Stefano Lonardi - Publications, H-index & Citations

Stefano Lonardi

keck graduate institute of applied life sciences

55H指数

272论文数

2.0W被引数

收录论文 48

发表时间

Prediction of DNA Methylation With Long-Range State-Space Models 基于长程状态空间模型的DNA甲基化预测

IEEE Transactions on Computational Biology and Bioinformatics

IF0

2025-11-19

PREAI

Hao Feng; Sakshar Chakravarty; Stefano Lonardi

Impact of Single Point Mutations in the SARS-CoV-2 Spike Protein RBD on B-Cell Receptor Diversity and Cross-Reactivity

JOURNAL OF IMMUNOLOGY

IF3.4

2025-11-01

PREAI

Olatoyinbo, Peace O.; Paco, Karen; Ray, Animesh; Hernandez, Jennifer; Zhang, Zihao; Zebardast, Sanaz; Patel, Dhruv; Roman, Isabel Condori; Felix, Jonathan; Yang, Tristan; Lonardi, Stefano; Tolstorukov, Ilya; Sazinsky, Matthew H.; Alam, Rashid M.; West, Ashwin; Ife Tugbiyele, Deborah Omosalewa; Mendivil, Mariana Paco; Lay, Jordan

ASPred: identification of antigen apecific B-cell receptors from single V(D)J sequences using large language models ASPred: 使用大型语言模型从单个V(D)J序列中鉴定抗原特异性b细胞受体

JOURNAL OF IMMUNOLOGY

IF3.4

2025-11-01

PREAI

Paco, Karen; Mendivil, Mariana Paco; Zhang, Zihao; Roman, Isabel Condori; Zebardast, Sanaz; Olatoyinbo, Peace O.; Alam, Rashid M.; Davila Ojeda, Christian; Patel, Dhruv; Felix, Jonathan; Yang, Tristan; Bin Ashraf, Faisal; Lay, Jordan; Tolstorukov, Ilya; Le Roch, Karine; Sazinsky, Matthew H.; Hernandez, Jeniffer; Lonardi, Stefano; Barroso da Silva, Fernando L.; Ray, Animesh

A drug repurposing approach reveals targetable epigenetic pathways in Plasmodium vivax hypnozoites 药物重定位方法揭示了恶性疟原虫休眠子中可靶向的表观遗传通路

ELIFE

IF0

2025-09-30

PREAI

Maher, Steven P.; Bakowski, Malina A.; Vantaux, Amelie; Flannery, Erika L.; Andolina, Chiara; Gupta, Mohit; Antonova-Koch, Yevgeniya; Argomaniz, Magdalena; Cabrera-Mora, Monica; Campo, Brice; Chao, Alexander T.; Chatterjee, Arnab K.; Cheng, Wayne T.; Chuenchob, Vorada; Cooper, Caitlin A.; Cottier, Karissa; Galinski, Mary R.; Harupa-Chung, Anke; Ji, Hana; Joseph, Sean B.; Lenz, Todd; Lonardi, Stefano; Matheson, Jessica; Mikolajczak, Sebastian A.; Moeller, Timothy; Orban, Agnes; Padin-Irizarry, Vivian; Pan, Kastin; Peneau, Julie; Prudhomme, Jacques; Roesch, Camille; Ruberto, Anthony; Sabnis, Saniya S.; Saney, Celia L.; Sattabongkot, Jetsumon; Sereshki, Saleh; Suriyakan, Sangrawee; Ubalee, Ratawan; Wang, Yinsheng; Wasisakun, Praphan; Yin, Jiekai; Popovici, Jean; McNamara, Case W.; Joyner, Chester; Nosten, Francois H.; Witkowski, Benoit; Le Roch, Karine G.; Kyle, Dennis E.

Balanced Training Sets Improve Deep Learning-Based Prediction of CRISPR sgRNA Activity

ACS SYNTHETIC BIOLOGY

IF3.9

2024-11-04

OAAI

Trivedi, Varun; Mohseni, Amirsadra; Lonardi, Stefano; Wheeldon, Ian

Insights into the evolution, virulence and speciation of Babesia MO1 and Babesia divergens through multiomics analyses

EMERGING MICROBES & INFECTIONS

IF7.5

2024-09-01

OAAI

Singh, Pallavi; Vydyam, Pratap; Fang, Tiffany; Estrada, Karel; Gonzalez, Luis Miguel; Grande, Ricardo; Kumar, Madelyn; Chakravarty, Sakshar; Berry, Vincent; Ranwez, Vincent; Carcy, Bernard; Depoix, Delphine; Sanchez, Sergio; Cornillot, Emmanuel; Abel, Steven; Ciampossin, Loic; Lenz, Todd; Harb, Omar; Sanchez-Flores, Alejandro; Montero, Estrella; Le Roch, Karine G.; Lonardi, Stefano; Mamoun, Choukri Ben

Properties and predicted functions of large genes and proteins of apicomplexan parasites 顶复门寄生虫的大基因和蛋白质的性质和预测功能

genomics proteomics bioinformatics

IF2.8

2024-04-04

OAAI

Fang, Tiffany; Mohseni, Amir; Lonardi, Stefano; Ben Mamoun, Choukri

Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes

GENOME RESEARCH

IF5.5

2024-03-01

OAAI

Yu, Wenjuan; Luo, Haohui; Yang, Jinbao; Zhang, Shengchen; Jiang, Heling; Zhao, Xianjia; Hui, Xingqi; Sun, Da; Li, Liang; Wei, Xiu-qing; Lonardi, Stefano; Pan, Weihua

Identification of Candidate Genes Controlling Red Seed Coat Color in Cowpea (Vigna unguiculata [L.] Walp)鉴定控制cow豆 (Vigna unguiculata [L.] Walp) 红色种皮颜色的候选基因

HORTICULTURAE

IF3

2024-02-09

OAAI

Herniter, Ira A.; Munoz-Amatriain, Maria; Lo, Sassoum; Guo, Yi-Ning; Lonardi, Stefano; Close, Timothy J.

Babesia BdFE1 esterase is required for the anti-parasitic activity of the ACE inhibitor fosinopril ACE抑制剂福辛普利的抗寄生虫活性需要巴贝斯虫BdFE1酯酶

JOURNAL OF BIOLOGICAL CHEMISTRY

IF3.9

2023-11-01

OAAI

Vydyam, Pratap; Choi, Jae-Yeon; Gihaz, Shalev; Chand, Meenal; Gewirtz, Meital; Thekkiniath, Jose; Lonardi, Stefano; Gennaro, Joseph C.; Ben Mamoun, Choukri

Seed coat pattern QTL and development in cowpea (Vigna unguiculata [L.] Walp.) (vol 10, 1346, 2019)

FRONTIERS IN PLANT SCIENCE

IF4.8

2023-11-01

OAAI

Herniter, Ira A.; Lo, Ryan; Munoz-Amatriain, Maria; Lo, Sassoum; Guo, Yi-Ning; Huynh, Bao-Lam; Lucas, Mitchell; Jia, Zhenyu; Roberts, Philip A.; Lonardi, Stefano; Close, Timothy J.

acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens acCRISPR: 一种提高CRISPR筛选准确性的活性校正方法

COMMUNICATIONS BIOLOGY

IF5.1

2023-06-08

OAAI

Ramesh, Adithya; Trivedi, Varun; Lee, Sangcheon; Tafrishi, Aida; Schwartz, Cory; Mohseni, Amirsadra; Li, Mengwan; Lonardi, Stefano; Wheeldon, Ian

On the prediction of non-CG DNA methylation using machine learning 基于机器学习的非CG DNA甲基化预测研究

genomics proteomics bioinformatics

IF2.8

2023-05-17

OAAI

Sereshki, Saleh; Lee, Nathan; Omirou, Michalis; Fasoula, Dionysia; Lonardi, Stefano

A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)

PLANT GENOME

IF3.8

2023-03-22

OAAI

Liang, Qihua; Munoz-Amatriain, Maria; Shu, Shengqiang; Lo, Sassoum; Wu, Xinyi; Carlson, Joseph W.; Davidson, Patrick; Goodstein, David M.; Phillips, Jeremy; Janis, Nadia M.; Lee, Elaine J.; Liang, Chenxi; Morrell, Peter L.; Farmer, Andrew D.; Xu, Pei; Close, Timothy J.; Lonardi, Stefano

Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly

PLOS PATHOGENS

IF4.9

2022-10-10

OAAI

Matson, Michael E. H.; Liang, Qihua; Lonardi, Stefano; Judelson, Howard S.

Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and-Cas12a guides in Yarrowia lipolytica 全基因组功能筛选可以预测解脂耶氏酵母中的高活性CRISPR-Cas9 and-Cas12a指南

NATURE COMMUNICATIONS

IF15.7

2022-02-17

OAAI

Baisya, Dipankar; Ramesh, Adithya; Schwartz, Cory; Lonardi, Stefano; Wheeldon, Ian

Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation 小胡子: 使用尺度空间表示从hi-c和micro-c图对染色质环进行多尺度检测

GENOME BIOLOGY

IF9.4

2020-09-30

112

OAAI

Roayaei Ardakany, Abbas; Gezer, Halil Tuvan; Lonardi, Stefano; Ay, Ferhat

Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.)Cow豆 (Vigna unguiculata [L.] Walp。) 的种皮模式QTL和发育

FRONTIERS IN PLANT SCIENCE

IF4.8

2019-10-25

OAAI

Herniter, Ira A.; Lo, Ryan; Munoz-Amatriain, Maria; Lo, Sassoum; Guo, Yi-Ning; Bao-Lam Huynh; Lucas, Mitchell; Jia, Zhenyu; Roberts, Philip A.; Lonardi, Stefano; Close, Timothy J.

Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica 验证全基因组CRISPR-Cas9功能可改善产油酵母Yarrowia lipolytica的筛选

METABOLIC ENGINEERING

IF6.8

2019-09-01

OAAI

Schwartz, Cory; Cheng, Jan-Fang; Evans, Robert; Schwartz, Christopher A.; Wagner, James M.; Anglin, Scott; Beitz, Adam; Pan, Weihua; Lonardi, Stefano; Blenner, Mark; Alper, Hal S.; Yoshikuni, Yasuo; Wheeldon, Ian

The genome of cowpea (Vigna unguiculata [L.] Walp.)

PLANT JOURNAL

IF5.7

2019-05-28

237

OAAI

Lonardi, Stefano; Munoz-Amatriain, Maria; Liang, Qihua; Shu, Shengqiang; Wanamaker, Steve I.; Lo, Sassoum; Tanskanen, Jaakko; Schulman, Alan H.; Zhu, Tingting; Luo, Ming-Cheng; Alhakami, Hind; Ounit, Rachid; Hasan, Abid Md.; Verdier, Jerome; Roberts, Philip A.; Santos, Jansen R. P.; Ndeve, Arsenio; Dolezel, Jaroslav; Vrana, Jan; Hokin, Samuel A.; Farmer, Andrew D.; Cannon, Steven B.; Close, Timothy J.

研究方向