Jian Peng

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2020

Deriving high-spatiotemporal-resolution leaf area index for agroecosystems in the U.S. Corn Belt using Planet Labs CubeSat and STAIR fusion data

Kimm, H., Guan, K., Jiang, C., Peng, B., Gentry, L. F., Wilkin, S. C., Wang, S., Cai, Y., Bernacchi, C. J., Peng, J. & Luo, Y., Mar 15 2020, In : Remote Sensing of Environment. 239, 111615.

Research output: Contribution to journalArticle

2019

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

AstraZeneca-Sanger Drug Combination DREAM Consortium, Dec 1 2019, In : Nature communications. 10, 1, 2674.

Research output: Contribution to journalArticle

Open Access

Identification of pathways associated with chemosensitivity through network embedding

Wang, S., Huang, E., Cairns, J., Peng, J., Wang, L. & Sinha, S., Mar 2019, In : PLoS computational biology. 15, 3, e1006864.

Research output: Contribution to journalArticle

Open Access

Integrating satellite and climate data to predict wheat yield in Australia using machine learning approaches

Cai, Y., Guan, K., Lobell, D., Potgieter, A. B., Wang, S., Peng, J., Xu, T., Asseng, S., Zhang, Y., You, L. & Peng, B., Aug 15 2019, In : Agricultural and Forest Meteorology. 274, p. 144-159 16 p.

Research output: Contribution to journalArticle

Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction

Su, Y., Luo, Y., Zhao, X., Liu, Y. & Peng, J., Jan 1 2019, In : PLoS computational biology. 15, 9, e1007283.

Research output: Contribution to journalArticle

Open Access

Metagenomic binning through low-density hashing

Luo, Y., Yu, Y. W., Zeng, J., Berger, B. & Peng, J., Jan 15 2019, In : Bioinformatics. 35, 2, p. 219-226 8 p.

Research output: Contribution to journalArticle

Open Access

Robust single-cell Hi-C clustering by convolution- And random-walk–based imputation

Zhou, J., Ma, J., Chen, Y., Cheng, C., Bao, B., Peng, J., Sejnowski, T. J., Dixon, J. R. & Ecker, J. R., Jan 1 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 28, p. 14011-14018 8 p.

Research output: Contribution to journalArticle

Open Access

Stratification of amyotrophic lateral sclerosis patients: A crowdsourcing approach

The ALS Stratification Consortium & Peng, J., Jan 1 2019, In : Scientific reports. 9, 1, 690.

Research output: Contribution to journalArticle

Open Access

Toward building a transparent statistical model for improving crop yield prediction: Modeling rainfed corn in the U.S

Li, Y., Guan, K., Yu, A., Peng, B., Zhao, L., Li, B. & Peng, J., Mar 15 2019, In : Field Crops Research. 234, p. 55-65 11 p.

Research output: Contribution to journalArticle

2018

A high-performance and in-season classification system of field-level crop types using time-series Landsat data and a machine learning approach

Cai, Y., Guan, K., Peng, J., Wang, S., Seifert, C., Wardlow, B. & Li, Z., Jun 1 2018, In : Remote Sensing of Environment. 210, p. 35-47 13 p.

Research output: Contribution to journalArticle

DPPred: An Effective Prediction Framework with Concise Discriminative Patterns

Shang, J., Jiang, M., Tong, W., Xiao, J., Peng, J. & Han, J., Jul 1 2018, In : IEEE Transactions on Knowledge and Data Engineering. 30, 7, p. 1226-1239 14 p.

Research output: Contribution to journalArticle

Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks

Liu, Y., Palmedo, P., Ye, Q., Berger, B. & Peng, J., Jan 24 2018, In : Cell Systems. 6, 1, p. 65-74.e3

Research output: Contribution to journalArticle

Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks

Cho, H., Berger, B. & Peng, J., Aug 22 2018, In : Cell Systems. 7, 2, p. 185-191.e4

Research output: Contribution to journalArticle

Learning structural motif representations for efficient protein structure search

Liu, Y., Ye, Q., Wang, L. & Peng, J., Sep 1 2018, In : Bioinformatics. 34, 17, p. i773-i780

Research output: Contribution to journalArticle

Reconstructing spatial organizations of chromosomes through manifold learning

Zhu, G., Deng, W., Hu, H., Ma, R., Zhang, S., Yang, J., Peng, J., Kaplan, T. & Zeng, J., May 4 2018, In : Nucleic acids research. 46, 8, p. e50

Research output: Contribution to journalArticle

Open Access

Typing tumors using pathways selected by somatic evolution

Wang, S., Ma, J., Zhang, W., Shen, J. P., Huang, J., Peng, J. & Ideker, T., Dec 1 2018, In : Nature communications. 9, 1, 4159.

Research output: Contribution to journalArticle

2017

A DREAM challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration- resistant prostate cancer

Prostate Cancer DREAM Challenge Community, Jan 1 2017, In : JCO Clinical Cancer Informatics. 2017, 1, p. 1-15 15 p.

Research output: Contribution to journalArticle

Open Access

A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

Luo, Y., Zhao, X., Zhou, J., Yang, J., Zhang, Y., Kuang, W., Peng, J., Chen, L. & Zeng, J., Dec 1 2017, In : Nature communications. 8, 1, 573.

Research output: Contribution to journalArticle

Detection of complexes in biological networks through diversified dense subgraph mining

Ma, X., Zhou, G., Shang, J., Wang, J., Peng, J. & Han, J., Sep 2017, In : Journal of Computational Biology. 24, 9, p. 923-941 19 p.

Research output: Contribution to journalArticle

Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways

Khurana, V., Peng, J., Chung, C. Y., Auluck, P. K., Fanning, S., Tardiff, D. F., Bartels, T., Koeva, M., Eichhorn, S. W., Benyamini, H., Lou, Y., Nutter-Upham, A., Baru, V., Freyzon, Y., Tuncbag, N., Costanzo, M., San Luis, B. J., Schöndorf, D. C., Barrasa, M. I., Ehsani, S. & 10 others, Sanjana, N., Zhong, Q., Gasser, T., Bartel, D. P., Vidal, M., Deleidi, M., Boone, C., Fraenkel, E., Berger, B. & Lindquist, S., Feb 22 2017, In : Cell Systems. 4, 2, p. 157-170.e14

Research output: Contribution to journalArticle

Network-assisted target identification for haploinsufficiency and homozygous profiling screens

Wang, S. & Peng, J., Jun 2017, In : PLoS computational biology. 13, 6, e1005553.

Research output: Contribution to journalArticle

On the interpretability of conditional probability estimates in the agnostic setting

Gao, Y., Parameswaran, A. & Peng, J., Jan 1 2017, In : Electronic Journal of Statistics. 11, 2, p. 5198-5231 34 p.

Research output: Contribution to journalArticle

2016

Compact Integration of Multi-Network Topology for Functional Analysis of Genes

Cho, H., Berger, B. & Peng, J., Dec 21 2016, In : Cell Systems. 3, 6, p. 540-548.e5

Research output: Contribution to journalArticle

DWCox: A density-weighted Cox model for outlier-robust prediction of prostate cancer survival

Xiao, J., Wang, S., Shang, J., Lin, H., Xin, D., Ren, X., Han, J. & Peng, J., Jan 1 2016, In : F1000Research. 5, 2806.

Research output: Contribution to journalArticle

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

Wang, S., Peng, J., Ma, J. & Xu, J., Jan 11 2016, In : Scientific reports. 6, 18962.

Research output: Contribution to journalArticle

Reconstructing causal biological networks through active learning

Cho, H., Berger, B. & Peng, J., Mar 1 2016, In : PloS one. 11, 3, e0150611.

Research output: Contribution to journalArticle

2015

Discovering What Dimensionality Reduction Really Tells Us about RNA-Seq Data

Simmons, S., Peng, J., Bienkowska, J. & Berger, B., Aug 1 2015, In : Journal of Computational Biology. 22, 8, p. 715-728 14 p.

Research output: Contribution to journalArticle

Exploiting ontology graph for predicting sparsely annotated gene function

Wang, S., Cho, H., Zhai, C. X., Berger, B. & Peng, J., Jun 15 2015, In : Bioinformatics. 31, 12, p. i357-i364

Research output: Contribution to journalArticle

Widespread macromolecular interaction perturbations in human genetic disorders

Sahni, N., Yi, S., Taipale, M., Fuxman Bass, J. I., Coulombe-Huntington, J., Yang, F., Peng, J., Weile, J., Karras, G. I., Wang, Y., Kovács, I. A., Kamburov, A., Krykbaeva, I., Lam, M. H., Tucker, G., Khurana, V., Sharma, A., Liu, Y. Y., Yachie, N., Zhong, Q. & 28 others, Shen, Y., Palagi, A., San-Miguel, A., Fan, C., Balcha, D., Dricot, A., Jordan, D. M., Walsh, J. M., Shah, A. A., Yang, X., Stoyanova, A. K., Leighton, A., Calderwood, M. A., Jacob, Y., Cusick, M. E., Salehi-Ashtiani, K., Whitesell, L. J., Sunyaev, S., Berger, B., Barabási, A. L., Charloteaux, B., Hill, D. E., Hao, T., Roth, F. P., Xia, Y., Walhout, A. J. M., Lindquist, S. & Vidal, M., Apr 23 2015, In : Cell. 161, 3, p. 647-660 14 p.

Research output: Contribution to journalArticle

2014

A community computational challenge to predict the activity of pairs of compounds

Bansal, M., Yang, J., Karan, C., Menden, M. P., Costello, J. C., Tang, H., Xiao, G., Li, Y., Allen, J., Zhong, R., Chen, B., Kim, M., Wang, T., Heiser, L. M., Realubit, R., Mattioli, M., Alvarez, M. J., Shen, Y., Gallahan, D., Singer, D. & 32 others, Saez-Rodriguez, J., Xie, Y., Stolovitzky, G., Califano, A., Abbuehl, J. P., Altman, R. B., Balcome, S., Bell, A., Bender, A., Berger, B., Bernard, J., Bieberich, A. A., Borboudakis, G., Chan, C., Chen, T. H., Choi, J., Coelho, L. P., Creighton, C. J., Dampier, W., Davisson, V. J., Deshpande, R., Diao, L., Di Camillo, B., Dundar, M., Ertel, A., Goswami, C. P., Gottlieb, A., Gould, M. N., Goya, J., Peng, J., Cellworks Group & NCI-DREAM Community, Dec 1 2014, In : Nature Biotechnology. 32, 12, p. 1213-1222 10 p.

Research output: Contribution to journalArticle

A community effort to assess and improve drug sensitivity prediction algorithms

NCI-DREAM Community, Dec 1 2014, In : Nature Biotechnology. 32, 12, p. 1202-1212 11 p.

Research output: Contribution to journalArticle

A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways

Taipale, M., Tucker, G., Peng, J., Krykbaeva, I., Lin, Z. Y., Larsen, B., Choi, H., Berger, B., Gingras, A. C. & Lindquist, S., Jul 17 2014, In : Cell. 158, 2, p. 434-448 15 p.

Research output: Contribution to journalArticle

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

Berger, E., Yorukoglu, D., Peng, J. & Berger, B., Mar 2014, In : PLoS computational biology. 10, 3, e1003502.

Research output: Contribution to journalArticle

HIV control is mediated in part by CD8+ T-cell targeting of specific epitopes

Pereyra, F., Heckerman, D., Carlson, J. M., Kadie, C., Soghoian, D. Z., Karel, D., Goldenthal, A., Davis, O. B., DeZiel, C. E., Lin, T., Peng, J., Piechocka, A., Carrington, M. & Walker, B. D., Jan 1 2014, In : Journal of virology. 88, 22, p. 12937-12948 12 p.

Research output: Contribution to journalArticle

Selection bias at the heterosexual HIV-1 transmission bottleneck

Carlson, J. M., Schaefer, M., Monaco, D. C., Batorsky, R., Claiborne, D. T., Prince, J., Deymier, M. J., Ende, Z. S., Klatt, N. R., DeZiel, C. E., Lin, T. H., Peng, J., Seese, A. M., Shapiro, R., Frater, J., Ndung'u, T., Tang, J., Goepfert, P., Gilmour, J., Price, M. A. & 6 others, Kilembe, W., Heckerman, D., Goulder, P. J. R., Allen, T. M., Allen, S. & Hunter, E., Jan 1 2014, In : Science. 345, 6193, 1254031.

Research output: Contribution to journalArticle

2013

Compressive genomics for protein databases

Daniels, N. M., Gallant, A., Peng, J., Cowen, L. J., Baym, M. & Berger, B., Jul 1 2013, In : Bioinformatics. 29, 13, p. i283-i290

Research output: Contribution to journalArticle

Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B gag proteins

Boutwell, C. L., Carlson, J. M., Lin, T. H., Seese, A., Power, K. A., Peng, J., Tang, Y., Brumme, Z. L., Heckerman, D., Schneidewind, A. & Allen, T. M., Apr 1 2013, In : Journal of virology. 87, 7, p. 3952-3965 14 p.

Research output: Contribution to journalArticle

Protein structure alignment beyond spatial proximity

Wang, S., Ma, J., Peng, J. & Xu, J., Mar 25 2013, In : Scientific reports. 3, 1448.

Research output: Contribution to journalArticle

2012

A computational framework for boosting confidence in high-throughput protein-protein interaction datasets

Hosur, R., Peng, J., Vinayagam, A., Stelzl, U., Xu, J., Perrimon, N., Bienkowska, J. & Berger, B., Jan 1 2012, In : Genome biology. 13, 8, p. R76

Research output: Contribution to journalArticle

A conditional neural fields model for protein threading

Ma, J., Peng, J., Wang, S. & Xu, J., Jun 1 2012, In : Bioinformatics. 28, 12, p. i59-i66 bts213.

Research output: Contribution to journalArticle

Modeling large regions in proteins: Applications to loops, termini, and folding

Adhikari, A. N., Peng, J., Wilde, M., Xu, J., Freed, K. F. & Sosnick, T. R., Jan 1 2012, In : Protein Science. 21, 1, p. 107-121 15 p.

Research output: Contribution to journalArticle

Template-based protein structure modeling using the RaptorX web server

Källberg, M., Wang, H., Wang, S., Peng, J., Wang, Z., Lu, H. & Xu, J., Aug 1 2012, In : Nature Protocols. 7, 8, p. 1511-1522 12 p.

Research output: Contribution to journalArticle

2011

Alignment of distantly related protein structures: Algorithm, bound and implications to homology modeling

Wang, S., Peng, J. & Xu, J., Sep 1 2011, In : Bioinformatics. 27, 18, p. 2537-2545 9 p., btr432.

Research output: Contribution to journalArticle

A multiple-template approach to protein threading

Peng, J. & Xu, J., Jun 1 2011, In : Proteins: Structure, Function and Bioinformatics. 79, 6, p. 1930-1939 10 p.

Research output: Contribution to journalArticle

Protein 8-class secondary structure prediction using conditional neural fields

Wang, Z., Zhao, F., Peng, J. & Xu, J., Oct 1 2011, In : Proteomics. 11, 19, p. 3786-3792 7 p.

Research output: Contribution to journalArticle

Raptorx: Exploiting structure information for protein alignment by statistical inference

Peng, J. & Xu, J., Oct 12 2011, In : Proteins: Structure, Function and Bioinformatics. 79, SUPPL. 10, p. 161-171 11 p.

Research output: Contribution to journalArticle

2010

A probabilistic and continuous model of protein conformational space for template-free modeling

Zhao, F., Peng, J., Debartolo, J., Freed, K. F., Sosnick, T. R. & Xu, J., Jun 1 2010, In : Journal of Computational Biology. 17, 6, p. 783-798 16 p.

Research output: Contribution to journalArticle

Fragment-free approach to protein folding using conditional neural fields

Zhao, F., Peng, J. & Xu, J., Jun 1 2010, In : Bioinformatics. 26, 12, p. i310-i317 btq193.

Research output: Contribution to journalArticle

Low-homology protein threading

Peng, J. & Xu, J., Jun 1 2010, In : Bioinformatics. 26, 12, p. i294-i300 btq192.

Research output: Contribution to journalArticle