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Items: 1 to 50 of 107

1.

Integrating multi-omics longitudinal data to reconstruct networks underlying lung development.

Ding J, Ahangari F, Espinoza CR, Chhabra D, Nicola T, Yan X, Lal CV, Hagood JS, Kaminski N, Bar-Joseph Z, Ambalavanan N.

Am J Physiol Lung Cell Mol Physiol. 2019 Aug 21. doi: 10.1152/ajplung.00554.2018. [Epub ahead of print]

PMID:
31432713
2.

Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains.

Rashid S, Long Z, Singh S, Kohram M, Vashistha H, Navlakha S, Salman H, Oltvai ZN, Bar-Joseph Z.

Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11770-11775. doi: 10.1073/pnas.1816315116. Epub 2019 May 24.

PMID:
31127043
3.

Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data.

Lin C, Bar-Joseph Z.

Bioinformatics. 2019 Apr 30. pii: btz296. doi: 10.1093/bioinformatics/btz296. [Epub ahead of print]

PMID:
31038684
4.

Protein interaction disruption in cancer.

Ruffalo M, Bar-Joseph Z.

BMC Cancer. 2019 Apr 23;19(1):370. doi: 10.1186/s12885-019-5532-5.

5.

Dynamic interaction network inference from longitudinal microbiome data.

Lugo-Martinez J, Ruiz-Perez D, Narasimhan G, Bar-Joseph Z.

Microbiome. 2019 Apr 2;7(1):54. doi: 10.1186/s40168-019-0660-3.

6.

Cell lineage inference from SNP and scRNA-Seq data.

Ding J, Lin C, Bar-Joseph Z.

Nucleic Acids Res. 2019 Jun 4;47(10):e56. doi: 10.1093/nar/gkz146.

7.

Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data.

Rashid S, Shah S, Bar-Joseph Z, Pandya R.

Bioinformatics. 2019 Feb 15. pii: btz095. doi: 10.1093/bioinformatics/btz095. [Epub ahead of print]

PMID:
30768159
8.

Network-guided prediction of aromatase inhibitor response in breast cancer.

Ruffalo M, Thomas R, Chen J, Lee AV, Oesterreich S, Bar-Joseph Z.

PLoS Comput Biol. 2019 Feb 11;15(2):e1006730. doi: 10.1371/journal.pcbi.1006730. eCollection 2019 Feb.

9.

Predicting protein targets for drug-like compounds using transcriptomics.

Pabon NA, Xia Y, Estabrooks SK, Ye Z, Herbrand AK, Süß E, Biondi RM, Assimon VA, Gestwicki JE, Brodsky JL, Camacho CJ, Bar-Joseph Z.

PLoS Comput Biol. 2018 Dec 7;14(12):e1006651. doi: 10.1371/journal.pcbi.1006651. eCollection 2018 Dec.

10.

A web server for comparative analysis of single-cell RNA-seq data.

Alavi A, Ruffalo M, Parvangada A, Huang Z, Bar-Joseph Z.

Nat Commun. 2018 Nov 13;9(1):4768. doi: 10.1038/s41467-018-07165-2.

11.

Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.

Friedman CE, Nguyen Q, Lukowski SW, Helfer A, Chiu HS, Miklas J, Levy S, Suo S, Han JJ, Osteil P, Peng G, Jing N, Baillie GJ, Senabouth A, Christ AN, Bruxner TJ, Murry CE, Wong ES, Ding J, Wang Y, Hudson J, Ruohola-Baker H, Bar-Joseph Z, Tam PPL, Powell JE, Palpant NJ.

Cell Stem Cell. 2018 Oct 4;23(4):586-598.e8. doi: 10.1016/j.stem.2018.09.009.

PMID:
30290179
12.

Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer.

Ray M, Ruffalo MM, Bar-Joseph Z.

Genes Chromosomes Cancer. 2019 Jan;58(1):34-42. doi: 10.1002/gcc.22688. Epub 2018 Nov 18.

PMID:
30285311
13.

Hercules: a profile HMM-based hybrid error correction algorithm for long reads.

Firtina C, Bar-Joseph Z, Alkan C, Cicek AE.

Nucleic Acids Res. 2018 Nov 30;46(21):e125. doi: 10.1093/nar/gky724.

14.

iDREM: Interactive visualization of dynamic regulatory networks.

Ding J, Hagood JS, Ambalavanan N, Kaminski N, Bar-Joseph Z.

PLoS Comput Biol. 2018 Mar 14;14(3):e1006019. doi: 10.1371/journal.pcbi.1006019. eCollection 2018 Mar.

15.

Reconstructing differentiation networks and their regulation from time series single-cell expression data.

Ding J, Aronow BJ, Kaminski N, Kitzmiller J, Whitsett JA, Bar-Joseph Z.

Genome Res. 2018 Jan 9. doi: 10.1101/gr.225979.117. [Epub ahead of print]

16.

Network Design and the Brain.

Navlakha S, Bar-Joseph Z, Barth AL.

Trends Cogn Sci. 2018 Jan;22(1):64-78. doi: 10.1016/j.tics.2017.09.012. Epub 2017 Oct 17. Review.

PMID:
29054336
17.

MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor.

Ding J, Bar-Joseph Z.

Bioinformatics. 2017 Nov 1;33(21):3477-3479. doi: 10.1093/bioinformatics/btx449.

18.

Reconstructing cancer drug response networks using multitask learning.

Ruffalo M, Stojanov P, Pillutla VK, Varma R, Bar-Joseph Z.

BMC Syst Biol. 2017 Oct 10;11(1):96. doi: 10.1186/s12918-017-0471-8.

19.

Using neural networks for reducing the dimensions of single-cell RNA-Seq data.

Lin C, Jain S, Kim H, Bar-Joseph Z.

Nucleic Acids Res. 2017 Sep 29;45(17):e156. doi: 10.1093/nar/gkx681.

20.

Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study.

Herazo-Maya JD, Sun J, Molyneaux PL, Li Q, Villalba JA, Tzouvelekis A, Lynn H, Juan-Guardela BM, Risquez C, Osorio JC, Yan X, Michel G, Aurelien N, Lindell KO, Klesen MJ, Moffatt MF, Cookson WO, Zhang Y, Garcia JGN, Noth I, Prasse A, Bar-Joseph Z, Gibson KF, Zhao H, Herzog EL, Rosas IO, Maher TM, Kaminski N.

Lancet Respir Med. 2017 Nov;5(11):857-868. doi: 10.1016/S2213-2600(17)30349-1. Epub 2017 Sep 21.

21.

TASIC: determining branching models from time series single cell data.

Rashid S, Kotton DN, Bar-Joseph Z.

Bioinformatics. 2017 Aug 15;33(16):2504-2512. doi: 10.1093/bioinformatics/btx173.

PMID:
28379537
22.

Selecting the most appropriate time points to profile in high-throughput studies.

Kleyman M, Sefer E, Nicola T, Espinoza C, Chhabra D, Hagood JS, Kaminski N, Ambalavanan N, Bar-Joseph Z.

Elife. 2017 Jan 26;6. pii: e18541. doi: 10.7554/eLife.18541.

23.

Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men.

Venkatachari NJ, Jain S, Walker L, Bivalkar-Mehla S, Chattopadhyay A, Bar-Joseph Z, Rinaldo C, Ragin A, Seaberg E, Levine A, Becker J, Martin E, Sacktor N, Ayyavoo V.

AIDS. 2017 Mar 13;31(5):623-633. doi: 10.1097/QAD.0000000000001379.

24.

A transcription factor hierarchy defines an environmental stress response network.

Song L, Huang SC, Wise A, Castanon R, Nery JR, Chen H, Watanabe M, Thomas J, Bar-Joseph Z, Ecker JR.

Science. 2016 Nov 4;354(6312). pii: aag1550.

25.

Genome wide predictions of miRNA regulation by transcription factors.

Ruffalo M, Bar-Joseph Z.

Bioinformatics. 2016 Sep 1;32(17):i746-i754. doi: 10.1093/bioinformatics/btw452.

PMID:
27587697
26.

Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments.

Sefer E, Kleyman M, Bar-Joseph Z.

Cell Syst. 2016 Jul;3(1):35-42. doi: 10.1016/j.cels.2016.06.007. Epub 2016 Jul 21.

27.

Reconstructing the temporal progression of HIV-1 immune response pathways.

Jain S, Arrais J, Venkatachari NJ, Ayyavoo V, Bar-Joseph Z.

Bioinformatics. 2016 Jun 15;32(12):i253-i261. doi: 10.1093/bioinformatics/btw254.

28.

Unbiased, High-Throughput Electron Microscopy Analysis of Experience-Dependent Synaptic Changes in the Neocortex.

Chandrasekaran S, Navlakha S, Audette NJ, McCreary DD, Suhan J, Bar-Joseph Z, Barth AL.

J Neurosci. 2015 Dec 16;35(50):16450-62. doi: 10.1523/JNEUROSCI.1573-15.2015.

29.

Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch.

Venkatachari NJ, Zerbato JM, Jain S, Mancini AE, Chattopadhyay A, Sluis-Cremer N, Bar-Joseph Z, Ayyavoo V.

Retrovirology. 2015 Oct 6;12:85. doi: 10.1186/s12977-015-0211-3.

30.

De novo ChIP-seq analysis.

He X, Cicek AE, Wang Y, Schulz MH, Le HS, Bar-Joseph Z.

Genome Biol. 2015 Sep 23;16:205. doi: 10.1186/s13059-015-0756-4.

31.

The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease Progression.

Gitter A, Bar-Joseph Z.

Methods Mol Biol. 2016;1303:493-506. doi: 10.1007/978-1-4939-2627-5_30.

PMID:
26235087
32.

Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks.

Navlakha S, Barth AL, Bar-Joseph Z.

PLoS Comput Biol. 2015 Jul 28;11(7):e1004347. doi: 10.1371/journal.pcbi.1004347. eCollection 2015 Jul.

33.

cDREM: inferring dynamic combinatorial gene regulation.

Wise A, Bar-Joseph Z.

J Comput Biol. 2015 Apr;22(4):324-33. doi: 10.1089/cmb.2015.0010.

34.

Multitask learning of signaling and regulatory networks with application to studying human response to flu.

Jain S, Gitter A, Bar-Joseph Z.

PLoS Comput Biol. 2014 Dec 18;10(12):e1003943. doi: 10.1371/journal.pcbi.1003943. eCollection 2014 Dec.

35.

SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data.

Wise A, Bar-Joseph Z.

Bioinformatics. 2015 Apr 15;31(8):1250-7. doi: 10.1093/bioinformatics/btu800. Epub 2014 Dec 4.

36.

ModuleBlast: identifying activated sub-networks within and across species.

Zinman GE, Naiman S, O'Dee DM, Kumar N, Nau GJ, Cohen HY, Bar-Joseph Z.

Nucleic Acids Res. 2015 Feb 18;43(3):e20. doi: 10.1093/nar/gku1224. Epub 2014 Nov 26.

37.

Gene expression in relation to exhaled nitric oxide identifies novel asthma phenotypes with unique biomolecular pathways.

Modena BD, Tedrow JR, Milosevic J, Bleecker ER, Meyers DA, Wu W, Bar-Joseph Z, Erzurum SC, Gaston BM, Busse WW, Jarjour NN, Kaminski N, Wenzel SE.

Am J Respir Crit Care Med. 2014 Dec 15;190(12):1363-72. doi: 10.1164/rccm.201406-1099OC.

38.

Topological properties of robust biological and computational networks.

Navlakha S, He X, Faloutsos C, Bar-Joseph Z.

J R Soc Interface. 2014 Apr 30;11(96):20140283. doi: 10.1098/rsif.2014.0283. Print 2014 Jul 6.

39.

Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells.

Zhou Y, Vazquez A, Wise A, Warita T, Warita K, Bar-Joseph Z, Oltvai ZN.

BMC Syst Biol. 2013 Dec 12;7:138. doi: 10.1186/1752-0509-7-138.

40.

Predicting tissue specific transcription factor binding sites.

Zhong S, He X, Bar-Joseph Z.

BMC Genomics. 2013 Nov 15;14:796. doi: 10.1186/1471-2164-14-796.

41.

Future directions in idiopathic pulmonary fibrosis research. An NHLBI workshop report.

Blackwell TS, Tager AM, Borok Z, Moore BB, Schwartz DA, Anstrom KJ, Bar-Joseph Z, Bitterman P, Blackburn MR, Bradford W, Brown KK, Chapman HA, Collard HR, Cosgrove GP, Deterding R, Doyle R, Flaherty KR, Garcia CK, Hagood JS, Henke CA, Herzog E, Hogaboam CM, Horowitz JC, King TE Jr, Loyd JE, Lawson WE, Marsh CB, Noble PW, Noth I, Sheppard D, Olsson J, Ortiz LA, O'Riordan TG, Oury TD, Raghu G, Roman J, Sime PJ, Sisson TH, Tschumperlin D, Violette SM, Weaver TE, Wells RG, White ES, Kaminski N, Martinez FJ, Wynn TA, Thannickal VJ, Eu JP.

Am J Respir Crit Care Med. 2014 Jan 15;189(2):214-22. doi: 10.1164/rccm.201306-1141WS.

42.

ExpressionBlast: mining large, unstructured expression databases.

Zinman GE, Naiman S, Kanfi Y, Cohen H, Bar-Joseph Z.

Nat Methods. 2013 Oct;10(10):925-6. doi: 10.1038/nmeth.2630. No abstract available.

PMID:
24076985
43.

Reconstructing dynamic microRNA-regulated interaction networks.

Schulz MH, Pandit KV, Lino Cardenas CL, Ambalavanan N, Kaminski N, Bar-Joseph Z.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15686-91. doi: 10.1073/pnas.1303236110. Epub 2013 Aug 28.

44.

A high-throughput framework to detect synapses in electron microscopy images.

Navlakha S, Suhan J, Barth AL, Bar-Joseph Z.

Bioinformatics. 2013 Jul 1;29(13):i9-17. doi: 10.1093/bioinformatics/btt222.

45.

Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation.

Le HS, Bar-Joseph Z.

Bioinformatics. 2013 Jul 1;29(13):i89-97. doi: 10.1093/bioinformatics/btt231.

46.

Identifying proteins controlling key disease signaling pathways.

Gitter A, Bar-Joseph Z.

Bioinformatics. 2013 Jul 1;29(13):i227-36. doi: 10.1093/bioinformatics/btt241.

47.

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis.

Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR.

Elife. 2013 Jun 11;2:e00675. doi: 10.7554/eLife.00675.

48.

MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts.

Duskova K, Nagilla P, Le HS, Iyer P, Thalamuthu A, Martinson J, Bar-Joseph Z, Buchanan W, Rinaldo C, Ayyavoo V.

BMC Infect Dis. 2013 May 30;13:250. doi: 10.1186/1471-2334-13-250.

49.

Probabilistic error correction for RNA sequencing.

Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z.

Nucleic Acids Res. 2013 May 1;41(10):e109. doi: 10.1093/nar/gkt215. Epub 2013 Apr 4.

50.

Linking the signaling cascades and dynamic regulatory networks controlling stress responses.

Gitter A, Carmi M, Barkai N, Bar-Joseph Z.

Genome Res. 2013 Feb;23(2):365-76. doi: 10.1101/gr.138628.112. Epub 2012 Oct 11.

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