Recent Publications:

Remarks: the topics in the list of publications:

- Bioinformatics and Computational Biology

- Secretory systems and neurotransmitter release

- Biotechnology and Technical Report

- Reviews and Books

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

2008:

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).

Submissions

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).

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

2007:

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).

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

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

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.

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

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. ,

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.

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

2006:

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

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

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]

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

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]

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]

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 ,

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

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]

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

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

2005:

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

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

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

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.

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

Bahir, I., Linial, M (2005) ProTeus: identifying signatures in protein termini. Nucleic Acids Research, 2005, Vol. 33

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

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

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

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.

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2004:

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

Inberg, A. Linial, M. (2004) Evolutional insights on uncharacterized SARS coronavirus genes. FEBS Lett. 577, 159-164.

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).

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

Kaplan, N. Friedlich, M. Fromer, M. Linial, M Functionally-Valid Unsupervised Compression of the Protein Space (2004)

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.

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).

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

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2003:

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

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

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.

Linial M. (2003) How incorrect annotations evolve - the case of short ORFs. Trends Biotechnol. 21, 298-300.

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.

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.

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

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

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.

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2002:

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.

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

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

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.

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.

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.

- 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).

- 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).

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2001:

Linial M, (2001) SNARE Proteins - From Membranes to Genomes.
Current Genomics, 2001, 2, 337-347

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.

- 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.

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

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2000:

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

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

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.

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

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

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

- 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.

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1999:

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.

- 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.

- 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.

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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.

- 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.

- 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.

- 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.

- "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.

- 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.

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1997:

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.

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.

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

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.

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

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.

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.

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

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1996:

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

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1995:

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

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

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