Metalign: efficient alignment-based metagenomic profiling via containment min hash

by LaPierre, Nathan, Alser, Mohammed, Eskin, Eleazar, Koslicki, David, Mangul, Serghei
Published in Genome Biology

Accounting for isoform expression increases power to identify genetic regulation of gene expression

by LaPierre, Nathan, Pimentel, Harold
Published in PLoS computational biology

Identifying causal variants by fine mapping across multiple studies

by LaPierre, Nathan, Taraszka, Kodi, Huang, Helen, He, Rosemary, Hormozdiari, Farhad, Eskin, Eleazar
Published in PLoS genetics

MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction

by LaPierre, Nathan, Ju, Chelsea J.-T., Zhou, Guangyu, Wang, Wei
Published in Methods (San Diego, Calif.)

De novo Nanopore read quality improvement using deep learning

by LaPierre, Nathan, Egan, Rob, Wang, Wei, Wang, Zhong
Published in BMC bioinformatics

MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples

by LaPierre, Nathan, Mangul, Serghei, Alser, Mohammed, Mandric, Igor, Wu, Nicholas C, Koslicki, David, Eskin, Eleazar
Published in BMC genomics

Robust Mendelian randomization in the presence of residual population stratification, batch effects and horizontal pleiotropy

by Cinelli, Carlos, LaPierre, Nathan, Hill, Brian L, Sankararaman, Sriram, Eskin, Eleazar
Published in Nature communications

Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice

by Khan, Arshad H., Bagley, Jared R., LaPierre, Nathan, Gonzalez-Figueroa, Carlos, Spencer, Tadeo C., Choudhury, Mudra, Xiao, Xinshu, Eskin, Eleazar, Jentsch, James D., Smith, Desmond J.
Published in Cell reports (Cambridge)

Leveraging family data to design Mendelian randomization that is provably robust to population stratification

by LaPierre, Nathan, Fu, Boyang, Turnbull, Steven, Eskin, Eleazar, Sankararaman, Sriram
Published in Genome research

Phenotype Prediction from Metagenomic Data Using Clustering and Assembly with Multiple Instance Learning (CAMIL)

by Rahman, Mohammad Arifur, LaPierre, Nathan, Rangwala, Huzefa
Published in IEEE/ACM transactions on computational biology and bioinformatics

Critical Assessment of Metagenome Interpretation: the second round of challenges

by Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo, Koslicki, David, Lesker, Till Robin, Gurevich, Alexey, Robertson, Gary, Alser, Mohammed, Antipov, Dmitry, Beghini, Francesco, Bertrand, Denis, Brito, Jaqueline J, Brown, C. Titus, Buchmann, Jan, Buluç, Aydin, Chen, Bo, Chikhi, Rayan, Cristian, Alexandru, Dabrowski, Piotr Wojciech, Darling, Aaron E, Egan, Rob, Eskin, Eleazar, Georganas, Evangelos, Goltsman, Eugene, Gray, Melissa A, Hansen, Lars Hestbjerg, Hofmeyr, Steven, Huang, Pingqin, Irber, Luiz, Jia, Huijue, Jørgensen, Tue Sparholt, Kieser, Silas D, Klemetsen, Terje, Kola, Axel, Kolmogorov, Mikhail, Korobeynikov, Anton, Kwan, Jason, LaPierre, Nathan, Lemaitre, Claire, Li, Chenhao, Limasset, Antoine, Malcher-Miranda, Fabio, Mangul, Serghei, Marijon, Pierre, Meleshko, Dmitry, Mende, Daniel R, Milanese, Alessio, Nagarajan, Niranjan, Nissen, Jakob, Nurk, Sergey, Oliker, Leonid, Paoli, Lucas, Peterlongo, Pierre, Piro, Vitor C, Porter, Jacob S, Rasmussen, Simon, Rees, Evan R, Reinert, Knut, Renard, Bernhard, Robertsen, Espen Mikal, Rosen, Gail L, Ruscheweyh, Hans-Joachim, Sarwal, Varuni, Segata, Nicola, Seiler, Enrico, Shi, Lizhen, Sun, Fengzhu, Sunagawa, Shinichi, Sørensen, Søren Johannes, Thomas, Ashleigh, Tong, Chengxuan, Trajkovski, Mirko, Tremblay, Julien, Uritskiy, Gherman, Vicedomini, Riccardo, Wang, Zhengyang, Wang, Ziye, Wang, Zhong, Warren, Andrew, Willassen, Nils Peder, Yelick, Katherine, You, Ronghui, Zeller, Georg, Zhao, Zhengqiao, Zhu, Shanfeng, Zhu, Jie, Garrido-Oter, Ruben, Gastmeier, Petra, Hacquard, Stephane, Häußler, Susanne, Khaledi, Ariane, Maechler, Friederike, Mesny, Fantin, Radutoiu, Simona, Schulze-Lefert, Paul, Smit, Nathiana, Strowig, Till, Bremges, Andreas, Sczyrba, Alexander, McHardy, Alice Carolyn
Published in Nature methods

Predicting Clinical Phenotype Using OTU-Based Metagenome Representation

by LaPierre, Nathan, Rangwala, Huzefa

Evolution of A-Type Macrosegregation in Large Size Steel Ingot After Multistep Forging and Heat Treatment

by Loucif, Abdelhalim, Ben Fredj, Emna, Harris, Nathan, Shahriari, Davood, Jahazi, Mohammad, Lapierre-Boire, Louis-Philippe
Published in Metallurgical and materials transactions. B, Process metallurgy and materials processing science

Whole genome sequencing of human Borrelia burgdorferi isolates reveals linked blocks of accessory genome elements located on plasmids and associated with human dissemination

by Lemieux, Jacob E, Huang, Weihua, Hill, Nathan, Cerar, Tjasa, Freimark, Lisa, Hernandez, Sergio, Luban, Matteo, Maraspin, Vera, Bogovič, Petra, Ogrinc, Katarina, Ruzič-Sabljič, Eva, Lapierre, Pascal, Lasek-Nesselquist, Erica, Singh, Navjot, Iyer, Radha, Liveris, Dionysios, Reed, Kurt D, Leong, John M, Branda, John A, Steere, Allen C, Wormser, Gary P, Strle, Franc, Sabeti, Pardis C, Schwartz, Ira, Strle, Klemen
Published in PLoS pathogens

Levofloxacin to Prevent Bacterial Infection in Patients with Acute Myeloid Leukemia Treated By Azacitidine and Venetoclax: A Study from the Dataml Registry

by Brousse, Xavier, Rasandisona, Nicolas, Leroy, Harmony, Delavigne, Karen, Mottal, Nathan, Tavitian, Suzanne, Leguay, Thibaut, Lapierre, Leopoldine, Delabesse, Eric, Bidet, Audrey, Gauthier, Martin, Lara, Diane, Calmettes, Claire, Sarry, Audrey, Gadaud, Noemie, Branco, Benoit, de Grande, anne-Charlotte, Beranger, Clementine, Recher, Christian, Pigneux, Arnaud, Bertoli, Sarah, Dumas, Pierre-Yves
Published in Blood

Whole genome sequencing of human Borrelia burgdorferi isolates reveals linked blocks of accessory genome elements located on plasmids and associated with human dissemination

by Jacob E Lemieux, Weihua Huang, Nathan Hill, Tjasa Cerar, Lisa Freimark, Sergio Hernandez, Matteo Luban, Vera Maraspin, Petra Bogovič, Katarina Ogrinc, Eva Ruzič-Sabljič, Pascal Lapierre, Erica Lasek-Nesselquist, Navjot Singh, Radha Iyer, Dionysios Liveris, Kurt D Reed, John M Leong, John A Branda, Allen C Steere, Gary P Wormser, Franc Strle, Pardis C Sabeti, Ira Schwartz, Klemen Strle
Published in PLoS pathogens

Atmospheric observations made at Oliktok Point, Alaska, as part of the Profiling at Oliktok Point to Enhance YOPP Experiments (POPEYE) campaign

by de Boer, Gijs, Dexheimer, Darielle, Mei, Fan, Hubbe, John, Longbottom, Casey, Carroll, Peter J, Apple, Monty, Goldberger, Lexie, Oaks, David, Lapierre, Justin, Crume, Michael, Bernard, Nathan, Shupe, Matthew D, Solomon, Amy, Intrieri, Janet, Lawrence, Dale, Doddi, Abhiram, Holdridge, Donna J, Hubbell, Michael, Ivey, Mark D, Schmid, Beat
Published in Earth system science data

Increasing accuracy of lake nutrient predictions in thousands of lakes by leveraging water clarity data

by Wagner, Tyler, Lottig, Noah R., Bartley, Meridith L., Hanks, Ephraim M., Schliep, Erin M., Wikle, Nathan B., King, Katelyn B. S., McCullough, Ian, Stachelek, Joseph, Cheruvelil, Kendra S., Filstrup, Christopher T., Lapierre, Jean Francois, Liu, Boyang, Soranno, Patricia A., Tan, Pang‐Ning, Wang, Qi, Webster, Katherine, Zhou, Jiayu
Published in Limnology and oceanography letters

Using co-creation focus groups to customise a remote multidomain programme designed to increase dementia literacy

by Wittich, Walter, Kröger, Edeltraut, Aubin, Gabrielle, Fadhlaoui, Asma, Anderson, Nicole D, Ben Gaied, Nouha, Itzhak, Inbal, Belleville, Sylvie
Published in BMJ open

Abstract

by Chhina, Tejinder S., Lapierre, Harry, Jackson, Zane S., Teitel, Jerome M., Latter, David A., Gross, Peter L., Abbas, Sherif, Anastakis, Dimitri, Drolet, Pierre, Lacroix, Mélanie, Elliot, Erin M., Lau, Bertrand, Tsui, Ban C. H., Mollison, Heather L., Patel, Rajesh, Negraeff, October, Yang, H., Campbell, David C., Katznelson, Rita, Karkouti, Keyvan, Carroll, Jo, McCluskey, Stuart, Karski, Jacek, Qu, Rong, Song, Dajun, Chung, Frances, Sibbick, Carolyn, Cleave-Hogg, Doreen, Torok-Both, Clint J., Chawla, Rajiv, Goldstein, David H., Tod, Deborah A., Sourovtseva, Elena, Sawyer, Jason, Lukitto, Karolinah, Quader, Keya, Kawatra, Rakhi, Mak, Peter H., Deschamps, Alain, Kanai, Akifumi, Samy, Winnie, Stockton, E., Gowrie-Mohan, S., Ramanayake, P. U., Cunningham, Kirsten, Desai, Sunil, Torok-Both, Clint, Cheverie, Ronald, Côté, Dany, Wijeysundera, Duminda N., Djaiani, George, Yang, Homer, Duke, Peter C., Nathan, Howard, Masters, Roy, Chamchad, Dmitri, Wijeysundera, Duminda, Ivano, Joan, Sullivan, Kristen M., Al-Abdulhadi, Osama A., Hong, Jeong-Yeon, Halpern, Stephen H., Yee, Jennifer A., Goldszmidt, Eric, Kern, Ralph, Macarthur, Alison, Purdie, Niall L., Angle, Pamela J., Lie, Lie Ming, Kronberg, Jean E., Lu, Wei-Yang, Prahbu, Atul, Potyomkina, Zoya, Peirovy, Javad, Chung, Frances F., Kayumov, Leonid, Sinclair, David R., Moller, Henry J., Cheng, Patrick, Kanji, Salmaan, Oxner, Adam D., Buth, Karen J., Denault, A., Carrier, M., Fortier, A., Tardif, J. C., Slinger, Peter, Blaise, Gilbert, Poonwala, Humara, Guay, Joanne, Son, Soochang, Yamashita, Masao, Barbour, Sean J., Vandebeek, Christine A., Montgomery, Carolyne J., Court, Colleen A., Crawford, Mark W., Carter, Clifford, Tang, Cathy, Tan, Juliana M.
Published in Canadian journal of anesthesia