ISA

Revision as of 11:32, 1 February 2016 by Micha (talk | contribs)



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

Leaune E, Rouzé H, Lestienne L, Bislimi K, Morgiève M, Chalancon B, Lau-Taï P, Vaiva G, Grandgenèvre P, Haesebaert J, Poulet E
The use of social media after bereavement by suicide: results from a French online survey.
BMC Psychiatry: 2024 Apr 23, 24(1);306
[PubMed:38654345] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Jansen TS, Güney G, Ganse B, Monje MHG, Schulz JB, Dafotakis M, Hoog Antink C, Braczynski AK
Video-based analysis of the blink reflex in Parkinson's disease patients.
Biomed Eng Online: 2024 Apr 23, 23(1);43
[PubMed:38654246] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Lin W, Hou L, Tang J, Huang A, Jia Z
Mir-195-5p targets Smad7 regulation of the Wnt/β-catenin pathway to promote osteogenic differentiation of vascular smooth muscle cells.
BMC Cardiovasc Disord: 2024 Apr 23, 24(1);221
[PubMed:38654161] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Lee D, Ruf M, Karadimitriou N, Steeb H, Manousidaki M, Varouchakis EA, Tzortzakis S, Yiotis A
Development of stochastically reconstructed 3D porous media micromodels using additive manufacturing: numerical and experimental validation.
Sci Rep: 2024 Apr 23, 14(1);9375
[PubMed:38654100] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Zhi Y, Bie H, Wang J, Ren L
Masked autoencoders with generalizable self-distillation for skin lesion segmentation.
Med Biol Eng Comput: 2024 Apr 24;
[PubMed:38653880] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Singh G, Goel R, Shapira Y, Hewitt J, Ovenden C, Selva D
Dacryocystorhinostomy videos on YouTube as a source of patient education.
Int Ophthalmol: 2024 Apr 23, 44(1);192
[PubMed:38653839] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Gangneux JP, Miossec C, Machouart M, Gits-Muselli M, Benderdouche M, Ranque S, Botterel F, Brun S, SFMM Tinea capitis study group
Epidemiology and management of tinea capitis in France: a 6-year nationwide retrospective survey.
Med Mycol: 2024 Apr 23;
[PubMed:38653717] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ha S, Jang Y, Lee BK, Hong Y, Kim BK, Park S, Yoo SK, Chang HJ
Simultaneous Viability Assessment and Invasive Coronary Angiography Using a Therapeutic CT System in Chronic Myocardial Infarction Patients.
Yonsei Med J: 2024 May, 65(5);257-264
[PubMed:38653564] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Richa Y, Asif A, Burton O, Richards H, Hennessey D
Changes in information seeking patterns of medical students in the social media and artificial intelligence age: preliminary findings.
Clin Teach: 2024 Apr 23;e13772
[PubMed:38653544] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Shu B, Riedel J, Lacher M, Mayer S
The top ranked 101 articles in Pediatric Surgical Journals from an Altmetric Perspective.
Eur J Pediatr Surg: 2024 Apr 23;
[PubMed:38653480] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Huang Z, Liu G, Zhang Y, Yuan Y, Xi B, Tan W
Assessing the impacts and contamination potentials of landfill leachate on adjacent groundwater systems.
Sci Total Environ: 2024 Apr 21;172664
[PubMed:38653413] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Carneiro MA, Pintor AMA, Boaventura RAR, Botelho CMS
Arsenic and antimony desorption in water treatment processes: Scaling up challenges with emerging adsorbents.
Sci Total Environ: 2024 Apr 21;172602
[PubMed:38653411] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Owonikoko WM, Alimba CG
Systematic literature review of heavy metal contamination of the Nigerian environment from E-waste management: associated health and carcinogenic risk assessment.
Toxicology: 2024 Apr 21;153811
[PubMed:38653375] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Al Teneiji AS, Abu Salim TY, Riaz Z
Factors impacting the adoption of big data in healthcare: A systematic literature review.
Int J Med Inform: 2024 Apr 20, 187;105460
[PubMed:38653062] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Gebhardt R, Hohn C, Asaduzzaman M
Stabilizing interactions of casein microparticles after a thermal post-treatment.
Food Chem: 2024 Apr 16, 450;139369
[PubMed:38653051] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Genserová L, Duška F, Krajčová A
β-hydroxybutyrate exposure restores mitochondrial function in skeletal muscle satellite cells of critically ill patients.
Clin Nutr: 2024 Apr 9, 43(6);1250-1260
[PubMed:38653008] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Ghosh A, Payton A, Gallant SC, Rogers KL Jr, Mascenik T, Hickman E, Love CA, Schichlein KD, Smyth TR, Kim YH, Rager JE, Gilmour MI, Randell SH, Jaspers I
Burn Pit Smoke Condensate-Mediated Toxicity in Human Airway Epithelial Cells.
Chem Res Toxicol: 2024 Apr 23;
[PubMed:38652897] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Mroz G, Mazhary H, Painter J
What's cooking? The normalization of meat in YouTube recipe videos consumed by South Asian British Muslims.
Food Cult Soc: 2023 Apr 11;1-19
[PubMed:38652831] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Benson P, Kathios N, Loui P
Predictive coding in musical anhedonia: A study of groove.
PLoS One: 2024, 19(4);e0301478
[PubMed:38652721] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Garrett C, Aghaei A, Aggarwal A, Qiao S
The Role of Social Media in the Experiences of COVID-19 Among Long-Hauler Women: Qualitative Study.
JMIR Hum Factors: 2024 Apr 23, 11;e50443
[PubMed:38652515] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Sharetts R, Moein ST, Khan R, Doty RL
Long-Term Taste and Smell Outcomes After COVID-19.
JAMA Netw Open: 2024 Apr 1, 7(4);e247818
[PubMed:38652477] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Reynolds KE, Huang E, Sabbineni M, Wiseman E, Murtaza N, Ahuja D, Napier M, Murphy KM, Singh KK, Scott AL
Purinergic Signalling Mediates Aberrant Excitability of Developing Neuronal Circuits in the Fmr1 Knockout Mouse Model.
Mol Neurobiol: 2024 Apr 23;
[PubMed:38652351] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Lijassi I, Arahou F, Mansouri Z, Wahby A, Rhazi L, Wahby I
Comparative Analysis of Effect of Culture Conditions on Growth and C-Phycocyanin Production in Helical and Linear Spirulina.
Curr Microbiol: 2024 Apr 23, 81(6);152
[PubMed:38652305] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Lenkinski RE, Rofsky NM
Contrast Media-driven Anthropogenic Gadolinium: Knowns and Unknowns.
Radiology: 2024 Apr, 311(1);e240020
[PubMed:38652027] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Mugumbate R, Gopaldasani V, Kidson P, Ravulo J
'We Were an Afterthought': Corona Virus Disease 2019 (COVID-19) Pandemic in Culturally and Linguistically Diverse (CALD) Communities in New South Wales, Australia.
Soc Work Public Health: 2024 Apr 23;1-13
[PubMed:38652020] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Gtari M, Beauchemin NJ, Sarker I, Sen A, Ghodhbane-Gtari F, Tisa LS
An overview of Parafrankia (Nod+/Fix+) and Pseudofrankia (Nod+/Fix-) interactions through genome mining and experimental modeling in co-culture and co-inoculation of Elaeagnus angustifolia.
Appl Environ Microbiol: 2024 Apr 23;e0028824
[PubMed:38651928] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Kou-Gi S, Wang BW, Pan CM, Fang WJ, Lin CM
Exosomal MALAT1 from macrophages treated with high levels of glucose upregulates LC3B expression via miR-204-5p downregulation.
J Chin Med Assoc: 2024 Apr 23;
[PubMed:38651895] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Chhetri A, Biswas A, Podder S, Dey RS, Mitra J
Strategic design of VO(2) encased in N-doped carbon as an efficient electrocatalyst for the nitrogen reduction reaction in neutral and acidic media.
Nanoscale: 2024 Apr 23;
[PubMed:38651787] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Lam B, Velasquez M, Ogiyama T, Godines K, Szu FY, Velasquez-Mao AJ, AlGhuraibawi W, Wang J, Messersmith PB, Vandsburger MH
Imaging of adeno-associated viral capsids for purposes of gene editing using CEST NMR/MRI.
Magn Reson Med: 2024 Apr 23;
[PubMed:38651648] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Obana KK, Law C, Mastroianni MA, Abdelaziz A, Alexander FJ, Ahmad CS, Trofa DP
What are our patients asking google about posterior cruciate ligament injuries? - frequently asked online questions and quality of online resources.
Phys Sportsmed: 2024 Apr 23;
[PubMed:38651524] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Liu Z, Chao Y, Zheng Z, Zhu L
Spontaneous oscillation of an active filament under viscosity gradients.
Soft Matter: 2024 Apr 23;
[PubMed:38651457] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Zhao M, Subudeng G, Zhao Y, Hao S, Li H
Effect of Cyclic Adenosine Monophosphate on Connexin 37 Expression in Sheep Cumulus-Oocyte Complexes.
J Dev Biol: 2024 Mar 27, 12(2);
[PubMed:38651455] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Rašiová M, Schlager O, Heiss C, Brodmann M, Mircea Olinic D, Boc V, Buso G, Belch J, Mazzolai L, Madaric J
Adverse reactions after intravascular iodinated contrast media administration and their management.
Vasa: 2024 Apr 23;
[PubMed:38651340] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Antony JS, Herranz AM, Mohammadian Gol T, Mailand S, Monnier P, Rottenberger J, Roig-Merino A, Keller B, Gowin C, Milla M, Beyer TA, Mezger M
Accelerated generation of gene-engineered monoclonal CHO cell lines using FluidFM nanoinjection and CRISPR/Cas9.
Biotechnol J: 2024 Apr, 19(4);e2300505
[PubMed:38651269] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Muzika NS, Kamai T, Williams LE, Kleiman M
Characterization of gelling agents in callus inducing media: Physical properties and their effect on callus growth.
Physiol Plant: 2024 Mar-Apr, 176(2);e14312
[PubMed:38651242] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Bergenfeld I
What can public health communicators learn from Reddit? A perspective for the next pandemic.
Front Public Health: 2024, 12;1348095
[PubMed:38651132] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Wehrli S, Irrgang C, Scott M, Arnrich B, Boender TS
The role of the (in)accessibility of social media data for infodemic management: a public health perspective on the situation in the European Union in March 2024.
Front Public Health: 2024, 12;1378412
[PubMed:38651120] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Charkhgard N
The Impact of Peer Groups and Media on Increasing Trends in Substance Use and Abuse Among the General Population During COVID-19.
Addict Health: 2024 Feb, 16(1);67-68
[PubMed:38651021] [WorldCat.org: ISSN ESSN ] [DOI] ( o)

Roda-Segarra J, Mengual-Andrés S, Payà Rico A
Analysis of social metrics on scientific production in the field of emotion-aware education through artificial intelligence.
Front Artif Intell: 2024, 7;1401162
[PubMed:38650962] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Galily Y, Samuel-Azran T, Laor T
The surprising role of marital status on sport second-screening: demographic influences during the 2022 world cup viewing in Israel.
Front Sports Act Living: 2024, 6;1329364
[PubMed:38650840] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Mahfouz HA, Alhazmi NF, Almatrafi MK, Almehmadi SS, Alharbi JK, Qadi LR, Tawakul A
The Influence of Lifestyle on Academic Performance Among Health Profession Students at Umm Al-Qura University.
Cureus: 2024 Mar, 16(3);e56759
[PubMed:38650788] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Alhusayni MA, Alzahrani AA, Alhomaidi FM, Alotaibi RN, Abu Rukbah LK, Alotaibi GF, Alnofaie MF
Interest in Rhinoplasty and Awareness of Postoperative Complications Among Female High School Students in Taif, Saudi Arabia.
Cureus: 2024 Mar, 16(3);e56741
[PubMed:38650772] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Chowdhury AH, Rad D, Rahman MS
Predicting anxiety, depression, and insomnia among Bangladeshi university students using tree-based machine learning models.
Health Sci Rep: 2024 Apr, 7(4);e2037
[PubMed:38650723] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Yulfo-Soto G, McCormick S, Chen H, Bai G, Trick HN, Hao G
Reduction of Fusarium head blight and trichothecene contamination in transgenic wheat expressing Fusarium graminearum trichothecene 3-O-acetyltransferase.
Front Plant Sci: 2024, 15;1389605
[PubMed:38650698] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Thang NN, Trang PT
Employer branding, organization's image and reputation, and intention to apply: the moderating role of the availability of organizational information on social media.
Front Sociol: 2024, 9;1256733
[PubMed:38650696] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Schuuring MJ, Anwer S, Petersen SE, Moharem-Elgamal S, Muraru D
Social media for cardiac imagers: a review.
Eur Heart J Cardiovasc Imaging: 2024 Apr 23;
[PubMed:38650541] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Gu W, Huang J, Lu Y, Lin W, Xu W, Chen FJ
Synthesis of Glycoconjugates through Chlorooxime-Thiol Conjugation.
J Org Chem: 2024 Apr 22;
[PubMed:38650458] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Wang W, Li C, Zhou C, Xiao X, Li F, Huang NY, Li L, Gu MD, Xu Q
Enrooted-type metal-support interaction boosting oxygen evolution reaction in acidic media.
Angew Chem Int Ed Engl: 2024 Apr 22;e202406947
[PubMed:38650436] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Strbo N, Rodriguez S, Padula L, Fisher E, Lyons A, Rodriguez C, Rivas K, Ibrahim M, Paidas M, Attia G
Assessment of immune cells in the uterine fluid at the time of the embryo transfer.
Am J Reprod Immunol: 2024 Apr, 91(4);e13842
[PubMed:38650366] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Kharey GS, Palace V, Whyte L, Greer CW
Influence of heavy Canadian crude oil on pristine freshwater boreal lake ecosystems in an experimental oil spill.
FEMS Microbiol Ecol: 2024 Apr 22;
[PubMed:38650065] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Odongo DO, Osir E, Awandu SS
An evaluation of physical access barriers to COVID-19 vaccines uptake among persons with physical disabilities in western Kenya.
BMC Public Health: 2024 Apr 22, 24(1);1112
[PubMed:38649905] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Ramadan A, Aboeldahab H, Bashir MN, Belal MM, Wageeh A, Atia A, Elbanna M, Alhejazi TJ, Abouzid M, Atef H, Khalid E, Elaziz OAA, Eldeeb MI, Kamel Omar DO, Refaey N, Setouhi A, Mohammed AK
Evaluating knowledge, attitude, and physical activity levels related to cardiovascular disease in Egyptian adults with and without cardiovascular disease: a community-based cross-sectional study.
BMC Public Health: 2024 Apr 22, 24(1);1107
[PubMed:38649883] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Malik G, Singh D, Bansal R
Exploring the Complex Dynamics: Examining the Influence of Deviant Personas in Online Gambling.
J Gambl Stud: 2024 Apr 22;
[PubMed:38649656] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Mykhaylyuk N
Digitalization: New era of dentistry.
J Prosthet Dent: 2024 Apr 21;
[PubMed:38649318] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Messina DM, Gross EL, Partido BB, Kearney RC
Social Media Use by Dental Hygiene Educators.
J Dent Hyg: 2024 Apr, 98(2);21-29
[PubMed:38649292] [WorldCat.org: ISSN ESSN ] ( p)

Yan ZB, Wu XM, Zhang N, Yang ZH, Zhu Z, Yu HM, Jia XQ, Yang XF
Effect of moxibustion on the SIRT1/FOXO3a signaling pathway in ApoE(-/-) mice with atherosclerosis.
Zhen Ci Yan Jiu: 2024 Apr 25, 49(4);376-383
[PubMed:38649205] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Pineau L, Alfa M, Radix C
ENDOSCOPE SAMPLING AND CULTURING METHODS.
J Hosp Infect: 2024 Apr 20;
[PubMed:38649121] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Zhou S, Song J, Sun H, Jiang Y, Jia H, Wang J, Yin X
Transport of polyethylene and polypropylene microplastics under the action of agricultural chemicals: Role of pesticide adjuvants and neonicotinoid active ingredients.
Environ Res: 2024 Apr 20;118975
[PubMed:38649018] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Jin SL, Kolis J, Parker J, Proctor DA, Prybylski D, Wardle C, Abad N, Brookmeyer KA, Voegeli C, Chiou H
Social histories of public health misinformation and infodemics: case studies of four pandemics.
Lancet Infect Dis: 2024 Apr 19;
[PubMed:38648811] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Korta Martiartu N, Salemi Yolgunlu P, Frenz M, Jaeger M
Pulse-echo ultrasound attenuation tomography.
Phys Med Biol: 2024 Apr 22;
[PubMed:38648803] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Dholakia A, Burdick KJ, Kreatsoulas C, Monuteaux MC, Tsai J, Subramanian SV, Fleegler EW
Historical Redlining and Present-Day Nonsuicide Firearm Fatalities.
Ann Intern Med: 2024 Apr 23;
[PubMed:38648643] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Pandit S, Seth D
Graphene Oxide-Induced Prototropism and Enhancement of Fluorescence Yield of Organic Molecules in Solutions: Recent Advances.
Langmuir: 2024 Apr 22;
[PubMed:38648496] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Xia C, Johnson NF
Nonlinear spreading behavior across multi-platform social media universe.
Chaos: 2024 Apr 1, 34(4);
[PubMed:38648381] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Díaz-Coello S, Winkler D, Griesser C, Moser T, Rodríguez JL, Kunze-Liebhäuser J, García G, Pastor E
Highly Active W(2)C-Based Composites for the HER in Alkaline Solution: the Role of Surface Oxide Species.
ACS Appl Mater Interfaces: 2024 Apr 22;
[PubMed:38648335] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Hasan S, Ahlgren CD, Lipphardt M, Chrumka A, Zaman R, Khan R, Waheed M, Higginbotham DO, Saleh E, McCarty SA
#lowbackpain on TikTok: A New Frontier for Orthopaedic Medical Education.
J Am Acad Orthop Surg Glob Res Rev: 2024 Apr 1, 8(4);
[PubMed:38648295] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Zhang B, Liu T, Ke Z, Li Y, Silamu W
Rumor detection based on Attention Graph Adversarial Dual Contrast Learning.
PLoS One: 2024, 19(4);e0290291
[PubMed:38648224] [WorldCat.org: ISSN ESSN ] [DOI] ( )

Lyons AC, Kersey K, Emslie C, Dimova E, Burrows A
Digital alcohol marketing and gender: A narrative synthesis.
Drug Alcohol Rev: 2024 Apr 22;
[PubMed:38648191] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Gill N, Banta JE, Gashugi L, Young SD
Analysis of Participant Stigma and Associated Costs of a Peer-Led Social Media HIV Intervention.
AIDS Educ Prev: 2024 Apr, 36(2);113-128
[PubMed:38648178] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Ingavat N, Wang X, Liew JM, Mahfut FB, But KP, Kok YJ, Bi X, Yang Y, Shintaro K, Tsoumpra M, Zhang W
Harnessing ceramic hydroxyapatite as an effective polishing strategy to remove product- and process-related impurities in bispecific antibody purification.
Bioresour Bioprocess: 2023 Dec 13, 10(1);93
[PubMed:38647984] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Kusumawati N, Sumarlan SH, Zubaidah E, Wardani AK
Isolation of xylose-utilizing yeasts from oil palm waste for xylitol and ethanol production.
Bioresour Bioprocess: 2023 Oct 13, 10(1);71
[PubMed:38647966] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Volkmar M, Maus AL, Weisbrodt M, Bohlender J, Langsdorf A, Holtmann D, Ulber R
Municipal green waste as substrate for the microbial production of platform chemicals.
Bioresour Bioprocess: 2023 Jul 22, 10(1);43
[PubMed:38647939] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Michalska K, Brown RK, Schröder U
Carbon source priority and availability limit bidirectional electron transfer in freshwater mixed culture electrochemically active bacterial biofilms.
Bioresour Bioprocess: 2023 Sep 20, 10(1);64
[PubMed:38647932] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Reyes Castillo N, Díaz CE, Andres MF, Imperial J, Valcárcel F, González Coloma AA
Optimization of fungicidal and acaricidal metabolite production by endophytic fungus Aspergillus sp. SPH2.
Bioresour Bioprocess: 2024 Mar 5, 11(1);28
[PubMed:38647905] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Wang C, Chang D, Zhang Q, Yu Z
Enhanced bioethanol production by evolved Escherichia coli LGE2-H in a microbial electrolysis cell system.
Bioresour Bioprocess: 2024 Jan 3, 11(1);4
[PubMed:38647898] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Shan C, Xia T, Liu J, Wang Y, Bai P, Xu L, Li Z, Zhao J, Bao X
The impacts of nicotinamide and inositol on the available cells and product performance of industrial baker's yeasts.
Bioresour Bioprocess: 2023 Jul 22, 10(1);41
[PubMed:38647809] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Smith SM, Bais B, Ismaili M'hamdi H, Schermer MH, Steegers-Theunissen RP
Stimulating Preconception Care Uptake by Women With a Vulnerable Health Status Through a Mobile Health App (Pregnant Faster): Pilot Feasibility Study.
JMIR Hum Factors: 2024 Apr 22, 11;e53614
[PubMed:38648092] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Shabahang R, Kim S, Chen X, Aruguete MS, Zsila Á
Downloading appetite? Investigating the role of parasocial relationship with favorite social media food influencer in followers' disordered eating behaviors.
Eat Weight Disord: 2024 Apr 22, 29(1);28
[PubMed:38647734] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Ruhluel D, Fisher L, Barton TE, Leighton H, Kumar S, Morillo PA, O'Brien S, Fothergill JL, Neill DR
Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments.
ISME J: 2024 Apr 22;
[PubMed:38647527] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Fernandez SV, Kim JH, Sadat D, Marcus C, Suh E, Mclntosh R, Shah A, Dagdeviren C
A Dynamic Ultrasound Phantom with Tissue-Mimicking Mechanical and Acoustic Properties.
Adv Sci (Weinh): 2024 Apr 22;e2400271
[PubMed:38647427] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Kerci SG, Sahan B
An Analysis of ChatGPT4 to Respond to Glaucoma-Related Questions.
J Glaucoma: 2024 Apr 23;
[PubMed:38647417] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Brown OI, Bridge KI, Straw S, Makava N, Scragg J, Limumpornpetch S, Luk C, Smith J, Skromna A, Bruns AF, Sukumar P, Roberts LD, Cubbon R, Witte KK, Wheatcroft S, Kearney MT
Studying Adipose Endothelial Cell/Adipocyte Cross-Talk in Human Subcutaneous Adipose Tissue.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647333] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Roets B, Abrahamse H, Crous A
Three-Dimensional Cell Culture of Adipose-Derived Stem Cells in a Hydrogel with Photobiomodulation Augmentation.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647328] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Charpentier M, Bloy N, Formenti SC, Galluzzi L, Demaria S
Live Imaging to Quantify Cellular Radiosensitivity in Patient-Derived Tumor Organoids.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647326] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Shimizu K, Kuze-Arata S, Kikusui T, Mogi K
Analysis of Electrocardiograms and Behavior in Mice from Pregnancy to Lactation Period.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647323] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Page-Dumroese DS, Tirocke JM, Anderson NM, Archuleta JG, McCollum DW, Morisette J, Pierson DN, Rodriguez-Franco C
Continuous In-woods Production of Biochar Using a Trailer-mounted Air Curtain Burner.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647320] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Alzoubi D, Rich W, Reilly MA
Automated Compression Testing of the Ocular Lens.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647316] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Budkov YA, Kalikin NN, Brandyshev PE
Surface tension of aqueous electrolyte solutions. A thermomechanical approach.
J Chem Phys: 2024 Apr 28, 160(16);
[PubMed:38647306] [WorldCat.org: ISSN ESSN ] [DOI] ( p)

Jockisch RD, Davey CR, Keller SMP, Lahoti S, Bramlet MT
Pioneering Patient-Specific Approaches for Precision Surgery Using Imaging and Virtual Reality.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647284] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Lopes MM, Lopes SM, Baganha R, Henriques C, Silva AC, Lobo DD, Cortes L, de Almeida LP, Nobre RJ
Isolation of Adeno-associated Viral Vectors Through a Single-step and Semi-automated Heparin Affinity Chromatography Protocol.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647283] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Molehin D, Guinan J, Lopez B
Generation of a Bovine Primary Enteroid-Derived Two-Dimensional Monolayer Culture System for Applications in Translational Biomedical Research.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647281] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Hu J, Hu C
Metacarpal Small Incision for Carpal Tunnel Syndrome.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647277] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Tan Z, Yeung TC, Ding Y, Wang CC
Establishment of an Experimental Mouse Model of Endometrioma to Study its Related Infertility.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647276] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Ni Z, Cao J, Shan M, Zhang Y, Shi L
Swimming Exercise Protocol and Care Methods for Pregnant Rats.
J Vis Exp: 2024 Apr 5, (206);
[PubMed:38647274] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Pinto M, Machado CS, Barreiro S, Otero-Espinar FJ, Remião F, Borges F, Fernandes C
Rescuing a Troubled Tolcapone with PEGylated PLGA Nanoparticles: Design, Characterization, and Hepatotoxicity Evaluation.
ACS Appl Mater Interfaces: 2024 Apr 22;
[PubMed:38647198] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Voinov MA, Nunn N, Rana R, Davidsson A, Smirnov AI, Smirnova TI
Measuring local pH at interfaces from molecular tumbling: A concept for designing EPR-active pH-sensitive labels and probes.
Org Biomol Chem: 2024 Apr 22;
[PubMed:38647161] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Farzad M, Naqui Z, MacDermid J, Cuypers S
Sustainable practices in hand therapy: a global perspective.
J Hand Surg Eur Vol: 2024 Apr 22;17531934241246451
[PubMed:38647160] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Paredes J, D'Anna L, Ramirez LD, Mayhan KT, Rhee JU, Timberlake DS
A qualitative assessment of blunt smokers' perceptions and receptivity to non-tobacco blunt wraps.
J Stud Alcohol Drugs: 2024 Apr 22;
[PubMed:38647093] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Guarducci G, Chiti M, Fattore DC, Caldararo R, Messina G, Filidei P, Nante N
Development of a network model to implement the HPV vaccination coverage.
Ann Ig: 2024 Apr 11;
[PubMed:38647091] [WorldCat.org: ISSN ESSN ] [DOI] ( a)

Waltz TB, Chao D, Prodoehl EK, Enders JD, Ehlers VL, Dharanikota BS, Dahms NM, Isaeva E, Hogan QH, Pan B, Stucky CL
Fabry disease Schwann cells release p11 to induce sensory neuron hyperactivity.
JCI Insight: 2024 Mar 7, 9(8);
[PubMed:38646936] [WorldCat.org: ISSN ESSN ] [DOI] ( e)

Wang C, Jiang H, Zhu J, Jin Y
A new agent for contrast-enhanced intravascular ultrasound imaging in vitro: polybutylcyanoacrylate nanoparticles with drug-carrying capacity.
Artif Cells Nanomed Biotechnol: 2024 Dec, 52(1);218-228
[PubMed:38646876] [WorldCat.org: ISSN ESSN ] [DOI] ( o) 

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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