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Prof. Michal Linial

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Recent Publications:

(over 120 publications in peer-reviewed journals and around 200 abstracts and presentations)

Remarks: the topics in the list of publications:
Bioinformatics and Computational Biology - Bioinformatics and Computational Biology
Secretory systems and neurotransmitter release - Secretory systems and neurotransmitter release
Biotechnology and More - Biotechnology and Technical Report
Reviews and Books - Reviews and Books

Sorted by year:
2008, 2007, 2006, 2005, 2004, 2003, 2002, 2001, 2000, 1999, 1998, 1997, 1996, 1995 | Sort by topics

2008:

abstract PDF Gielchinsky, Y. Bogoch, Y. Rechavi, G. Yaacov-Hirsch, J. Amariglio, N. Shveiky, D. Linial, M. Laufer, N. (2008) Gene expression in women conceiving spontaneously over the age of 45 years. Fertility and Sterility (in press). Bioinformatics and Computational Biology

Submissions

abstract PDF Yaniv Loewenstein, Elon Portugaly, Menachem Fromer and Michal Linial, (2008) Efficient algorithms for exact hierarchical clustering of huge datasets: Tackling the entire protein space. Submitted to ISMB 2008 (Toronto). Bioinformatics and Computational Biology

abstract PDF Yaniv Loewenstein and Michal Linial, (2008) Connect the dots: Exposing hidden protein family connections from the entire sequence tree. Submitted to ECCB 2008 (Sardinia). Bioinformatics and Computational Biology

2007:

abstract PDF Bogoch Y, Linial M. (2007) Coordinated expression of cytoskeleton regulating genes in the accelerated neurite outgrowth of P19 embryonic carcinoma cells. Experimental Cell Research (in press). Bioinformatics and Computational Biology

abstract PDF Varshavsky R, Gottlieb A, Horn D, Linial M. (2007) Unsupervised feature selection under perturbations: meeting the challenges of biological data. Bioinformatics 23: 3343-3349. Bioinformatics and Computational Biology

abstract PDF Varshavsky, R. Horn, D. Linial, M. (2007) Clustering Algorithms Optimizer: A Framework for Large Datasets. ISBRA, Lecture Notes in Bioinformatics (4463), 85-96 Bioinformatics and Computational Biology

abstract PDF Varshavsky, R. Fromer, M. Man, A. Linial, M. (2007) When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features. (WABI). Lecture Notes in Computer Science (4645), 12-24. Bioinformatics and Computational Biology

abstract PDF Inberg, A. Bogoch, Y. Bledi, Y. Linial, M. (2007) Cellular processes underlying maturation of P19 neurons: Changes in protein folding regimen and cytoskeleton organization. Proteomics. 2007 7:910-920 Secretory systems and neurotransmitter release

abstract PDF Kaplan, N. Morpurgo, N. Linial, M. (2007) Novel Families of Toxin-like Peptides in Insects and Mammals: A Computational Approach, Journal Molecular Biology 369:553–566. Bioinformatics and Computational Biology, Secretory systems and neurotransmitter release

abstract PDF Bogoch, Y. Biala, YN. Linial, M. Weinstock, M. (2007) Anxiety induced by prenatal stress is associated with suppression of hippocampal genes involved in synaptic function. Journal of Neurochemistry, 101, 1018–1030. Secretory systems and neurotransmitter release

abstract PDF Portugaly, E. Linial, N. Linial, M. (2007) EVEREST: A collection of evolutionary conserved protein domains. Nucleic Acids Res. 35 (Database issue): D241-D246 Bioinformatics and Computational Biology

2006:

abstract Brachya, G. Yanay, C. Linial, M. (2006) Synaptic proteins as multi-sensor devices of neurotransmission. BMC Neurosci. 2006 Oct 30;7 Suppl 1:S4. Secretory systems and neurotransmitter release

abstract PDF Kaplan, N. Linial, M. contrinuted to
Insights into social insects from the genome of the honeybee Apis mellifera. The Honeybee Genome Sequencing Consortium Nature 444, 512 - 512 (23 Nov 2006) Corrigenda Secretory systems and neurotransmitter release

abstract Sasson, O. Kaplan, N. Linial, M. Functional annotation prediction: all for one and one for all. Protein Sci. 2006 Jun;15(6):1557-62. Epub 2006 May 2. PMID: 16672244 [PubMed - indexed for MEDLINE] Bioinformatics and Computational Biology

abstract PDF Portugaly, E. Harel, A. Linial, N. Linial, M. (2006) EVEREST: Automatic identification and classification of protein domains in all protein sequences. BMC Bioinformatics 2006, 7:277 Bioinformatics and Computational Biology

abstract PDF Kaplan, N. Linial, M. (2006) ProtoBee: hierarchical classification and annotation of the honey bee proteome. Genome Res. 2006 Nov;16(11):1431-8. Epub 2006 Oct 25. PMID: 17065614 [PubMed - indexed for MEDLINE] Bioinformatics and Computational Biology

abstract PDF Krispin, A. Bledi, Y. Atallah, M. Trahtemberg, U. Verbovetski, I. Nahari, E. Zelig, O. Linial, M. Mevorach, D. (2006) Apoptotic cell thrombospondin-1 and heparin binding domain lead to dendritic cell phagocytic and tolerizing states. Blood. 2006 Nov 15;108(10):3580-9. Epub 2006 Aug 1. PMID: 16882710 [PubMed - indexed for MEDLINE] Secretory systems and neurotransmitter release

abstract PDF Schueler-Furman, O. Glick, E. Segovia, J. Linial, M. (2006). Is GAS1 a co-receptor for the GDNF family of ligands? Trends Pharmacol Sci 27, 72-77 Bioinformatics and Computational Biology, Secretory systems and neurotransmitter release

abstract PDF Linial, M. (2006) The Secrets of a Functional Synapse ñ From a Computational and Experimental Viewpoint. BMC Bioinformatics, 7(Suppl 1):S6 Bioinformatics and Computational Biology

abstract PDF Varshavsky, R. Gottlieb, A. Linial, M. Horn, D. (2006) Novel Unsupervised Feature Filtering of Biological Data. Bioinformatics. 2006 Jul 15;22(14):e507-13. PMID: 16873514 [PubMed - indexed for MEDLINE] Bioinformatics and Computational Biology

abstract PDF Bahir, I., Linial, M (2006) Functional Grouping Based on Signatures in Protein Termini. PROTEINS: Structure, Function, and Bioinformatics 63:996ñ1004 Bioinformatics and Computational Biology

Linial, M. (2006) Computational biology tasks of a functional synapse. BMC bioinformatics 7 (in press)Bioinformatics and Computational Biology

2005:

abstract PDF Yudovin-Farber, I. Yanay, C. Azzam, T. Linial, M. Domb, A.J. (2005) Quaternary ammonium polysaccharides for gene delivery. Bioconjug Chem 16: 1196-1203. Biotechnology and More

abstract PDF Sasson. O, Kaplan. N, Linial. M, (2005) Functional annotations prediction: All for one and one for all. Protein Sci. 15: 1557-1562. Bioinformatics and Computational Biology

abstract PDF Kaplan N, Linial M. (2005) Automatic detection of false annotations via binary property clustering. BMC Bioinformatics 6, 46 (12 pages) Bioinformatics and Computational Biology

abstract PDF Varshavsky, R., Linial, M. Horn, D (2005) COMPACT - A Comparative Package for Clustering Assessment. In: Lecture Notes in Computer Science Algorithms, 3759, pp 159-167. Springer. G. Springer-Verlag Berlin Heidelberg. Bioinformatics and Computational Biology

abstract PDF Sasson, O. Linial, M. (2005) ProTarget: automatic prediction of protein structure novelty. Nucleic Acids Res. 33, W81-84. Bioinformatics and Computational Biology

abstract PDF Bahir, I., Linial, M (2005) ProTeus: identifying signatures in protein termini. Nucleic Acids Research, 2005, Vol. 33 Bioinformatics and Computational Biology

abstract PDF Bahir, I., Linial, M (2005) ProTeus: An Archive of Signatures in Proteins Termini Nucleic acids Research, 33, W277-280. Bioinformatics and Computational Biology

abstract PDF Kifer, I. Sasson, O. Linial, M. (2005) Predicting fold novelty based on ProtoNet hierarchical classification. Bioinformatics, 21, 1020-1027. Bioinformatics and Computational Biology

abstract PDF Sadka, T. Linial, M. Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domains. Bioinformatics 21, i378-i386. Bioinformatics and Computational Biology

abstract PDF Kaplan, N. Sasson, O. Inbar, U. Friedlich, M. Fromer, M. Fleischer, H. Portugaly, E. Linial, N. Linial, M. (2005) ProtoNet 4.0: A hierarchical classification of one million protein sequences. Nucleic Acids Research, 33, D216-D218. Bioinformatics and Computational Biology

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2004:

abstract PDF Kaplan, N. Friedlich, M. Fromer, Linial, M. (2004) A functional hierarchical organization of the protein sequence space. BMC Bioinformatics. 5, 196. Bioinformatics and Computational Biology

abstract PDF Inberg, A. Linial, M. (2004) Evolutional insights on uncharacterized SARS coronavirus genes. FEBS Lett. 577, 159-164. Bioinformatics and Computational Biology

abstract PDF Kaplan, N. Linial, M. (2004) False Annotations of Proteins: Automatic Detection via Keyword-Based Clustering. (12th International Conference on Intelligent Systems for Molecular Biology (ISMB) 3rd European Conference on Computational Biology (ECCB). Bioinformatics and Computational Biology

abstract PDF Shachar, O. Linial, M. A robust method to detect structural and functional remote homologues. Proteins: Structure, Function, and Bioinformatics (2004) 57, 532-538. Bioinformatics and Computational Biology

abstract PDF Kaplan, N. Friedlich, M. Fromer, M. Linial, M Functionally-Valid Unsupervised Compression of the Protein Space (2004) Bioinformatics and Computational Biology

abstract PDF Azzam T, Eliyahu H, Makovitzki A, Linial M, Domb AJ. Hydrophobized dextran-spermine conjugate as potential vector for in vitro gene transfection. Jornal Control Release (2004) 96, 309-323. Bioinformatics and Computational Biology

PDF Bogoch, Y. Bledi, Y. Tayar, S. and Linial, M. (2004) Unveiling the molecular events leading to a neurotransmitter phenotype switch in developing neurons (Cholinergic Mechanism, book chapter). Reviews and Books

abstract PDF Fromer, M. Friedlich, M. Kaplan, N. Linial, N. Linial, M. (2004) An Information - Theoretic Approach to the Supervised Partitioning of the Hierarchical Protein Space Bioinformatics and Computational Biology

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2003:

abstract PDF Kifer, I. Sasson, O. and Linial, M (2003) Target selection for structural genomics based on ProtoNet classification. Bioinformatics. Bioinformatics and Computational Biology

abstract PDF Linial, M. (2003) Fishing with (Proto)Net - a principled approach to protein target selection. Comparative Functional Genomics, 4, 542-554. Bioinformatics and Computational Biology

abstract PDF Kaplan N, Vaaknin A, Linial M. (2003) PANDORA: keyword-based analysis of protein sets by integration of annotation sources. Nucleic Acids Res. 31, 5617-5626. Bioinformatics and Computational Biology

abstract PDF Linial M. (2003) How incorrect annotations evolve - the case of short ORFs. Trends Biotechnol. 21, 298-300. Bioinformatics and Computational Biology

abstract PDF PowerPoint Sasson O, Vaaknin A, Fleischer H, Portugaly E, Bilu Y, Linial N, Linial M. (2003) ProtoNet: hierarchical classification of the protein space. Nucleic Acids Res. 31, 348-352. Bioinformatics and Computational Biology

abstract PDF Michaelevski, I, Chikvashvili, D, Tsuk, S, Singer-Lahat, D, Kang, Y, Linial, M, Gaisano, H.Y., Fili. O., Lotan, I. (2003)
Direct Interaction of Target SNAREs with the Kv2.1 Channel. Modal regulation of channel activation and inactivation gating. J Biol Chem. 278, 34320-34330. Secretory systems and neurotransmitter release

abstract PDF Bledi, Y., Inberg, A and Linial, M. (2003) A proteomic method for analysing plasma membrane proteins in living mammalian cells. Briefings in Functional Genomics and Proteomics 3, 254-265 Biotechnology and More

PDF Sasson O. and Linial M. (2003) Protein clustering and classification. In: Bioinformatics, Kluwer Academic Publishers, 29 pages (in press). Reviews and Books

PowerPoint Sasson O., Fleischer H, Portugaly E, Linial N and Linial M. (2003) ProtoNet: The system and a user guide. Technical report, School of Computer Science and Engineering. The Hebrew University of Jerusalem. Technical Report

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2002:

PDF Bilu, Y. and Linial , M. (2002) Functional consequences in metabolic pathways from phylogenetic profiles. in Lecture Notes in Computer Science vol. 2452, Algorithms in Bioinformatics, Springer (eds. Guigo, Gusfield) pp. 263-276. Bioinformatics and Computational Biology

abstract PDF Sasson O, Linial N, Linial M. (2002) The metric space of proteins-comparative study of clustering algorithms. Bioinformatics, 18, S14-21. Bioinformatics and Computational Biology

abstract PDF Portugaly E, Kifer I, Linial M. (2002) Selecting targets for structural determination by navigating in a graph of protein families. Bioinformatics, 18, 899-907. Bioinformatics and Computational Biology

abstract PDF Bilu Y, Linial M. (2002) The advantage of functional prediction based on clustering of yeast genes and its correlation with non-sequence based classifications. J Comput Biol. 9, 193-210. Bioinformatics and Computational Biology

abstract PDF Bloch-Shilderman E, Abu-Raya S, Trembovler V, Boschwitz H, Gruzman A, Linial M, Lazarovici P. (2002) Pardaxin Stimulation of Phospholipases A2 and Their Involvement in Exocytosis in PC-12 Cells cells. J Pharmacol Exp Ther. 301, 953-962. Secretory systems and neurotransmitter release

abstract PDF Azzam T, Eliyahu H, Shapira L, Linial M, Barenholz Y, Domb AJ. (2002) Polysaccharide-Oligoamine Based Conjugates for Gene Delivery. J. Med. Chem. 45, 1817-1824. Biotechnology and More

- Linial M. (2002) Large-scale protein prioritization of targets for Structural Genomics projects. "Methods in Molecular Biology" (Kennedy M.A., ed), Humana Press (in press). Reviews and Books

- Bogoch Y, Bledi Y, Tayar S, Linial M. (2002) Unveiling the molecular events leading to a neurotransmitter phenotype switch in developing neurons, Cholinergic Mechanisms (in press). Reviews and Books

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2001:

abstract PDF Linial M, (2001) SNARE Proteins - From Membranes to Genomes.
Current Genomics, 2001, 2, 337-347 Biotechnology and More

abstract PDF Bloch-Shilderman E, Jiang H, Abu-Raya S, Linial M, Lazarovici P. (2001) Involvement of Extracellular Signal-Regulated Kinase (ERK) in Pardaxin-Induced Dopamine Release from PC12 Cells. J Pharmacol Exp Ther. 296, 704-711. Secretory systems and neurotransmitter release

- Fili O, Michaelevski I, Bledi Y, Chikvashvili D, Singer-Lahat D, Boshwitz H, Linial M, Lotan I. (2001) Direct interaction of a brain voltage-gated K+ channel with syntaxin 1A: functional impact on channel gating. J Neurosci. 21, 1964-1974. Secretory systems and neurotransmitter release

abstract PDF Menichini P, Linial M. (2001) SUVi and BACH1: a new subfamily of mammalian helicases? Mutation Research 487, 67-71. Biotechnology and More

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2000:

abstract PDF Linial, M. and Yona, G. (2000) Methodologies for target selection in structural genomics. Progress in Biophysics & Molecular Biology 73, 297-320. Bioinformatics and Computational Biology

abstract PDF Friedman N, Linial M, Nachman I, Pe'er D. (2000) Using Bayesian networks to analyze expression data. J Comput Biol. 7, 601-620. Bioinformatics and Computational Biology

abstract PDF Portugaly E, Linial M. (2000) Estimating the probability for a protein to have a new fold: A statistical computational model. Proc Natl Acad Sci USA. 97, 5161-5166. Bioinformatics and Computational Biology

PDF Yona G, Linial N, Linial M. (2000) ProtoMap: automatic classification of protein sequences and hierarchy of protein families. Nucleic Acids Res. 28, 49-55. Bioinformatics and Computational Biology

abstract PDF Bledi Y, Domb AJ, Linial M. (2000) Culturing neuronal cells on surfaces coated by a novel polyethyleneimine-based polymer. Brain Research Protocols 5, 282ñ289 Biotechnology and More

- Linial M, Yona G. (2000) Methodologies for target selection in structural genomics. Prog Biophys Mol Biol. 73, 297-320. Reviews and Books

- Linial M. (2000) Neurotoxins as tools in dissecting the exocytic machinery. SubCellular Biochemistry. 34, (Harris and Hilderson, eds) Plenum Publishing Co, New York, 39-72. Reviews and Books

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1999:

abstract PDF Yona G, Linial N, Linial M. (1999) ProtoMap: Automatic Classification of Protein Sequences, a Hierarchy of Protein Families, and Local Maps of the Protein Space. PROTEINS: Structure, Function, and Genetics 37, 360ñ378. Bioinformatics and Computational Biology

- Ilouz N, Branski L, Parnis J, Parnas H, Linial M. (1999) Depolarization affects the binding properties of muscarinic acetylcholine receptors and their interaction with proteins of the exocytic apparatus. J Biol Chem. 274, 29519-29528. Secretory systems and neurotransmitter release

- Peleg G, Lewis A, Linial M, Loew LM. (1999) Nonlinear optical measurement of membrane potential around single molecules at selected cellular sites. Proc Natl Acad Sci USA. 96, 6700-6704. Biotechnology and More

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1998:

- Yona G, Linial N, Tishby N, Linial M. (1998) A map of the protein space - an automatic hierarchical classification of all protein sequences. Proc Int Conf Intell Syst Mol Biol. 212-221. Bioinformatics and Computational Biology

- Baram D, Linial M, Mekori YA, Sagi-Eisenberg R. (1998) Ca2+-dependent exocytosis in mast cells is stimulated by the Ca2+ sensor, synaptotagmin I. J Immunol. 161, 5120-5123. Secretory systems and neurotransmitter release

- Parnas D, Linial M. (1998) Highly sensitive ELISA-based assay for quantifying protein levels in neuronal cultures. Brain Res Brain Res Protoc. 2, 333-338. Secretory systems and neurotransmitter release

- Parnas D, Heldman E, Branski L, Feinstein N, Linial M. (1998) Expression and localization of muscarinic receptors in P19-derived neurons. J Mol Neurosci. 10, 17-29. Secretory systems and neurotransmitter release

- "Toxins and the Secretory System" (Linial, M. Grasso, A. Lazarowitz, P. eds) in Molecular and Cellular Mechanisms in Toxins Action (ed. P. Lazarowitz). (1998) Volume 2, Publishers: Harwood Academic Publishers GMBH, Switzerland, 480 pages. Reviews and Books

- Linial M. (1998) Neurotoxins and the safety-latches of the secretory process. in "Toxins and the Secretory System" (Linial, Grasso, Lazarowitz, eds) Vol. 2., Harwood Academic Publishers GMBH, Switzerland, 215-263. Reviews and Books

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1997:

abstract postscript Linial M, Linial N, Tishby N, Yona G. (1997) Global self-organization of all known protein sequences reveals inherent biological signatures. J Mol Biol. 268, 539-556. Bioinformatics and Computational Biology

abstract Linial M, Ilouz N, Parnas H. (1997) Voltage-dependent interaction between the muscarinic ACh receptor and proteins of the exocytic machinery. J Physiol. 504, 251-258. Secretory systems and neurotransmitter release

abstract Parnas D, Linial M. (1997) Acceleration of neuronal maturation of P19 cells by increasing culture density. Brain Res Dev Brain Res. 101, 115-124. Secretory systems and neurotransmitter release

abstract Benhar M, Boschwitz H, Linial M. (1997) Differential expression pattern of Rab-GDI isoforms during the parotid gland secretion cycle. Exp Cell Res. 233, 207-215. Secretory systems and neurotransmitter release

abstract Levius O, Feinstein N, Linial M. (1997) Expression and localization of synaptotagmin I in rat parotid gland. Eur J Cell Biol. 73, 81-92. Secretory systems and neurotransmitter release

abstract Parnas D, Linial M. (1997) Culture density regulates both the cholinergic phenotype and the expression of the CNTF receptor in P19 neurons. J Mol Neurosci. 8, 115-130. Secretory systems and neurotransmitter release

abstract Shalom S, Strinkovski A, Peleg G, Druckmann S, Krauss A, Lewis A, Linial M, Ottolenghi M. (1997) An optical submicrometer calcium sensor with conductance sensing capability. Anal Biochem. 244, 256-259. Biotechnology and More

abstract Linial M. (1997) SNARE proteins - why so many, why so few? J Neurochem. 69, 1781-1792. Reviews and Books

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1996:

- Linial M, Parnas D. (1996) Deciphering neuronal secretion: tools of the trade. Biochim Biophys Acta. 1286, 117-152. Secretory systems and neurotransmitter release

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1995:

abstract Parnas D, Linial M. (1995) Cholinergic properties of neurons differentiated from an embryonal carcinoma cell-line (P19). Int J Dev Neurosci. 13, 767-781. Secretory systems and neurotransmitter release

abstract Linial M. (1995) Bacterial neurotoxins - a thousand years later. Isr J Med Sci. 31, 591-595. Reviews and Books

 

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