J, Wynn SL, Foreman J, Firth H, Ingram J
Improving the care of children with GENetic Rare disease: Observational Cohort study (GenROC)-a study protocol.
BMJ Open: 2024 May 16, 14(5);e085237
[PubMed:38760043] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Sait MI, Christie RA, Cox C, Board M, Thomas S, O'Sullivan C, Davies C, Walker DM, Vassallo M, Sadler EA, Allen-Pick M, Moore P, Bradbury K, Murphy J
DIALOR (DIgitAL cOaching for fRailty): protocol for a single-arm mixed-methods feasibility study of a digital health coaching intervention for older people with frailty in primary care.
BMJ Open: 2024 May 16, 14(5);e080480
[PubMed:38760042] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Grudziąż-Sękowska J, Sękowski K, Pinkas J, Jankowski M
Preferred sources of information on diabetes prevention programmes: a population-based cross-sectional study in Poland.
BMJ Open: 2024 May 17, 14(5);e083362
[PubMed:38760035] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Mahawongkajit P, Bunprachoen K
Innovative push percutaneous endoscopic gastrostomy by means of gastropexy and Foley catheter in a patient with advanced head and neck and esophageal cancer.
Endoscopy: 2024 Dec, 56(S 01);E428-E429
[PubMed:38759974] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Ogura T, Okuda A, Ueno S, Nishioka N, Nishikawa H
Endoscopic ultrasound-guided hepaticogastrostomy stent exchange using a novel spiral plastic stent.
Endoscopy: 2024 Dec, 56(S 01);E426-E427
[PubMed:38759973] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Tamaru T, Oguro K, Yano T, Ono Y, Sakamoto H, Despott EJ, Yamamoto H
Clip-and-pull method: re-strangulation of a sizable small-bowel polyp for endoscopic ischemic polypectomy.
Endoscopy: 2024 Dec, 56(S 01);E424-E425
[PubMed:38759972] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Shiomi D, Sumi K, Kawasaki Y, Nomura N, Ushio J, Ito T, Inoue H
Endoscopic hand suturing of a covered self-expandable metal stent to prevent migration in malignant gastric outlet obstruction.
Endoscopy: 2024 Dec, 56(S 01);E422-E423
[PubMed:38759971] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Saito K, Ishikawa Y, Kitahara M, Nomura S, Fujisawa M, Kogure H
Novel rendezvous technique for covered metal stent placement using balloon-assisted endoscope in duodenal perforation.
Endoscopy: 2024 Dec, 56(S 01);E420-E421
[PubMed:38759970] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

DellʼAnna G, Mandarino FV, Biamonte P, Bernardi F, Annese V, Danese S, Azzolini F
Dual-channel endoscope for double-traction endoscopic device-assisted full-thickness resection of rectal superficial tumor.
Endoscopy: 2024 Dec, 56(S 01);E418-E419
[PubMed:38759969] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Takayanagi T, Sekino Y, Ueno K, Matsumoto S, Kasuga N, Nagase H
A case of endoscopic ultrasonography-guided choledochoduodenostomy for malignant distal bile duct obstruction with upside-down stomach.
Endoscopy: 2024 Dec, 56(S 01);E416-E417
[PubMed:38759968] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Kawakami Y, Masaki Y, Ishigami K, Hirano T, Murota A, Sugita S, Nakase H
Peroral cholangioscopy-guided biopsy with novel biopsy forceps in comprehensive cancer genomic profiling for cystic duct carcinoma.
Endoscopy: 2024 Dec, 56(S 01);E414-E415
[PubMed:38759967] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Okimoto K, Matsumura T, Akizue N, Ohta Y, Taida T, Kato J, Kato N
Novel self-assembling peptide for management of bleeding associated with colorectal angiodysplasia.
Endoscopy: 2024 Dec, 56(S 01);E412-E413
[PubMed:38759966] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Miyaguchi K, Mizuno S, Mochida S
Hemorrhage into the bile duct after endoscopic ultrasound-guided fine needle aspiration for pancreatic cancer.
Endoscopy: 2024 Dec, 56(S 01);E410-E411
[PubMed:38759965] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Tang L, Zhao H, Peng K, Lou J
Use of biliopancreatic duct imaging system in a 13-month-old girl to enable endoscopic removal of a foreign body in the appendix.
Endoscopy: 2024 Dec, 56(S 01);E408-E409
[PubMed:38759964] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Shi S, Ye J, Feng Q
Endoscopic submucosal dissection for a soft-palate lesion with use of a small-bore tracheal tube combined with floss traction.
Endoscopy: 2024 Dec, 56(S 01);E406-E407
[PubMed:38759963] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Wu Z, Liu Y, Song S, Li W, Ng H, He S, Wang G
Endoscopic hand suturing with clips for a large defect after endoscopic full-thickness resection of gastric gastrointestinal stromal tumor.
Endoscopy: 2024 Dec, 56(S 01);E402-E403
[PubMed:38759962] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Song L, Ma L, Wang L, Zhang G, Wang Y
Peroral endoscopic mediastinal tunneling myotomy for esophageal achalasia: the first case treated in mediastinal tunnel.
Endoscopy: 2024 Dec, 56(S 01);E400-E401
[PubMed:38759961] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Paida K, Gupta S
Ultrasound-guided removal of embedded fishbone.
Endoscopy: 2024 Dec, 56(S 01);E398-E399
[PubMed:38759960] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Zhang Q, Wang L, Wu Q
Occurrence and combined exposure of phthalate esters in urban soil, surface dust, atmospheric dustfall, and commercial food in the semi-arid industrial city of Lanzhou, Northwest China.
Environ Pollut: 2024 May 15, 354;124170
[PubMed:38759748] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Roche AI, Young A, Sabaque C, Kelpin SS, Sinicrope P, Pham C, Marsch LA, Campbell ANC, Venner K, Baker-DeKrey L, Wyatt T, WhiteHawk S, Nord T, Resnicow K, Young C, Brown A, Bart G, Patten C
Wiidookaage'win: Beta-test of a Facebook group intervention for native women to support opioid use recovery.
J Subst Use Addict Treat: 2024 May 15;209396
[PubMed:38759734] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Gateva A, Assyov Y, Karamfilova V, Kamenov Z
Common carotid artery intima media thickness (CIMT) in patients with prediabetes and newly diagnosed type 2 diabetes mellitus.
J Diabetes Complications: 2024 May 11, 38(7);108766
[PubMed:38759539] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Naseem K, Wakeel Manj Q, Akram S, Shabbir S, Noor A, Farooqi ZH, Urooge Khan S, Ali M, Faizan Nazar M, Haider S, Alam K
Spectroscopic monitoring of polyurethane-based nanocomposite as a potential catalyst for the reduction of dyes.
Spectrochim Acta A Mol Biomol Spectrosc: 2024 May 11, 317;124450
[PubMed:38759392] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Gao Y, Chen Q, Liu S, Wang J, Borthwick AGL, Ni J
The mystery of rich human gut antibiotic resistome in the Yellow River with hyper-concentrated sediment-laden flow.
Water Res: 2024 May 9, 258;121763
[PubMed:38759286] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Elling CL, Gomez HZ, Lee NK, Hirsch SD, Santos-Cortez RLP
The A2ml1-Knockout mouse as an animal model for non-syndromic otitis media.
Int J Pediatr Otorhinolaryngol: 2024 May 10, 181;111980
[PubMed:38759260] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Fernández-Fernández E, Brugarolas E, Monjo-Henry I, Novella-Navarro M, Balsa A, De Miguel E
The influence of the cardiac cycle on the halo sign and its impact on the ultrasound diagnosis of giant cell arteritis.
Rheumatology (Oxford): 2024 May 17;
[PubMed:38759208] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Keogh RR, Kozhukhov T, Thijssen K, Shendruk TN
Active Darcy's Law.
Phys Rev Lett: 2024 May 3, 132(18);188301
[PubMed:38759204] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

An S, Liu T, Cao L, Gu Z, Fan H, Zeng Y, Cheng L, Zhu J, Assouar B
Multibranch Elastic Bound States in the Continuum.
Phys Rev Lett: 2024 May 3, 132(18);187202
[PubMed:38759185] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Segal A, Doyle NW
Technology trends in practice: A survey of occupational therapy practitioners.
Work: 2024 May 16;
[PubMed:38759088] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Rana SS, Choudhury J
Orchestrated Octuple C-H Activation: A Bottom-Up Topology Engineering Approach toward Stimuli-Responsive Double-Heptagon-Embedded Wavy Polycyclic Heteroaromatics.
Angew Chem Int Ed Engl: 2024 May 17;e202406514
[PubMed:38758986] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Baudrit C, Fernandez C, Couteaux J, Ndiaye A
Electronic knowledge books (eK-Books) as a medium to capitalise on and transfer scientific, engineering, operational, technological and craft knowledge.
PLoS One: 2024, 19(5);e0299150
[PubMed:38758949] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Lee JH, Lee SE, Kwon YS
Exploring empathic engagement in immersive media: An EEG study on mu rhythm suppression in VR.
PLoS One: 2024, 19(5);e0303553
[PubMed:38758939] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Baral P, Afnan N, Ahmad Zahra M, Akter B, Rabia Prapti S, Muazzam Hossan M, Haque FKM
Bacteriological analysis and antibiotic resistance in patients with diabetic foot ulcers in Dhaka.
PLoS One: 2024, 19(5);e0301767
[PubMed:38758936] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Liu J, Liu Y, Chen V, Chee W, Im EO
Feasibility and acceptability of a home-based virtual group exercise program in global Asian adult population: Baseline characteristics of a cohort study.
Medicine (Baltimore): 2024 May 17, 103(20);e38121
[PubMed:38758883] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Daga P, Thurakkal B, Rawal S, Das T
Matrix stiffening promotes perinuclear clustering of mitochondria.
Mol Biol Cell: 2024 May 17;mbcE23040139
[PubMed:38758658] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Zhang Y, Fu J, Lai J, Deng S, Guo Z, Zhong C, Tang J, Cao W, Wu Y
Reporting of Ethical Considerations in Qualitative Research Utilizing Social Media Data on Public Health Care: Scoping Review.
J Med Internet Res: 2024 May 17, 26;e51496
[PubMed:38758590] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Ramsey WA, Cobler-Lichter MD, O'Neil CF, Ishii M, Satahoo SS, Kaufman JI, Pizano LR, Koru-Sengul T, Szapocznik J, Schulman CI
Mental Health Support Is an Unmet Need for Long-Term Burn Survivors: A Web-Based Survey.
J Burn Care Res: 2024 May 17;
[PubMed:38758544] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Rodrigues NT, Alves Aarão Reis FD
Adsorption of Diffusing Tracers, Apparent Tortuosity, and Application to Mesoporous Silica.
Langmuir: 2024 May 17;
[PubMed:38758366] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Mir NUD, Hossain S, Biswas S
A recyclable luminescent MOF sensor for on-site detection of insecticide dinotefuran and anti-Parkinson's drug entacapone in various environmental and biological specimens.
Chem Asian J: 2024 May 17;e202400377
[PubMed:38758347] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Reis FCG, Castelli RF, Kuczera D, Oliveira HC, Rodrigues ML
Analysis of Cryptococcus Extracellular Vesicles.
Methods Mol Biol: 2024, 2775;359-365
[PubMed:38758329] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Wilson PC, Hinz FO, Farrell I
Impacts of Fulvic Acid on the Toxicity of the Herbicide Atrazine to Lemna minor.
Bull Environ Contam Toxicol: 2024 May 17, 112(6);77
[PubMed:38758236] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Wang L, Zhang K, Zhang X, Tan Y, Guo L, Xia Y, Wang X
Mismatched Supramolecular Interactions Facilitate the Reprocessing of Super-Strong and Ultra-Tough Thermoset Elastomers.
Adv Mater: 2024 May 17;e2311758
[PubMed:38758171] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Snieder R, Deheuvels M
Energy partitioning among compressional and shear waves in three-dimensional attenuating elastic media.
J Acoust Soc Am: 2024 May 1, 155(5);3336-3344
[PubMed:38758054] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Côrte-Real L, Sergi B, Yildirim B, Colucas R, Starosta R, Fontrodona X, Romero I, André V, Acilan C, Correia I
Enhanced selectivity towards melanoma cells with zinc(II)-Schiff bases containing imidazole derivatives.
Dalton Trans: 2024 May 17;
[PubMed:38758025] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Furuyama T, Yamamoto R, Kato N, Ono M
Erratum: Modified Fear Conditioning for Inducing Flight Behaviors in Mice.
J Vis Exp: 2024 May 17, (207);
[PubMed:38758020] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Landers S, Parsh B
Risks of 'bone smashing' trend on social media.
Nursing: 2024 Jun 1, 54(6);11
[PubMed:38757990] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Romer D, Patterson ST, Jamieson PE, Jamieson KH
What Caused the Narrowing of Black-White COVID-19 Vaccination Disparity in the US? A Test of 5 Hypotheses.
J Health Commun: 2024 May 17;1-12
[PubMed:38757709] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Bai K, Tan KH
The Influence of Online Social and Physical Presence on User Consumption Decisions in TikTok Livestreaming: A Scoping Review.
Cyberpsychol Behav Soc Netw: 2024 May 17;
[PubMed:38757705] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ansari S, Azeem A, Khan I, Iqbal N
Association of Phubbing Behavior and Fear of Missing Out: A Systematic Review and Meta-Analysis.
Cyberpsychol Behav Soc Netw: 2024 May 17;
[PubMed:38757677] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Wang T, Wang Y, Fu Y, Chen Z, Jiang C, Ji YE, Lu Y
Angle-Multiplexed 3D Photonic Superstructures with Multi-Directional Switchable Structural Color for Information Transformation, Storage, and Encryption.
Adv Sci (Weinh): 2024 May 17;e2400442
[PubMed:38757669] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Moghaddam M, Godeffroy L, Jasielec JJ, Kostopoulos N, Noël JM, Piquemal JY, Lemineur JF, Peljo P, Kanoufi F
Scanning Electrochemical Microscopy Meets Optical Microscopy: Probing the Local Paths of Charge Transfer Operando in Booster-Microparticles for Flow Batteries.
Small: 2024 May 17;e2309607
[PubMed:38757541] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Yılmaz N, Deniz OG, Secgin S, Secgin Y, Bozduman F
Investigation of the effectiveness of atmospheric pressure cold plasma on sciatic nerve injury in rats.
Folia Morphol (Warsz): 2024 May 17;
[PubMed:38757499] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Tootoonchian P, Holló G, Uzunlar R, Lagzi I, Baytekin B
Periodic Stratification of Colloids in a Liquid Phase Produced by a Precipitation Reaction and Gel Swelling.
Langmuir: 2024 May 17;
[PubMed:38757442] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Gao Y, Huang Y, Ren C, Chou P, Wu C, Pan X, Quan G, Huang Z
Looking back, moving forward: protein corona of lipid nanoparticles.
J Mater Chem B: 2024 May 17;
[PubMed:38757190] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Yang TT, Zhang YQ, Xie MS, Tian Y, Wang DC, Guo HM
Dearomative [2 + 1] Spiroannulation of Bromophenols with Electron-Deficient Alkenes.
J Org Chem: 2024 May 17;
[PubMed:38757188] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Roberts AR, Vallabhaneni N, Russi B, Spence TL, Leiding JW, Sochet AA
Azithromycin for Pediatric Critical Asthma: A Multicenter Retrospective Cohort Study.
Hosp Pediatr: 2024 May 17;
[PubMed:38757173] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Murray C, Mitchell L, Tuke J, Mackay M
Revealing patient-reported experiences in healthcare from social media using thedesign-acquire-process-model-analyse-visualise framework.
Digit Health: 2024 Jan-Dec, 10;20552076241251715
[PubMed:38757085] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Pechlaner G
Biotechnology activism is dead; long live biotechnology activism! The lure and legacy of market-based food movement strategies.
Agric Human Values: 2024, 41(2);583-597
[PubMed:38756988] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Hennocq Q, Bongibault T, Garcelon N, Khonsari RH
Humanitarian Facial Recognition for Rare Craniofacial Malformations.
Plast Reconstr Surg Glob Open: 2024 May, 12(5);e5780
[PubMed:38756957] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Zhang Y, Chow EPF, Sudarto B, Wang D, Stoove M, Medland N, O'Donnell D, Keen P, Ong JJ, Phillips TR
HIV self-testing knowledge, attitudes, and practices among Asian-born gay, bisexual, and other men who have sex with men in Australia: a qualitative study.
Front Public Health: 2024, 12;1325081
[PubMed:38756874] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Walker AIB, Trani JF, Banks CF, Murphy SA, Zha W, Williams MM, Day GS, Zhu Y, Ances BM, Hill CV, Hudson DL, Babulal GM
Recruiting a prospective community cohort to study Alzheimer's disease and structural and social determinants of health among adults racialized as Black: The ARCHES cohort.
Alzheimers Dement (N Y): 2024 Apr-Jun, 10(2);e12473
[PubMed:38756718] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Suraseth C, Koraneekij P
Cyberbullying among secondary school students: Analyzing prediction and relationship with background, social status, and ICT use.
Heliyon: 2024 May 15, 10(9);e30775
[PubMed:38756584] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Wu Y, Mai C
Dynamic spillover between crude oil, gold, and Chinese stock market sectors -analysis of spillovers during financial crisis data during the last two decades.
Heliyon: 2024 May 15, 10(9);e30219
[PubMed:38756561] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Stieger S, Volsa S, Willinger D, Lewetz D, Batinic B
Laughter in everyday life: an event-based experience sampling method study using wrist-worn wearables.
Front Psychol: 2024, 15;1296955
[PubMed:38756489] [WorldCat.org: ISSN ESSN ] [DOI] ( ) 

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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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