My Google Scholar Page

2023

• Mayassa J Bou-Dargham, Linlin Sha, Drishty B Sarker, Martina Z Krakora-Compagno, Zhui Chen, Jinfeng Zhang, Qing-Xiang Amy Sang. TCGA RNA-Seq and Tumor-Infiltrating Lymphocyte Imaging Data Reveal Cold Tumor Signatures of Invasive Ductal Carcinomas and Estrogen Receptor-Positive Human Breast Tumors Int J Mol Sci. 24(11):9355 (2023)

2022

• Weissenbacher, Davy, ..., Qing Han, Jinfeng Zhang, ... Automatic Extraction of Medication Mentions from Tweets - Overview of the BioCreative VII Shared Task 3 Competition Database, accepted, 2022.
• Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Kai Wang, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Saipradeep VG, Zhiyong Lu.
  Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. Database, accepted, 2022.
• Chenran Wang, Yang Chen, Yuan Zhang, Keqiao Li, Menghan Lin, Feng Pan, Wei Wu, Jinfeng Zhang. A Reinforcement Learning Approach for Protein-Ligand Binding Pose Prediction. BMC Bioinformatics, In press, 2022.
• Arslan Erdengasileng, Qing Han, Tingting Zhao, Shubo Tian, Xin Sui, Keqiao Li, Wanjing Wang, Jian Wang, Ting Hu, Feng Pan, Yuan Zhang, Jinfeng Zhang. Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification. Database, Volume 2022, 2022, baac066, https://doi.org/10.1093/database/baac066

2021

• Xin Sui, Wanjing Wang, Jinfeng Zhang. Text Mining Drug-Protein Interactions using an Ensemble of BERT, Sentence BERT and T5 models. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 54, 2021.
• Arslan Erdengasileng, Keqiao Li, Qing Han, Shubo Tian, Jian Wang, Ting Hu, Jinfeng Zhang. A BERT-Based Hybrid System for Chemical Identification and Indexing in Full-Text Articles. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 130, 2021.
• Qing Han, Shubo Tian, Jinfeng Zhang. A PubMedBERT-based Classfier with Data Augmentation Strategy for Detecting Medication Mentions in Tweets. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 198, 2021.
• Meng-Han Chung, Jun Zhou, Xiaodong Pang, Yuchuan Tao, Jinfeng Zhang. BioKDE: a Deep Learning Powered Search Engine and Biomedical Knowledge Discovery Platform. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 254, 2021.
• Shubo Tian, Jinfeng Zhang.Multi-label topic classification for COVID-19 literature annotation using an ensemble model based on PubMedBERT. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 302, 2021.
• Kaixian Yu, Zihan Cui, Xin Sui, Xing, Qiu Jinfeng Zhang. Biological network inference with GRASP: a Bayesian network structure learning method using adaptive sequential Monte Carlo. Frontiers in Genetics, accepted.
• Zihan Cui, Yuhang Liu, Jinfeng Zhang, Xing Qiu, Super-delta2: An Enhanced Differential Expression Analysis Procedure for Multi-Group Comparisons of RNA-seq Data, Bioinformatics, 2021, btab155.
• Savannah D. Savadel, Thomas Hartwig, Zachary M. Turpin, Daniel L. Vera, Pei-Yau Lung, Xin Sui, Max Blank, Wolf B. Frommer, Jonathan H. Dennis, Jinfeng Zhang, Hank W. Bass. The native cistrome and sequence motif families of the maize ear. PLoS Genetics, 2021, 17(8):e1009689.
• Shubo Tian, Arslan Erdengasileng, Xi Yang, Yi Guo, Yonghui Wu, Jinfeng Zhang, Jiang Bian, Zhe He. Transformer-based named entity recognition for parsing clinical trial eligibility criteria. Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August, 2021, 49:1–6.
• Zahraa Khamis, Xiaodong Pang, Zihan Cui, Qingxiang Amy Sang, Jinfeng Zhang. Cytochrome P450-2D6: a novel biomarker in liver cancer health disparity PLoS One, accepted.

2020

• Jinchan Qu, Albert Steppi, Dongrui Zhong, Jie Hao, Jian Wang, Pei-Yau Lung, Tingting Zhao, Zhe He, Jinfeng Zhang. Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach. BMC Genomics, 2020, 21(1):773. doi: 10.1186/s12864-020-07185-7.
• Pei-Yau Lung, Dongrui Zhong, Xiaodong Pang, Yan Li, Jinfeng Zhang. Maximizing the Reusability of Gene Expression Data by Predicting Missing Metadata. PLoS Computational Biology, 2020, 16(11):e1007450.
• Avishek Mukherjee, Yaoguang Zhong, Zhenghao Zhang, Tingting Zhao, Jinfeng Zhang. Vecsim: Carrier-based, Privacy-Preserving Cellphone Contact Tracing. ACM Proceedings MobiWac’20, November 16–20, 2020, Alicante, Spain.
• Tingting Zhao, Zihan Cui, Mary Grace McClellan, Disa Yu, Qing-Xiang Amy Sang, Jinfeng Zhang. Identifying county-level factors for female breast cancer incidence rate through a large-scale population study. Applied Geography, accepted.
• Yan Li, Xiaodong Pang, Zihan Cui, Yidong Zhou, Feng Mao, Yan Lin, Xiaohui Zhang, Songjie Shen, Peixin Zhu, Tingting Zhao, Qiang Sun, Jinfeng Zhang. Genetic factors associated with cancer racial disparity - an integrative study across twenty-one cancer types. Molecular Oncology, accepted.
• Rajiv K Parvathaneni, Edoardo Bertolini, Md Shamimuzzaman, Daniel Vera, Pei-Yau Lung, Brian R Rice, Jinfeng Zhang, Patrick J Brown, Alexander E Lipka, Hank W Bass, Andrea L Eveland. The regulatory landscape of early maize inflorescence development. Genome Biology, 2020; 21: 165.
• Mayassa J. Bou-Dargham, Linlin Sha, Qing-Xiang Amy Sang, Jinfeng Zhang. Immune landscape of human prostate cancer: Immune evasion mechanisms and biomarkers for personalized immunotherapy. BMC Cancer, 20, Article number: 572 (2020).
• Yuan Zhang, Xin Sui, Scott Stagg, Jinfeng Zhang. FTIP: An Accurate and Efficient Method for Global Protein Surface Comparison. Bioinformatics, 2020; 36(10):3056-3063.
• Serin Zhang, Jiang Shao, Disa Yu, Xing Qiu, Jinfeng Zhang. MatchMixeR: A Cross-platform Normalization Method for Gene Expression Data Integration. Bioinformatics, 2020;36(8):2486-2491.

2019

• Yuan Zhang, Yang Chen, Chenran Wang, Chun-Chao Lo, Xiuwen Liu, Wei Wu, Jinfeng Zhang. ProDCoNN: Protein Design Using a Convolutional Neural Network. Proteins, In press.
• Jie Hao, Xing Wang, Shuming Shi, Jinfeng Zhang, Zhaopeng Tu. Multi-Granularity Self-Attention for Neural Machine Translation. EMNLP 2019
• Jie Hao, Xing Wang, Shuming Shi, Jinfeng Zhang, Zhaopeng Tu. Towards better modeling hierarchical structure for self-attention with ordered nuerons. EMNLP 2019
• Jie Hao, Xing Wang, Baosong Yang, Longyue Wang, Jinfeng Zhang, Zhaopeng Tu. Modeling recurrence for transformer. NAACL-HLT 2019.
• Rezarta Islamaj Dogan,..., Jinfeng Zhang, ..., Zhiyong Lu. Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database, 2019, bay147.
• Pei-Yau Lung, Zhe He, Tingting Zhao, Disa Yu, Jinfeng Zhang. Extracting chemical–protein interactions from literature using sentence structure analysis and feature engineering. Database, 2019, bay138.

2018

• Mayassa J. Bou-Dargham, Yuhang Liu, Qing-Xiang Amy Sang, Jinfeng Zhang. Subgrouping breast cancer patients based on immune evasion mechanisms unravels a high involvement of transforming growth factor-beta and decoy receptor 3. PLoS ONE 13(12): e0207799. https://doi.org/10.1371/journal.pone.0207799.
• Zachary M. Turpin, Daniel L. Vera, Savannah D. Savadel, Pei-Yau Lung, Emily E. Wear, Leigh Mickelson-Young, William F. Thompson, Linda Hanley-Bowdoin, Jonathan H. Dennis, Jinfeng Zhang, Hank W. Bass, Chromatin Structure Profile Data from DNS-seq: Differential Nuclease Sensitivity Mapping of Four Reference Tissues of B73 Maize (Zea mays L) , Data in Brief, 2018.
• Kaixian Yu, Pei-Yau Lung, Tingting Zhao, Peixiang Zhao, Yan-Yuan Tseng and Jinfeng Zhang. Automatic extraction of protein-protein interactions using grammatical relationship graph, BMC Medical Informatics and Decision Making, 2018, 18 (Suppl 2) :42
• Hamdy EA Ali, Pei-Yau Lung, Andrew B Sholl, Shaimaa A Gad, Juan J Bustamante, Hamed I Ali, Johng S Rhim, Gagan Deep, Jinfeng Zhang, Zakaria Y Abd Elmageed, Dysregulated gene expression predicts tumor aggressiveness in African-American prostate cancer patients, Scientific Reports, 2018, 8, 16335.
• Albert Steppi, Jinchan Qu, Minjing Tao, Tingting Zhao, Xiaodong Pang, Jinfeng Zhang, Simulation Study on a New Peer Review Approach, arXiv preprint arXiv:1806.08663
• Senthil Girimurugan, Yuhang Liu, Pei-Yau Lung, Daniel Vera, Jonathan Dennis, Hank Bass, Jinfeng Zhang, iSeg: an efficient algorithm for segmentation of genomic and epigenomic data. BMC Bioinformatics, 2018, 19(1):131. doi: 10.1186/s12859-018-2140-3.

2017

• Yuhang Liu, Jinfeng Zhang*, Xing Qiu*. Super-delta: a new differential gene expression analysis procedure with robust data normalization BMC Bioinformatics, 2017, 18:582, https://doi.org/10.1186/s12859-017-1992-2.
• Yan Li, Albert Steppi, Yidong Zhou, Feng Mao, Philip Craig Miller, Max M. He, Tingting Zhao, Qiang Sun, Jinfeng Zhang*. Tumoral expression of drug and xenobiotic metabolizing enzymes in breast cancer patients of different ethnicities with implications to personalized medicine . Scientific Reports, 2017 7:4747. doi:10.1038/s41598-017-04250-2.
• Kaixian Yu, Qing-Xiang Amy Sang, Pei-Yau Lung, Winston Tan, Ty Lively, Cedric Sheffield, Mayassa Bou Dargham, Jun S. Liu, Jinfeng Zhang. Personalized chemotherapy selection for breast cancer using gene expression profiles. Scientific Reports, 2017 3;7:43294. doi: 10.1038/srep43294.
• K Tang, J Zhang, J Liang. Distance-Guided Forward and Backward Chain-Growth Monte Carlo Method for Conformational Sampling and Structural Prediction of Antibody CDR-H3 Loops. Journal of Chemical Theory and Computation, 2017, 13 (1), 380–388.
• Y Shi, A Steppi, Y Cao, J Wang, MM He, L Li, J Zhang. Integrative comparison of mRNA expression patterns in breast cancers from Caucasian and Asian Americans with implications for precision medicine. Cancer Research, 2017; 77(2):423-433.

2016

• Peng Zou, Longhua Liu, Louise Zheng, Kyle Payne, Masoud H. Manjili, Michael O. Idowu, Jinfeng Zhang, Eva Maria Schmelz and Zhiyong Cheng. Coordinated upregulation of mitochondrial biogenesis and turnover in breast cancer cells: the role of dynamin related protein-1 and implication for breast cancer treatment. Oxidative Medicine and Cellular Longevity, 2016, 4085727.

2015

• Ke Tang, Samuel Wong, Jun S. Liu, Jinfeng Zhang, Jie Liang, (2015) Conformational sampling and structure prediction of multiple interacting loops in soluble and beta-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method. Bioinformatics, (2015) 31 (16): 2646-2652.

2014

• Daniel L. Vera, Thelma F. Madzima, Jonathan D. Labonne, Mohammad P. Alam, Gregg G. Hoffman, S.B. Girimurugan, Jinfeng Zhang, Karen M. McGinnis, Jonathan H. Dennis and Hank W. Bass. Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. The Plant Cell, 2014, 26(10):3883-93.
• G He, A Steppi, J Laborde, A Srivastava, P Zhao, J Zhang, (2014) RASS: A webserver for RNA alignment in the joint sequence-structure space. Nucleic Acids Research, W377-81.
• K Tang, J Zhang, J Liang. (2014) Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method. PLoS Computational Biology, 10(4): e1003539. doi:10.1371/journal.pcbi.1003539.

2013

• Sexton, B.S., Avey, D., Druliner, B. R., Fincher, J. A., Grau, D. J., Borowsky, M. L., Gupta, S., Girimurugan, S., Chicken, E., Zhang , J., Noble, W.S., Zhu, F., Kingston, R. E., and Dennis, J. H. (2013) The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed. Genome Research, 10.1101/gr.160150.113.
• Paul A. Stewart, Jennifer Luks, Mark D. Roycik, Qing-Xiang Amy Sang, and Jinfeng Zhang (2013) Differentially Expressed Transcripts and Dysregulated Signaling Pathways and Networks in African American Breast Cancer. PLoS One, 8(12): e82460.
• Wei Wu, Anuj Srivastava, Jose Laborde, Jinfeng Zhang, An Efficient Multiple Protein Structure Comparison Method and its Application to Structure Clustering and Outlier Detection, IEEE, BIBM, 2013, 69-73.
• Jose Laborde, Daniel Robinson, Anuj Srivastava, Eric Klassen and Jinfeng Zhang, RNA global alignment in the joint sequence-structure space using Elastic Shape Analysis, Nucl. Acids Res. (2013) 41 (11): e114. doi: 10.1093/nar/gkt187
• Rajesh Chowdhary, Jinfeng Zhang, Sin Lam Tan, Daniel Osborne, Vladimir B Bajic, Jun S Liu, PIMiner: a web tool for extraction of protein interactions from biomedical literature, IJDMB, (2013) 7 (4): 450-462.

2012

• Leif Ellingson, Jinfeng Zhang, Protein Surface Matching by Combining Local and Global Geometric Information, PLoS ONE, 2012, 7(7): e40540.
• Chi Zhang, Rajesh Chowdhary, Jinfeng Zhang, Biological pathway discovery through text mining and data integration, IEEE-EMBS, 2012, 5466-5469.
• Shreyas Karnik, Sin Lam Tan, Bess Berg, Ingrid Glurich, Humberto J Vidaillet, C. David Page, Jinfeng Zhang, Rajesh Chowdhary, Predicting Atrial Fibrillation and Flutter using Electronic Health Records, IEEE-EMBS, 2012, 5562-5565.
• Tingting Zhao, Lindsey Bell, Mark W. Horner, John Sulik, Jinfeng Zhang, Consumer Responses towards Home Energy Financial Incentives: A Survey-Based Study , Energy policy, (2012), 47:291-297.
• Rajesh Chowdhary, Sin Lam Tan, Jinfeng Zhang, Vladimir B. Bajic and Jun S. Liu, Context-specific Protein Network Miner - an online system for exploring context-specific protein interaction networks from the literature , PLoS One, 2012, 7(4): e34480. doi:10.1371/journal.pone.0034480.
• Sentil Balaji, Charles Mcclendon, Rajesh Chowdhary, Jun S Liu and Jinfeng Zhang, IMID: Integrated molecular interaction database , Bioinformatics, (2012) 28 (5): 747-749.

2011

• Jose Laborde, Anuj Srivastava, Jinfeng Zhang. Structure-based RNA function prediction using elastic shape analysis, IEEE-BIBM, 2011, 16-21.
• Tyrone Ryba, Ichiro Hiratani, Dana Battaglia, Micheal Kulik, Jinfeng Zhang, Stephen Dalton, and David M Gilbert. Replication timing: a fingerprint for cell identity and pluripotency, PLoS Computational Biology, 2011, 7(10): e1002225.
• Zhiyong Cheng, Jinfeng Zhang, David P Ballou, Charles H Williams, Jr, Reactivity of thioredoxin as a protein thiol-disulfide oxidoreductase , Chemical Review, 2011, 111 (9), 5768-5783.
• Lindsey Bell, Rajesh Chowdhary, Jun S Liu, Xufeng Niu, Jinfeng Zhang. Integrated bio-entity network: a system for biological knowledge discovery. PLoS ONE, 2011, 6(6): e21474, doi:10.1371/journal.pone.0021474.
• Lindsey Bell, Jinfeng Zhang, Xufeng Niu. Mixture of logistic models and an ensemble approach for extracting protein-protein interactions. ACM-BCB, 371-375, (2011).
• Leif Ellingson, Jinfeng Zhang. An efficient algorithm for matching protein binding sites for protein function prediction. ACM-BCB, 289-293, (2011).
• Wei Liu, Anuj Srivastava, Jinfeng Zhang. A mathematical framework for protein structure comparison, PLoS Computational Biology 7(2), (2011): e1001075. doi:10.1371/journal.pcbi.1001075

2010

• Yue Li, Gary Tyson, Jinfeng Zhang. Effect of sequences on the shape of protein energy landscapes , ACM-BCB, 35-42, (2010).
• Wei Liu, Anuj Srivastava, Jinfeng Zhang. Protein structure alignment using elastic shape analysis, ACM-BCB, 62-70, (2010).
• Tyrone Ryba, Ichiro Hiratani, Junjie Lu, Mari Itoh, Michael Kulik, Jinfeng Zhang, Stephen Dalton, David M. Gilbert. Evolutionarily conserved replication timing profiles distinguish closely related cell types and predict long range chromatin interactions , Genome Research, 20(6):761-70 (2010).

2009

• Rajesh Chowdhary, Jinfeng Zhang, Jun S Liu. Bayesian Inference of Protein-protein Interactions from Biological Literature , Bioinformatics, 25(12), 1536-1542 (2009).

• Jie Liang, Sema Kachalo, Xiang Li, Zheng Ouyang, Yan-Yuan Tseng, Jinfeng Zhang. Geometric structures of proteins for understanding folding, discriminating natives and predicting biochemical functions . The World Is a Jigsaw (Ed. Rien van de Weygaert), 2009, Springer.

2007

• Jinfeng Zhang, Sam C Kou, Jun S Liu. Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo Journal of Chemical Physics, 126, 225101 (2007).

• Jinfeng Zhang, Ming Lin, Rong Chen, Jie Liang, Jun S Liu. Monte Carlo sampling of near-native structures of proteins and applications, Proteins, 66, 61-68, (2007)

-2006

• Jinfeng Zhang, Jun S Liu. On side-chain conformational entropy of proteins. PLoS Computational Biology, (2006) 2(12): e168. doi:10.1371/journal.pcbi.0020168.

• Jinfeng Zhang, Rong Chen, Jie Liang. Empirical Potential Function for Simplified Protein Models: Combining Contact and Local Sequence-Structure Descriptors. Proteins. 63(4), 949-960, (2006)

• Jinfeng Zhang, Yu Chen, Rong Chen, Jie Liang. Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models. J. Chem. Phys. 121:592-603, (2004).

• Jinfeng Zhang, Rong Chen, Chao Tang, Jie Liang. Origin of scaling behavior of protein packing density: A sequential Monte Carlo study of compact long chain polymers. J. Chem. Phys. 118(13):6102-6109, (2003).

• Jie Liang, Jinfeng Zhang, Rong Chen. Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method. J. Chem. Phys., 117:3511-3521, (2002).