Works by Jianlin Cheng

Results: 174

RECURSIVE PROTEIN MODELING:: A DIVIDE AND CONQUER STRATEGY FOR PROTEIN STRUCTURE PREDICTION AND ITS CASE STUDY IN CASP9.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 3, p. 1242003-1, doi. 10.1142/S0219720012420036

By:

CHENG, JIANLIN;
EICKHOLT, JESSE;
WANG, ZHENG;
DENG, XIN

Publication type:

Article

l‐Cysteine modified silver nanoparticles‐based colorimetric sensing for the sensitive determination of Hg<sup>2+</sup> in aqueous solutions.

Published in:

Luminescence: Journal of Biological & Chemical Luminescence, 2021, v. 36, n. 3, p. 698, doi. 10.1002/bio.3990

By:

Fan, Pengfei;
He, Shunzhen;
Cheng, Jianlin;
Hu, Congcong;
Liu, Can;
Yang, Shengyuan;
Liu, Jinquan

Publication type:

Article

Correction to: GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data.

Published in:

2020

By:

Oluwadare, Oluwatosin;
Highsmith, Max;
Turner, Douglass;
Lieberman Aiden, Erez;
Cheng, Jianlin

Publication type:

Correction Notice

GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data.

Published in:

BMC Molecular & Cell Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12860-020-00304-y

By:

Oluwadare, Oluwatosin;
Highsmith, Max;
Turner, Douglass;
Lieberman-Aiden, Erez;
Cheng, Jianlin

Publication type:

Article

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-40558-y

By:

McKay, Cole E.;
Cheng, Jianlin;
Tanner, John J.

Publication type:

Article

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-40558-y

By:

McKay, Cole E.;
Cheng, Jianlin;
Tanner, John J.

Publication type:

Article

The SEPALLATA-like gene HrSEP1 in Hippophae rhamnoides regulates flower development by interacting with other MADS-box subfamily genes.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2024.1503346

By:

Cong, Di;
Zhao, Xue;
Ni, Chang;
Li, Mengru;
Han, Luwen;
Cheng, Jianlin;
Liu, Hongzhang;
Liu, Huijing;
Yao, Dan;
Liu, Shuying;
Chen, Guoshuang

Publication type:

Article

NNcon: improved protein contact map prediction using 2D-recursive neural networks.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_2, p. W515, doi. 10.1093/nar/gkp305

By:

Tegge, Allison N.;
Wang, Zheng;
Eickholt, Jesse;
Cheng, Jianlin

Publication type:

Article

DOMAC: an accurate, hybrid protein domain prediction server.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W354, doi. 10.1093/nar/gkm390

By:

Cheng, Jianlin

Publication type:

Article

Protein structure accuracy estimation using geometry‐complete perceptron networks.

Published in:

Protein Science: A Publication of the Protein Society, 2024, v. 33, n. 3, p. 1, doi. 10.1002/pro.4932

By:

Morehead, Alex;
Liu, Jian;
Cheng, Jianlin

Publication type:

Article

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment.

Published in:

BMC Structural Biology, 2014, v. 14, p. 1, doi. 10.1186/1472-6807-14-13

By:

Renzhi Cao;
Zheng Wang;
Jianlin Cheng

Publication type:

Article

Designing and benchmarking the MULTICOM protein structure prediction system.

Published in:

BMC Structural Biology, 2013, v. 13, p. 1, doi. 10.1186/1472-6807-13-2

By:

Jilong Li;
Xin Deng;
Eickholt, Jesse;
Jianlin Cheng

Publication type:

Article

A multi-template combination algorithm for protein comparative modeling.

Published in:

BMC Structural Biology, 2008, v. 8, p. 1, doi. 10.1186/1472-6807-8-18

By:

Jianlin Cheng

Publication type:

Article

DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM.

Published in:

BMC Bioinformatics, 2020, v. 21, n. 1, p. N.PAG, doi. 10.1186/s12859-020-03809-7

By:

Al-Azzawi, Adil;
Ouadou, Anes;
Max, Highsmith;
Duan, Ye;
Tanner, John J.;
Cheng, Jianlin

Publication type:

Article

AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2926-y

By:

Al-Azzawi, Adil;
Ouadou, Anes;
Tanner, John J.;
Cheng, Jianlin

Publication type:

Article

Nursing Care of pregnant women complicated with iron deficiency anemia.

Published in:

Chinese Nursing Research, 2014, v. 28, n. 12C, p. 4576

By:

Cheng Jianlin

Publication type:

Article

Reconstructing 3D chromosome structures from single-cell Hi-C data with SO(3)-equivariant graph neural networks.

Published in:

NAR Genomics & Bioinformatics, 2025, v. 7, n. 1, p. 1, doi. 10.1093/nargab/lqaf027

By:

Wang, Yanli;
Cheng, Jianlin

Publication type:

Article

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-92395-6

By:

Wu, Tianqi;
Liu, Jian;
Guo, Zhiye;
Hou, Jie;
Cheng, Jianlin

Publication type:

Article

DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-91827-7

By:

Quadir, Farhan;
Roy, Raj S.;
Halfmann, Randal;
Cheng, Jianlin

Publication type:

Article

Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-90303-6

By:

Chen, Xiao;
Liu, Jian;
Guo, Zhiye;
Wu, Tianqi;
Hou, Jie;
Cheng, Jianlin

Publication type:

Article

VEHiCLE: a Variationally Encoded Hi-C Loss Enhancement algorithm for improving and generating Hi-C data.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-88115-9

By:

Highsmith, Max;
Cheng, Jianlin

Publication type:

Article

Deciphering the association between gene function and spatial gene-gene interactions in 3D human genome conformation.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2093-0

By:

Renzhi Cao;
Jianlin Cheng

Publication type:

Article

Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells.

Published in:

BMC Genomics, 2012, v. 13, n. 1, p. 1, doi. 10.1186/1471-2164-13-437

By:

Zhu, Mingzhu;
Deng, Xin;
Joshi, Trupti;
Xu, Dong;
Stacey, Gary;
Cheng, Jianlin

Publication type:

Article

Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics.

Published in:

BMC Genomics, 2012, v. 13, n. Suppl 1, p. 1, doi. 10.1186/1471-2164-13-S1-S15

By:

Joshi, Trupti;
Patil, Kapil;
Fitzpatrick, Michael R.;
Franklin, Levi D.;
Yao, Qiuming;
Cook, Jeffrey R.;
Wang, Zheng;
Libault, Marc;
Brechenmacher, Laurent;
Valliyodan, Babu;
Wu, Xiaolei;
Cheng, Jianlin;
Stacey, Gary;
Nguyen, Henry T.;
Xu, Dong

Publication type:

Article

Deep learning methods for protein function prediction.

Published in:

Proteomics, 2025, v. 25, n. 1-2, p. 1, doi. 10.1002/pmic.202300471

By:

Boadu, Frimpong;
Lee, Ahhyun;
Cheng, Jianlin

Publication type:

Article

Genome sequence of the palaeopolyploid soybean.

Published in:

2010

By:

Schmutz, Jeremy;
Cannon, Steven B.;
Schlueter, Jessica;
Ma, Jianxin;
Mitros, Therese;
Nelson, William;
Hyten, David L.;
Song, Qijian;
Thelen, Jay J.;
Cheng, Jianlin;
Xu, Dong;
Hellsten, Uffe;
May, Gregory D.;
Yu, Yeisoo;
Sakurai, Tetsuya;
Umezawa, Taishi;
Bhattacharyya, Madan K.;
Sandhu, Devinder;
Valliyodan, Babu;
Lindquist, Erika

Publication type:

Correction Notice

Genome sequence of the palaeopolyploid soybean.

Published in:

Nature, 2010, v. 463, n. 7278, p. 178, doi. 10.1038/nature08670

By:

Schmutz, Jeremy;
Cannon, Steven B.;
Schlueter, Jessica;
Jianxin Ma;
Mitros, Therese;
Nelson, William;
Hyten, David L.;
Qijian Song;
Thelen, Jay J.;
Jianlin Cheng;
Dong Xu;
Hellsten, Uffe;
May, Gregory D.;
Yu, Yeisoo;
Sakurai, Tetsuya;
Umezawa, Taishi;
Bhattacharyya, Madan K.;
Sandhu, Devinder;
Valliyodan, Babu;
Lindquist, Erika

Publication type:

Article

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures.

Published in:

Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03299-9

By:

Giri, Nabin;
Wang, Liguo;
Cheng, Jianlin

Publication type:

Article

DIPS-Plus: The enhanced database of interacting protein structures for interface prediction.

Published in:

Scientific Data, 2023, v. 10, n. 1, p. 1, doi. 10.1038/s41597-023-02409-3

By:

Morehead, Alex;
Chen, Chen;
Sedova, Ada;
Cheng, Jianlin

Publication type:

Article

DIPS-Plus: The enhanced database of interacting protein structures for interface prediction.

Published in:

Scientific Data, 2023, v. 10, n. 1, p. 1, doi. 10.1038/s41597-023-02409-3

By:

Morehead, Alex;
Chen, Chen;
Sedova, Ada;
Cheng, Jianlin

Publication type:

Article

Genomic imbalance determines positive and negative modulation of gene expression in diploid maize.

Published in:

Plant Cell, 2021, v. 33, n. 4, p. 917, doi. 10.1093/plcell/koab030

By:

Shi, Xiaowen;
Yang, Hua;
Chen, Chen;
Hou, Jie;
Hanson, Katherine M;
Albert, Patrice S;
Ji, Tieming;
Cheng, Jianlin;
Birchler, James A

Publication type:

Article

Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize.

Published in:

Plant Cell, 2021, v. 33, n. 4, p. 901, doi. 10.1093/plcell/koab029

By:

Yang, Hua;
Shi, Xiaowen;
Chen, Chen;
Hou, Jie;
Ji, Tieming;
Cheng, Jianlin;
Birchler, James A

Publication type:

Article

Effect of aneuploidy of a non‐essential chromosome on gene expression in maize.

Published in:

Plant Journal, 2022, v. 110, n. 1, p. 193, doi. 10.1111/tpj.15665

By:

Shi, Xiaowen;
Yang, Hua;
Chen, Chen;
Hou, Jie;
Ji, Tieming;
Cheng, Jianlin;
Birchler, James A.

Publication type:

Article

Dissection of a Down syndrome-associated trisomy to separate the gene dosage-dependent and -independent effects of an extra chromosome.

Published in:

Human Molecular Genetics, 2023, v. 32, n. 13, p. 2205, doi. 10.1093/hmg/ddad056

By:

Xing, Zhuo;
Li, Yichen;
Cortes-Gomez, Eduardo;
Jiang, Xiaoling;
Gao, Shuang;
Pao, Annie;
Shan, Jidong;
Song, Yinghui;
Perez, Amanda;
Yu, Tao;
Highsmith, Max R;
Boadu, Frimpong;
Conroy, Jeffrey M;
Singh, Prashant K;
Bakin, Andrei V;
Cheng, Jianlin;
Duan, Zhijun;
Wang, Jianmin;
Liu, Song;
Tycko, Benjamin

Publication type:

Article

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49647-6

By:

Giri, Nabin;
Cheng, Jianlin

Publication type:

Article

Hydrocarbon Resin-Based Composites with Low Thermal Expansion Coefficient and Dielectric Loss for High-Frequency Copper Clad Laminates.

Published in:

Polymers (20734360), 2022, v. 14, n. 11, p. 2200, doi. 10.3390/polym14112200

By:

Dong, Jiaojiao;
Wang, Hao;
Zhang, Qilong;
Yang, Hui;
Cheng, Jianlin;
Xia, Zhaoyue

Publication type:

Article

Modeling and Optimization of a Cooling Tower-Assisted Heat Pump System.

Published in:

Energies (19961073), 2017, v. 10, n. 5, p. 733, doi. 10.3390/en10050733

By:

Xiaoqing Wei;
Nianping Li;
Jinqing Peng;
Jianlin Cheng;
Jinhua Hu;
Meng Wang

Publication type:

Article

Performance Analyses of Counter-Flow Closed Wet Cooling Towers Based on a Simplified Calculation Method.

Published in:

Energies (19961073), 2017, v. 10, n. 3, p. 282, doi. 10.3390/en10030282

By:

Xiaoqing Wei;
Nianping Li;
Jinqing Peng;
Jianlin Cheng;
Jinhua Hu;
Meng Wang

Publication type:

Article

Transcriptomic analysis identifies gene networks regulated by estrogen receptor α (ERα) and ERβ that control distinct effects of different botanical estrogens.

Published in:

Nuclear Receptor Signaling, 2014, v. 12, p. 1, doi. 10.1621/nrs.12001

By:

Ping Gong;
Madak-Erdogan, Zeynep;
Jilong Li;
Jianlin Cheng;
Greenlief, C. Michael;
Helferich, William;
Katzenellenbogen, John A.;
Katzenellenbogen, Benita S.

Publication type:

Article

A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data.

Published in:

BMC Genomics, 2018, v. 19, p. 1, doi. 10.1186/s12864-018-4546-8

By:

Oluwadare, Oluwatosin;
Yuxiang Zhang;
Jianlin Cheng

Publication type:

Article

A deep auto-encoder model for gene expression prediction.

Published in:

BMC Genomics, 2017, v. 18, p. 39, doi. 10.1186/s12864-017-4226-0

By:

Rui Xie;
Jia Wen;
Quitadamo, Andrew;
Jianlin Cheng;
Xinghua Shi

Publication type:

Article

CONFOLD2: improved contact-driven ab initio protein structure modeling.

Published in:

BMC Bioinformatics, 2018, v. 19, p. 1, doi. 10.1186/s12859-018-2032-6

By:

Adhikari, Badri;
Jianlin Cheng

Publication type:

Article

ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1931-2

By:

Oluwadare, Oluwatosin;
Jianlin Cheng

Publication type:

Article

Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challenges.

Published in:

Human Genetics, 2025, v. 144, n. 2/3, p. 265, doi. 10.1007/s00439-024-02724-8

By:

Turina, Paola;
Petrosino, Maria;
Enriquez Sandoval, Carlos A.;
Novak, Leonore;
Pasquo, Alessandra;
Alexov, Emil;
Alladin, Muttaqi Ahmad;
Ascher, David B.;
Babbi, Giulia;
Bakolitsa, Constantina;
Casadio, Rita;
Cheng, Jianlin;
Fariselli, Piero;
Folkman, Lukas;
Kamandula, Akash;
Katsonis, Panagiotis;
Li, Minghui;
Li, Dong;
Lichtarge, Olivier;
Mahmud, Sajid

Publication type:

Article

A large expert-curated cryo-EM image dataset for machine learning protein particle picking.

Published in:

Scientific Data, 2023, v. 10, n. 1, p. 1, doi. 10.1038/s41597-023-02280-2

By:

Dhakal, Ashwin;
Gyawali, Rajan;
Wang, Liguo;
Cheng, Jianlin

Publication type:

Article

An overview of bioinformatics methods for modeling biological pathways in yeast.

Published in:

Briefings in Functional Genomics, 2016, v. 15, n. 2, p. 95, doi. 10.1093/bfgp/elv040

By:

Jie Hou;
Lipi Acharya;
Dongxiao Zhu;
Jianlin Cheng

Publication type:

Article

Heme oxygenase promotes B‐Raf‐dependent melanosphere formation.

Published in:

Pigment Cell & Melanoma Research, 2020, v. 33, n. 6, p. 850, doi. 10.1111/pcmr.12905

By:

Jasmer, Kimberly J.;
Hou, Jie;
Mannino, Philip;
Cheng, Jianlin;
Hannink, Mark

Publication type:

Article

Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteins.

Published in:

Virology Journal, 2019, v. 16, n. 1, p. N.PAG, doi. 10.1186/s12985-018-1106-4

By:

Olaya, Cristian;
Adhikari, Badri;
Raikhy, Gaurav;
Cheng, Jianlin;
Pappu, Hanu R.

Publication type:

Article

Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells.

Published in:

BMC Molecular Biology, 2015, v. 16, p. 1, doi. 10.1186/s12867-015-0049-1

By:

Yuan Lu;
Jilong Li;
Jianlin Cheng;
Lubahn, Dennis B.

Publication type:

Article

Genes targeted by the Hedgehog-signaling pathway can be regulated by Estrogen related receptor β.

Published in:

BMC Molecular Biology, 2015, v. 16, p. 1, doi. 10.1186/s12867-015-0047-3

By:

Yuan Lu;
Jilong Li;
Jianlin Cheng;
Lubahn, Dennis B.

Publication type:

Article