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Items: 1 to 50 of 269

1.

A cell-based probabilistic approach unveils the concerted action of miRNAs.

Mahlab-Aviv S, Linial N, Linial M.

PLoS Comput Biol. 2019 Dec 2;15(12):e1007204. doi: 10.1371/journal.pcbi.1007204. eCollection 2019 Dec.

2.

Serine substitutions are linked to codon usage and differ for variable and conserved protein regions.

Schwartz GW, Shauli T, Linial M, Hershberg U.

Sci Rep. 2019 Nov 21;9(1):17238. doi: 10.1038/s41598-019-53452-3.

3.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I.

Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8.

4.

Simian Foamy Virus Co-Infections.

Murray SM, Linial ML.

Viruses. 2019 Sep 27;11(10). pii: E902. doi: 10.3390/v11100902. Review.

5.

Substantial batch effects in TCGA exome sequences undermine pan-cancer analysis of germline variants.

Rasnic R, Brandes N, Zuk O, Linial M.

BMC Cancer. 2019 Aug 7;19(1):783. doi: 10.1186/s12885-019-5994-5.

6.

Quantifying gene selection in cancer through protein functional alteration bias.

Brandes N, Linial N, Linial M.

Nucleic Acids Res. 2019 Jul 26;47(13):6642-6655. doi: 10.1093/nar/gkz546.

7.

Giant Viruses-Big Surprises.

Brandes N, Linial M.

Viruses. 2019 Apr 30;11(5). pii: E404. doi: 10.3390/v11050404. Review.

8.

Human genes escaping X-inactivation revealed by single cell expression data.

Wainer Katsir K, Linial M.

BMC Genomics. 2019 Mar 12;20(1):201. doi: 10.1186/s12864-019-5507-6.

9.

Corrigendum to "Spumaretroviruses: Updated taxonomy and nomenclature" [Virology 516 (2018) 158-164].

Khan AS, Bodem J, Buseyne F, Gessain A, Johnson W, Kuhn JH, Kuzmak J, Lindemann D, Linial ML, Löchelt M, Materniak-Kornas M, Soares MA, Switzer WM.

Virology. 2019 Feb;528. pii: S0042-6822(18)30390-8. doi: 10.1016/j.virol.2018.12.018. Epub 2019 Jan 20. No abstract available.

10.

Age-Induced Spatial Memory Deficits in Rats Are Correlated with Specific Brain Region Alterations in Microglial Morphology and Gene Expression.

Shoham S, Linial M, Weinstock M.

J Neuroimmune Pharmacol. 2019 Jun;14(2):251-262. doi: 10.1007/s11481-018-9817-2. Epub 2018 Oct 20.

PMID:
30343448
11.

Characteristics of myeloproliferative neoplasms in patients exposed to ionizing radiation following the Chernobyl nuclear accident.

Poluben L, Puligandla M, Neuberg D, Bryke CR, Hsu Y, Shumeiko O, Yuan X, Voznesensky O, Pihan G, Adam M, Fraenkel E, Rasnic R, Linial M, Klymenko S, Balk SP, Fraenkel PG.

Am J Hematol. 2019 Jan;94(1):62-73. doi: 10.1002/ajh.25307. Epub 2018 Oct 31.

12.

Small RNA sequences derived from pre-microRNAs in the supraspliceosome.

Mahlab-Aviv S, Boulos A, Peretz AR, Eliyahu T, Carmel L, Sperling R, Linial M.

Nucleic Acids Res. 2018 Nov 16;46(20):11014-11029. doi: 10.1093/nar/gky791.

13.

Spumaretroviruses: Updated taxonomy and nomenclature.

Khan AS, Bodem J, Buseyne F, Gessain A, Johnson W, Kuhn JH, Kuzmak J, Lindemann D, Linial ML, Löchelt M, Materniak-Kornas M, Soares MA, Switzer WM.

Virology. 2018 Mar;516:158-164. doi: 10.1016/j.virol.2017.12.035. Review. Erratum in: Virology. 2019 Feb;528:.

14.

Foamy virus zoonotic infections.

Pinto-Santini DM, Stenbak CR, Linial ML.

Retrovirology. 2017 Dec 2;14(1):55. doi: 10.1186/s12977-017-0379-9. Review.

15.

Overlooked Short Toxin-Like Proteins: A Shortcut to Drug Design.

Linial M, Rappoport N, Ofer D.

Toxins (Basel). 2017 Oct 29;9(11). pii: E350. doi: 10.3390/toxins9110350.

16.

Enhancing identification of cancer types via lowly-expressed microRNAs.

Rasnic R, Linial N, Linial M.

Nucleic Acids Res. 2017 May 19;45(9):5048-5060. doi: 10.1093/nar/gkx210.

17.

ASAP: a machine learning framework for local protein properties.

Brandes N, Ofer D, Linial M.

Database (Oxford). 2016 Oct 2;2016. pii: baw133. Print 2016.

18.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

19.

Gene overlapping and size constraints in the viral world.

Brandes N, Linial M.

Biol Direct. 2016 May 21;11:26. doi: 10.1186/s13062-016-0128-3.

20.

Trends in genome dynamics among major orders of insects revealed through variations in protein families.

Rappoport N, Linial M.

BMC Genomics. 2015 Aug 7;16:583. doi: 10.1186/s12864-015-1771-2.

21.

ProFET: Feature engineering captures high-level protein functions.

Ofer D, Linial M.

Bioinformatics. 2015 Nov 1;31(21):3429-36. doi: 10.1093/bioinformatics/btv345. Epub 2015 Jun 30.

PMID:
26130574
22.

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.

Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B.

F1000Res. 2015 Jan 15;4:12. doi: 10.12688/f1000research.6038.1. eCollection 2015.

23.

A Seminomadic Population in Bangladesh with Extensive Exposure to Macaques Does Not Exhibit High Levels of Zoonotic Simian Foamy Virus Infection.

Craig KL, Hasan MK, Jackson DL, Engel GA, Soliven K, Feeroz MM, Wang X, Jones-Engel L, Linial ML.

J Virol. 2015 Jul;89(14):7414-6. doi: 10.1128/JVI.01065-15. Epub 2015 Apr 29.

24.

ProtoBug: functional families from the complete proteomes of insects.

Rappoport N, Linial M.

Database (Oxford). 2015 Apr 24;2015:bau122. doi: 10.1093/database/bau122. Print 2015.

25.

Extended fertility and longevity: the genetic and epigenetic link.

Wainer-Katsir K, Zou JY, Linial M.

Fertil Steril. 2015 May;103(5):1117-24. doi: 10.1016/j.fertnstert.2015.02.008. Epub 2015 Mar 18. Review.

PMID:
25796320
26.

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.

Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B.

Bioinformatics. 2015 Feb 15;31(4):616-7. doi: 10.1093/bioinformatics/btv019. Epub 2015 Feb 2.

PMID:
25644272
27.

Obituary: Axel Rethwilm (1959-2014).

Berkhout B, Bodem J, Erlwein O, Herchenröder O, Khan AS, Lever AM, Lindemann D, Linial ML, Löchelt M, McClure MO, Scheller C, Weiss RA.

Retrovirology. 2014 Sep 25;11:85. doi: 10.1186/s12977-014-0085-9. No abstract available.

28.

Entropy-driven partitioning of the hierarchical protein space.

Rappoport N, Stern A, Linial N, Linial M.

Bioinformatics. 2014 Sep 1;30(17):i624-30. doi: 10.1093/bioinformatics/btu478.

29.

miRror-Suite: decoding coordinated regulation by microRNAs.

Friedman Y, Karsenty S, Linial M.

Database (Oxford). 2014 Jun 6;2014. pii: bau043. doi: 10.1093/database/bau043. Print 2014.

30.

NeuroPID: a classifier of neuropeptide precursors.

Karsenty S, Rappoport N, Ofer D, Zair A, Linial M.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W182-6. doi: 10.1093/nar/gku363. Epub 2014 May 3.

31.

The automated function prediction SIG looks back at 2013 and prepares for 2014.

Wass MN, Mooney SD, Linial M, Radivojac P, Friedberg I.

Bioinformatics. 2014 Jul 15;30(14):2091-2. doi: 10.1093/bioinformatics/btu117. Epub 2014 Mar 3. No abstract available.

32.

A novel Bayesian method for detection of APOBEC3-mediated hypermutation and its application to zoonotic transmission of simian foamy viruses.

Matsen FA 4th, Small CT, Soliven K, Engel GA, Feeroz MM, Wang X, Craig KL, Hasan MK, Emerman M, Linial ML, Jones-Engel L.

PLoS Comput Biol. 2014 Feb 27;10(2):e1003493. doi: 10.1371/journal.pcbi.1003493. eCollection 2014 Feb.

33.

Speed controls in translating secretory proteins in eukaryotes--an evolutionary perspective.

Mahlab S, Linial M.

PLoS Comput Biol. 2014 Jan;10(1):e1003294. doi: 10.1371/journal.pcbi.1003294. Epub 2014 Jan 2.

34.

miRror2.0: a platform for assessing the joint action of microRNAs in cell regulation.

Friedman Y, Linial M.

J Bioinform Comput Biol. 2013 Dec;11(6):1343012. doi: 10.1142/S0219720013430129.

PMID:
24372041
35.

NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes.

Ofer D, Linial M.

Bioinformatics. 2014 Apr 1;30(7):931-40. doi: 10.1093/bioinformatics/btt725. Epub 2013 Dec 13.

PMID:
24336809
36.

New World simian foamy virus infections in vivo and in vitro.

Stenbak CR, Craig KL, Ivanov SB, Wang X, Soliven KC, Jackson DL, Gutierrez GA, Engel G, Jones-Engel L, Linial ML.

J Virol. 2014 Jan;88(2):982-91. doi: 10.1128/JVI.03154-13. Epub 2013 Nov 6.

37.

Simian foamy virus infection of rhesus macaques in Bangladesh: relationship of latent proviruses and transcriptionally active viruses.

Soliven K, Wang X, Small CT, Feeroz MM, Lee EG, Craig KL, Hasan K, Engel GA, Jones-Engel L, Matsen FA 4th, Linial ML.

J Virol. 2013 Dec;87(24):13628-39. doi: 10.1128/JVI.01989-13. Epub 2013 Oct 9.

38.

Zoonotic simian foamy virus in Bangladesh reflects diverse patterns of transmission and co-infection.

Engel GA, Small CT, Soliven K, Feeroz MM, Wang X, Kamrul Hasan M, Oh G, Rabiul Alam SM, Craig KL, Jackson DL, Matsen Iv FA, Linial ML, Jones-Engel L.

Emerg Microbes Infect. 2013 Sep;2(9):e58. doi: 10.1038/emi.2013.60. Epub 2013 Sep 4.

39.

Short toxin-like proteins attack the defense line of innate immunity.

Tirosh Y, Ofer D, Eliyahu T, Linial M.

Toxins (Basel). 2013 Jul 23;5(7):1314-31. doi: 10.3390/toxins5071314.

40.

Population dynamics of rhesus macaques and associated foamy virus in Bangladesh.

Feeroz MM, Soliven K, Small CT, Engel GA, Andreina Pacheco M, Yee JL, Wang X, Kamrul Hasan M, Oh G, Levine KL, Rabiul Alam SM, Craig KL, Jackson DL, Lee EG, Barry PA, Lerche NW, Escalante AA, Matsen Iv FA, Linial ML, Jones-Engel L.

Emerg Microbes Infect. 2013 May;2(5):e29. doi: 10.1038/emi.2013.23. Epub 2013 May 22.

41.

ProtoNet: charting the expanding universe of protein sequences.

Rappoport N, Linial N, Linial M.

Nat Biotechnol. 2013 Apr;31(4):290-2. doi: 10.1038/nbt.2553. No abstract available.

PMID:
23563419
42.

Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex.

Rappoport N, Linial M.

BMC Bioinformatics. 2013;14 Suppl 3:S11. doi: 10.1186/1471-2105-14-S3-S11. Epub 2013 Feb 28.

43.

Foamy virus assembly with emphasis on pol encapsidation.

Lee EG, Stenbak CR, Linial ML.

Viruses. 2013 Mar 20;5(3):886-900. doi: 10.3390/v5030886. Review.

44.

Working together: combinatorial regulation by microRNAs.

Friedman Y, Balaga O, Linial M.

Adv Exp Med Biol. 2013;774:317-37. doi: 10.1007/978-94-007-5590-1_16. Review.

PMID:
23377980
45.

A large-scale evaluation of computational protein function prediction.

Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.

Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.

46.

Short toxin-like proteins abound in Cnidaria genomes.

Tirosh Y, Linial I, Askenazi M, Linial M.

Toxins (Basel). 2012 Nov 16;4(11):1367-84. doi: 10.3390/toxins4111367.

47.

Expression of prototype foamy virus pol as a Gag-Pol fusion protein does not change the timing of reverse transcription.

Jackson DL, Lee EG, Linial ML.

J Virol. 2013 Jan;87(2):1252-4. doi: 10.1128/JVI.02153-12. Epub 2012 Nov 7.

48.

Implicit biology in peptide spectral libraries.

Askenazi M, Linial M.

Anal Chem. 2012 Sep 18;84(18):7919-25. doi: 10.1021/ac301674y. Epub 2012 Aug 31.

PMID:
22909014
49.

Toward a combinatorial nature of microRNA regulation in human cells.

Balaga O, Friedman Y, Linial M.

Nucleic Acids Res. 2012 Oct;40(19):9404-16. doi: 10.1093/nar/gks759. Epub 2012 Aug 16.

50.

Paving the future: finding suitable ISMB venues.

Rost B, Gaasterland T, Lengauer T, Linial M, Markel S, Morrison McKay BJ, Schneider R, Horton P, Kelso J.

Bioinformatics. 2012 Oct 1;28(19):2556-9. Epub 2012 Jul 13.

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