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2. Detect influential points of feature rankings

Author

Wang, Shuo and Lu, Junyan

Subjects
Statistics - Applications, Statistics - Methodology
Abstract

Background Deriving feature rankings is essential in bioinformatics studies since the ordered features are important in guiding subsequent research. Feature rankings may be distorted by influential points (IP), but such effects are rarely mentioned in previous studies. This study aimed to investigate the impact of IPs on feature rankings and propose a new method to detect IPs. Method The present study utilized a case-deletion (i.e., leave-one-out) approach to assess the impact of cases. The influence of a case was measured by comparing the rank changes before and after the deletion of that case. We proposed a rank comparison method using adaptive top-prioritized weights that highlighted the rank changes of the top-ranked features. The weights were adjustable to the distribution of rank changes. Results Potential IPs could be observed in several datasets. The presence of IPs could significantly alter the results of the following analysis (e.g., enriched pathways), suggesting the necessity of IPs detection when deriving feature rankings. Compared with existing methods, the novel rank comparison method could identify rank changes of important (top-ranked) features because of employing the adaptive weights adjusted to the distribution of rank changes. Conclusions IPs detection should be routinely performed when deriving feature rankings. The new method for IPs detection exhibited favorable features compared with existing methods.

Published
2023

4. IAP dependency of T-cell prolymphocytic leukemia identified by high-throughput drug screening

Author

Pohly, Marcel Fabian, Putzker, Kerstin, Scheinost, Sebastian, Ben Taarit, Lena, Walther, Tatjana, Kummer, Sandra, Wertheimer, Tobias, Lin, Minqi, Do, Thi Huong Lan, Handler, Kristina, Michler, Jan, Kivioja, Jarno, Bach, Karsten, Kisele, Samanta, Kim, James, Dietrich, Sascha, Bornhauser, Beat, Wei-Lynn Wong, Wendy, Becher, Burkhard, Moor, Andreas, Lewis, Joe, Ficht, Xenia, Lu, Junyan, Huber, Wolfgang, and Zenz, Thorsten

Published
2025
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5. Dual biological role and clinical impact of de novo chromatin activation in chronic lymphocytic leukemia

Author

Chapaprieta, Vicente, Maiques-Diaz, Alba, Nadeu, Ferran, Clot, Guillem, Massoni-Badosa, Ramon, Mozas, Pablo, Mateos-Jáimez, Judith, Vidal, Anna, Charalampopoulou, Stella, Duran-Ferrer, Martí, Royo, Romina, Russiñol, Núria, Llaó-Cid, Laura, Piñeyroa, Juan A., Villamor, Neus, Heyn, Holger, Herbst, Sophie A., Lu, Junyan, Bryant, Dean J., Strefford, Jonathan C., Dietrich, Sascha, Zenz, Thorsten, Delgado, Julio, López-Guillermo, Armando, Campo, Elias, and Martin-Subero, Jose I.

Published
2025
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6. Ex vivo drug response profiling for response and outcome prediction in hematologic malignancies: the prospective non-interventional SMARTrial

Author

Liebers, Nora, Bruch, Peter-Martin, Terzer, Tobias, Hernandez-Hernandez, Miguel, Paramasivam, Nagarajan, Fitzgerald, Donnacha, Altmann, Heidi, Roider, Tobias, Kolb, Carolin, Knoll, Mareike, Lenze, Angela, Platzbecker, Uwe, Röllig, Christoph, Baldus, Claudia, Serve, Hubert, Bornhäuser, Martin, Hübschmann, Daniel, Müller-Tidow, Carsten, Stölzel, Friedrich, Huber, Wolfgang, Benner, Axel, Zenz, Thorsten, Lu, Junyan, and Dietrich, Sascha

Published
2023
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12. A Modified BiSeNet for Spinal Segmentation

Author

Deng, Yunjiao, Gu, Feng, Wang, Shuai, Zeng, Daxing, Lu, Junyan, Liu, Haitao, Hou, Yulei, Zhang, Qinghua, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Yang, Huayong, editor, Liu, Honghai, editor, Zou, Jun, editor, Yin, Zhouping, editor, Liu, Lianqing, editor, Yang, Geng, editor, Ouyang, Xiaoping, editor, and Wang, Zhiyong, editor

Published
2023
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14. Negative feedback regulation of MAPK signaling is an important driver of chronic lymphocytic leukemia progression

Author

Ecker, Veronika, Brandmeier, Lisa, Stumpf, Martina, Giansanti, Piero, Moreira, Aida Varela, Pfeuffer, Lisa, Fens, Marcel H.A.M., Lu, Junyan, Kuster, Bernhard, Engleitner, Thomas, Heidegger, Simon, Rad, Roland, Ringshausen, Ingo, Zenz, Thorsten, Wendtner, Clemens-Martin, Müschen, Markus, Jellusova, Julia, Ruland, Jürgen, and Buchner, Maike

Published
2023
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17. A Modified BiSeNet for Spinal Segmentation

Author

Deng, Yunjiao, primary, Gu, Feng, additional, Wang, Shuai, additional, Zeng, Daxing, additional, Lu, Junyan, additional, Liu, Haitao, additional, Hou, Yulei, additional, and Zhang, Qinghua, additional

Published
2023
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20. Proteogenomics refines the molecular classification of chronic lymphocytic leukemia

Author

Herbst, Sophie A., Vesterlund, Mattias, Helmboldt, Alexander J., Jafari, Rozbeh, Siavelis, Ioannis, Stahl, Matthias, Schitter, Eva C., Liebers, Nora, Brinkmann, Berit J., Czernilofsky, Felix, Roider, Tobias, Bruch, Peter-Martin, Iskar, Murat, Kittai, Adam, Huang, Ying, Lu, Junyan, Richter, Sarah, Mermelekas, Georgios, Umer, Husen Muhammad, Knoll, Mareike, Kolb, Carolin, Lenze, Angela, Cao, Xiaofang, Österholm, Cecilia, Wahnschaffe, Linus, Herling, Carmen, Scheinost, Sebastian, Ganzinger, Matthias, Mansouri, Larry, Kriegsmann, Katharina, Kriegsmann, Mark, Anders, Simon, Zapatka, Marc, Del Poeta, Giovanni, Zucchetto, Antonella, Bomben, Riccardo, Gattei, Valter, Dreger, Peter, Woyach, Jennifer, Herling, Marco, Müller-Tidow, Carsten, Rosenquist, Richard, Stilgenbauer, Stephan, Zenz, Thorsten, Huber, Wolfgang, Tausch, Eugen, Lehtiö, Janne, and Dietrich, Sascha

Published
2022
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21. Viral transduction of primary human lymphoma B cells reveals mechanisms of NOTCH-mediated immune escape

Author

Mangolini, Maurizio, Maiques-Diaz, Alba, Charalampopoulou, Stella, Gerhard-Hartmann, Elena, Bloehdorn, Johannes, Moore, Andrew, Giachetti, Giorgia, Lu, Junyan, Roamio Franklin, Valar Nila, Chilamakuri, Chandra Sekkar Reddy, Moutsopoulos, Ilias, Rosenwald, Andreas, Stilgenbauer, Stephan, Zenz, Thorsten, Mohorianu, Irina, D’Santos, Clive, Deaglio, Silvia, Hodson, Daniel J., Martin-Subero, Jose I., and Ringshausen, Ingo

Published
2022
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24. The protein landscape of chronic lymphocytic leukemia

Author

Meier-Abt, Fabienne, Lu, Junyan, Cannizzaro, Ester, Pohly, Marcel F., Kummer, Sandra, Pfammatter, Sibylle, Kunz, Laura, Collins, Ben C., Nadeu, Ferran, Lee, Kwang Seok, Xue, Peng, Gwerder, Myriam, Roiss, Michael, Hüllein, Jennifer, Scheinost, Sebastian, Dietrich, Sascha, Campo, Elias, Huber, Wolfgang, Aebersold, Ruedi, and Zenz, Thorsten

Published
2021
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29. Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia

Author

Lu, Junyan, Cannizzaro, Ester, Meier-Abt, Fabienne, Scheinost, Sebastian, Bruch, Peter-Martin, Giles, Holly A. R., Lütge, Almut, Hüllein, Jennifer, Wagner, Lena, Giacopelli, Brian, Nadeu, Ferran, Delgado, Julio, Campo, Elías, Mangolini, Maurizio, Ringshausen, Ingo, Böttcher, Martin, Mougiakakos, Dimitrios, Jacobs, Andrea, Bodenmiller, Bernd, Dietrich, Sascha, Oakes, Christopher C., Zenz, Thorsten, and Huber, Wolfgang

Published
2021
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30. Urodynamic analysis of the effect of electroacupuncture at different acupoints on the bladder after spinal cord injury.

Author

Lu, Junyan, Cheng, Bo, and Lin, Le

Subjects
SPINAL cord injuries, ACUPUNCTURE points, ELECTROACUPUNCTURE, NEUROGENIC bladder, URINARY organs
Abstract

Objective: Guanyuan (CV4), Zhongji (CV3) and Sanyinjiao (SP6) are the most frequently used acupoints for treating neurogenic bladder after spinal cord injury (SCI). However, there has been no investigation to clarify the differences in effects of these acupoints in different types of neurogenic bladder. Methods: The study was structured with a randomized, two‐phase cross over design with a washout period. A routine urodynamic examination was performed first, then, in the order of grouping, electroacupuncture was performed on CV4, CV3, and SP6, respectively，and urodynamic examination was performed to observe the changes of urodynamic indexes in real time. Results: When undergoing electroacupuncture at CV4, CV3, and SP6 in patients with neurogenic detrusor overactivity (DO), the bladder volume at the first occurrence of DO and maximum cystometric capacity increased (p < 0.05), but maximum detrusor pressure (Pdetmax) at DO decreased (p < 0.05), and the changes using CV4 and CV3 was more significantly than using SP6 (p < 0.05). And in patients with in neurogenic detrusor underactivity, there were no significant changes in maximum urinary flow rate and Pdetmax during urination (p > 0.05). Conclusion: The immediate relief effect of electroacupuncture at CV4, CV3 on DO was greater than at SP6. [ABSTRACT FROM AUTHOR]

Published
2024
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31. Revisiting the diagnostic and prognostic significance of high-frequency QRS analysis in cardiovascular diseases: a comprehensive review.

Author

Qiu, Shifeng, Liu, Tinghui, Zhan, Zijin, Li, Xue, Liu, Xuewei, Xin, Xiaoyu, Lu, Junyan, Wu, Lipei, Wang, Li, Cui, Kai, and Xiu, Jiancheng

Subjects
MYOCARDIAL ischemia, WORLD health, DIAGNOSIS, ELECTROCARDIOGRAPHY, PUBLIC health, CARDIOVASCULAR diseases
Abstract

Cardiovascular diseases (CVDs) present a significant global public health threat, contributing to a substantial number of cases involving morbidity and mortality. Therefore, the early and accurate detection of CVDs plays an indispensable role in enhancing patient outcomes. Decades of extensive research on electrocardiography at high frequencies have yielded a wealth of knowledge regarding alterations in the QRS complex during myocardial ischemia, as well as the methodologies to assess and quantify these changes. In recent years, the analysis of high-frequency QRS (HF-QRS) components has emerged as a promising non-invasive approach for diagnosing various cardiovascular conditions. Alterations in HF-QRS amplitude and morphology have demonstrated remarkable sensitivity as diagnostic indicators for myocardial ischemia, often surpassing measures of ST-T segment changes. This comprehensive review aims to provide an intricate overview of the current advancements, challenges, and prospects associated with HF-QRS analysis in the field of CVDs. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Leadership Reconfiguration in State-Acquired Privately Owned Enterprises: A Paradox between Institutional Control and Agency.

Author

Min, Yijie, Lu, Junyan, Wu, Yunke, and Zhang, Yanlong

Subjects
SENIOR leadership teams, INSTITUTIONAL logic, GOVERNMENT business enterprises, MERGERS & acquisitions, PARADOX
Abstract

Copyright of Management & Organization Review is the property of Cambridge University Press and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2024
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33. Construct prognostic models of multiple myeloma with pathway information incorporated.

Author

Wang, Shuo, Wang, ShanJin, Pan, Wei, Yi, YuYang, and Lu, Junyan

Subjects
MISSING data (Statistics), PROGNOSTIC models, BONE marrow cells, PREDICTION models, MULTIPLE myeloma
Abstract

Multiple myeloma (MM) is a hematological disease exhibiting aberrant clonal expansion of cancerous plasma cells in the bone marrow. The effects of treatments for MM vary between patients, highlighting the importance of developing prognostic models for informed therapeutic decision-making. Most previous models were constructed at the gene level, ignoring the fact that the dysfunction of the pathway is closely associated with disease development and progression. The present study considered two strategies that construct predictive models by taking pathway information into consideration: pathway score method and group lasso using pathway information. The former simply converted gene expression to sample-wise pathway scores for model fitting. We considered three methods for pathway score calculation (ssGSEA, GSVA, and z-scores) and 14 data sources providing pathway information. We implemented these methods in microarray data for MM (GSE136324) and obtained a candidate model with the best prediction performance in interval validation. The candidate model is further compared with the gene-based model and previously published models in two external data. We also investigated the effects of missing values on prediction. The results showed that group lasso incorporating Vax pathway information (Vax(grp)) was more competitive in prediction than the gene model in both internal and external validation. Immune information, including VAX pathways, seemed to be more predictive for MM. Vax(grp) also outperformed the previously published models. Moreover, the new model was more resistant to missing values, and the presence of missing values (<5%) would not evidently deteriorate its prediction accuracy using our missing data imputation method. In a nutshell, pathway-based models (using group lasso) were competitive alternatives to gene-based models for MM. These models were documented in an R package (https://github.com/ShuoStat/MMMs), where a missing data imputation method was also integrated to facilitate future validation. Author summary: Traditionally, prognostic models were mainly constructed at the gene level, ignoring the role of pathway functions in disease development and progression. Enlightened by this, we advocated guiding the model building with well-established prior knowledge (pathway information). We investigated several approaches that could incorporate pathway information in model building. The results showed that pathway-based models exhibit superior predictive capabilities compared to their gene-based counterparts. Furthermore, these pathway-based models were more robust to missing values. The proposed models also outperformed previously published gene-based models. Beyond their prediction performance, the pathway-based models can directly reveal the association between the pathway functions and survival outcomes, demonstrating their advantage in the model interpretability. This enhanced interpretability not only deepens our understanding of disease mechanisms but also facilitates informed decision-making in clinical and research settings. We urge for more attention to be given to developing modeling methods that incorporate prior knowledge. [ABSTRACT FROM AUTHOR]

Published
2024
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34. Changes in Spatiotemporal Pattern and Its Driving Factors of Suburban Forest Defoliating Pest Disasters.

Author

Jiang, Xuefei, Liu, Ting, Ding, Mingming, Zhang, Wei, Zhai, Chang, Lu, Junyan, He, Huaijiang, Luo, Ye, Bao, Guangdao, and Ren, Zhibin

Subjects
LEAF area index, CONIFEROUS forests, REMOTE-sensing images, REMOTE sensing, PINUS koraiensis
Abstract

Forest defoliating pests are significant global forest disturbance agents, posing substantial threats to forest ecosystems. However, previous studies have lacked systematic analyses of the continuous spatiotemporal distribution characteristics over a complete 3–5 year disaster cycle based on remote sensing data. This study focuses on the Dendrolimus superans outbreak in the Changbai Mountain region of northeastern China. Utilizing leaf area index (LAI) data derived from Sentinel-2A satellite images, we analyze the extent and dynamic changes of forest defoliation. We comprehensively examine the spatiotemporal patterns of forest defoliating pest disasters and their development trends across different forest types. Using the geographical detector method, we quantify the main influencing factors and their interactions, revealing the differential impacts of various factors during different growth stages of the pests. The results show that in the early stage of the Dendrolimus superans outbreak, the affected area is extensive but with mild severity, with newly affected areas being 23 times larger than during non-outbreak periods. In the pre-hibernation stage, the affected areas are smaller but more severe, with a cumulative area reaching up to 8213 hectares. The spatial diffusion characteristics of the outbreak follow a sequential pattern across forest types: Larix olgensis, Pinus sylvestris var. mongolica, Picea koraiensis, and Pinus koraiensis. The most significant influencing factor during the pest development phase was the relative humidity of the year preceding the outbreak, with a q-value of 0.27. During the mitigation phase, summer precipitation was the most influential factor, with a q-value of 0.12. The combined effect of humidity and the low temperatures of 2020 had the most significant impact on both the development and mitigation stages of the outbreak. This study's methodology achieves a high-precision quantitative inversion of long-term disaster spatial characteristics, providing new perspectives and tools for real-time monitoring and differentiated control of forest pest infestations. [ABSTRACT FROM AUTHOR]

Published
2024
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35. Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL

Author

Bruch, Peter‐Martin, Giles, Holly AR, Kolb, Carolin, Herbst, Sophie A, Becirovic, Tina, Roider, Tobias, Lu, Junyan, Scheinost, Sebastian, Wagner, Lena, Huellein, Jennifer, Berest, Ivan, Kriegsmann, Mark, Kriegsmann, Katharina, Zgorzelski, Christiane, Dreger, Peter, Zaugg, Judith B, Müller‐Tidow, Carsten, Zenz, Thorsten, Huber, Wolfgang, and Dietrich, Sascha

Published
2022
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38. The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome

Author

Duran-Ferrer, Martí, Clot, Guillem, Nadeu, Ferran, Beekman, Renée, Baumann, Tycho, Nordlund, Jessica, Marincevic-Zuniga, Yanara, Lönnerholm, Gudmar, Rivas-Delgado, Alfredo, Martín, Silvia, Ordoñez, Raquel, Castellano, Giancarlo, Kulis, Marta, Queirós, Ana C., Lee, Seung-Tae, Wiemels, Joseph, Royo, Romina, Puiggrós, Montserrat, Lu, Junyan, Giné, Eva, Beà, Sílvia, Jares, Pedro, Agirre, Xabier, Prosper, Felipe, López-Otín, Carlos, Puente, Xosé S., Oakes, Christopher C., Zenz, Thorsten, Delgado, Julio, López-Guillermo, Armando, Campo, Elías, and Martín-Subero, José Ignacio

Published
2020
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40. Developmental subtypes assessed by DNA methylation-iPLEX forecast the natural history of chronic lymphocytic leukemia

Author

Giacopelli, Brian, Zhao, Qiuhong, Ruppert, Amy S., Agyeman, Akwasi, Weigel, Christoph, Wu, Yue-Zhong, Gerber, Madelyn M., Rabe, Kari G., Larson, Melissa C., Lu, Junyan, Blachly, James S., Rogers, Kerry A., Wierda, William G., Brown, Jennifer R., Rai, Kanti R., Keating, Michael, Rassenti, Laura Z., Kipps, Thomas J., Zenz, Thorsten, Shanafelt, Tait D., Kay, Neil E., Abruzzo, Lynne V., Coombes, Kevin R., Woyach, Jennifer A., Byrd, John C., and Oakes, Christopher C.

Published
2019
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41. Supplementary Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma

Author

Tao, Hongru, primary, Jin, Chen, primary, Zhou, Liyuan, primary, Deng, Zhenzhong, primary, Li, Xiao, primary, Dang, Wenzhen, primary, Fan, Shijie, primary, Li, Bing, primary, Ye, Fei, primary, Lu, Junyan, primary, Kong, Xiangqian, primary, Liu, Chuanpeng, primary, Luo, Cheng, primary, and Zhang, Yuanyuan, primary

Published
2024
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42. Data from PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma

Author

Tao, Hongru, primary, Jin, Chen, primary, Zhou, Liyuan, primary, Deng, Zhenzhong, primary, Li, Xiao, primary, Dang, Wenzhen, primary, Fan, Shijie, primary, Li, Bing, primary, Ye, Fei, primary, Lu, Junyan, primary, Kong, Xiangqian, primary, Liu, Chuanpeng, primary, Luo, Cheng, primary, and Zhang, Yuanyuan, primary

Published
2024
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44. IGLV3-21R110 mutation has prognostic value in patients with treatment-naive chronic lymphocytic leukemia

Author

Syrykh, Charlotte, primary, Pons-Brun, Berta, additional, Russiñol, Núria, additional, Playa-Albinyana, Heribert, additional, Baumann, Tycho, additional, Duran-Ferrer, Martí, additional, Kulis, Marta, additional, Carbó-Meix, Anna, additional, Mozas, Pablo, additional, Alcoceba, Miguel, additional, González, Marcos, additional, Navarro-Bailón, Almudena, additional, Colado, Enrique, additional, Payer, Ángel R., additional, Aymerich, Marta, additional, Terol, María J., additional, Lu, Junyan, additional, Knisbacher, Binyamin A., additional, Hahn, Cynthia K., additional, Ruiz-Gaspà, Sílvia, additional, Enjuanes, Anna, additional, Wu, Catherine J., additional, Getz, Gad, additional, Zenz, Thorsten, additional, López-Guillermo, Armando, additional, Martín-Subero, José I., additional, Colomer, Dolors, additional, Delgado, Julio, additional, Campo, Elías, additional, and Nadeu, Ferran, additional

Published
2023
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47. PRMT1 inhibition activates the interferon pathway to potentiate antitumor immunity and enhance checkpoint blockade efficacy in melanoma

Author

Tao, Hongru, primary, Jin, Chen, additional, Zhou, Liyuan, additional, Deng, Zhenzhong, additional, Li, Xiao, additional, Dang, Wenzhen, additional, Fan, Shijie, additional, Li, Bing, additional, Ye, Fei, additional, Lu, JunYan, additional, Kong, Xiangqian, additional, Liu, Chuanpeng, additional, Luo, Cheng, additional, and Zhang, Yuanyuan, additional

Published
2023
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50. IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms

Author

Nadeu, Ferran, Mas-de-les-Valls, Rut, Navarro, Alba, Royo, Romina, Martín, Silvia, Villamor, Neus, Suárez-Cisneros, Helena, Mares, Rosó, Lu, Junyan, Enjuanes, Anna, Rivas-Delgado, Alfredo, Aymerich, Marta, Baumann, Tycho, Colomer, Dolors, Delgado, Julio, Morin, Ryan D., Zenz, Thorsten, Puente, Xose S., Campbell, Peter J., Beà, Sílvia, Maura, Francesco, and Campo, Elías

Published
2020
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