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2. Author Correction: Transcriptomic profiles and 5-year results from the randomized CLL14 study of venetoclax plus obinutuzumab versus chlorambucil plus obinutuzumab in chronic lymphocytic leukemia

Author

Al-Sawaf, Othman, Zhang, Can, Jin, Hyun Yong, Robrecht, Sandra, Choi, Yoonha, Balasubramanian, Sandhya, Kotak, Alex, Chang, Yi Meng, Fink, Anna Maria, Tausch, Eugen, Schneider, Christof, Ritgen, Matthias, Kreuzer, Karl-Anton, Chyla, Brenda, Paulson, Joseph N., Pallasch, Christian P., Frenzel, Lukas P., Peifer, Martin, Eichhorst, Barbara, Stilgenbauer, Stephan, Jiang, Yanwen, Hallek, Michael, and Fischer, Kirsten

Published
2023
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3. Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours

Author

Nabbi, Arash, Beck, Pengbo, Delaidelli, Alberto, Oldridge, Derek A., Sudhaman, Sumedha, Zhu, Kelsey, Yang, S. Y. Cindy, Mulder, David T., Bruce, Jeffrey P., Paulson, Joseph N., Raman, Pichai, Zhu, Yuankun, Resnick, Adam C., Sorensen, Poul H., Sill, Martin, Brabetz, Sebastian, Lambo, Sander, Malkin, David, Johann, Pascal D., Kool, Marcel, Jones, David T. W., Pfister, Stefan M., Jäger, Natalie, and Pugh, Trevor J.

Published
2023
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4. The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

Author

Ben Guebila, Marouen, Wang, Tian, Lopes-Ramos, Camila M., Fanfani, Viola, Weighill, Des, Burkholz, Rebekka, Schlauch, Daniel, Paulson, Joseph N., Altenbuchinger, Michael, Shutta, Katherine H., Sonawane, Abhijeet R., Lim, James, Calderer, Genis, van IJzendoorn, David G.P., Morgan, Daniel, Marin, Alessandro, Chen, Cho-Yi, Song, Qi, Saha, Enakshi, DeMeo, Dawn L., Padi, Megha, Platig, John, Kuijjer, Marieke L., Glass, Kimberly, and Quackenbush, John

Published
2023
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5. Transcriptomic profiles and 5-year results from the randomized CLL14 study of venetoclax plus obinutuzumab versus chlorambucil plus obinutuzumab in chronic lymphocytic leukemia

Author

Al-Sawaf, Othman, Zhang, Can, Jin, Hyun Yong, Robrecht, Sandra, Choi, Yoonha, Balasubramanian, Sandhya, Kotak, Alex, Chang, Yi Meng, Fink, Anna Maria, Tausch, Eugen, Schneider, Christof, Ritgen, Matthias, Kreuzer, Karl-Anton, Chyla, Brenda, Paulson, Joseph N., Pallasch, Christian P., Frenzel, Lukas P., Peifer, Martin, Eichhorst, Barbara, Stilgenbauer, Stephan, Jiang, Yanwen, Hallek, Michael, and Fischer, Kirsten

Published
2023
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7. Paenibacillus spp infection among infants with postinfectious hydrocephalus in Uganda: an observational case-control study

Author

Morton, Sarah U, Hehnly, Christine, Burgoine, Kathy, Ssentongo, Paddy, Ericson, Jessica E, Kumar, M Senthil, Hagmann, Cornelia, Fronterre, Claudio, Smith, Jasmine, Movassagh, Mercedeh, Streck, Nicholas, Bebell, Lisa M, Bazira, Joel, Kumbakumba, Elias, Bajunirwe, Francis, Mulondo, Ronald, Mbabazi-Kabachelor, Edith, Nsubuga, Brian K, Natukwatsa, Davis, Nalule, Esther, Magombe, Joshua, Erickson, Tim, Ngonzi, Joseph, Ochora, Moses, Olupot-Olupot, Peter, Onen, Justin, Ssenyonga, Peter, Mugamba, John, Warf, Benjamin C, Kulkarni, Abhaya V, Lane, Jessica, Whalen, Andrew J, Zhang, Lijun, Sheldon, Kathryn, Meier, Frederick A, Kiwanuka, Julius, Broach, James R, Paulson, Joseph N, and Schiff, Steven J

Published
2023
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8. A tumor volume and performance status model to predict outcome before treatment in diffuse large B-cell lymphoma

Author

Thieblemont, Catherine, Chartier, Loic, Dührsen, Ulrich, Vitolo, Umberto, Barrington, Sally F., Zaucha, Jan M., Vercellino, Laetitia, Gomes Silva, Maria, Patrocinio-Carvalho, Ines, Decazes, Pierre, Viailly, Pierre-Julien, Tilly, Herve, Berriolo-Riedinger, Alina, Casasnovas, Oliver, Hüttmann, Andreas, Ilyas, Hajira, Mikhaeel, N. George, Dunn, Joel, Cottereau, Anne-Ségolène, Schmitz, Christine, Kostakoglu, Lale, Paulson, Joseph N., Nielsen, Tina, and Meignan, Michael

Published
2022
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9. Cytomegalovirus infections in infants in Uganda: Newborn-mother pairs, neonates with sepsis, and infants with hydrocephalus

Author

Hehnly, Christine, Ssentongo, Paddy, Bebell, Lisa M., Burgoine, Kathy, Bazira, Joel, Fronterre, Claudio, Kumbakumba, Elias, Mulondo, Ronald, Mbabazi-Kabachelor, Edith, Morton, Sarah U., Ngonzi, Joseph, Ochora, Moses, Olupot-Olupot, Peter, Mugamba, John, Onen, Justin, Roberts, Drucilla J., Sheldon, Kathryn, Sinnar, Shamim A., Smith, Jasmine, Ssenyonga, Peter, Kiwanuka, Julius, Paulson, Joseph N., Meier, Frederick A., Ericson, Jessica E., Broach, James R., and Schiff, Steven J.

Published
2022
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10. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

Author

Oyserman, Ben O., Flores, Stalin Sarango, Griffioen, Thom, Pan, Xinya, van der Wijk, Elmar, Pronk, Lotte, Lokhorst, Wouter, Nurfikari, Azkia, Paulson, Joseph N., Movassagh, Mercedeh, Stopnisek, Nejc, Kupczok, Anne, Cordovez, Viviane, Carrión, Víctor J., Ligterink, Wilco, Snoek, Basten L., Medema, Marnix H., and Raaijmakers, Jos M.

Published
2022
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17. Immune activation during Paenibacillus brain infection in African infants with frequent cytomegalovirus co-infection

Author

Isaacs, Albert M., Morton, Sarah U., Movassagh, Mercedeh, Zhang, Qiang, Hehnly, Christine, Zhang, Lijun, Morales, Diego M., Sinnar, Shamim A., Ericson, Jessica E., Mbabazi-Kabachelor, Edith, Ssenyonga, Peter, Onen, Justin, Mulondo, Ronnie, Hornig, Mady, Warf, Benjamin C., Broach, James R., Townsend, R. Reid, Limbrick, David D., Jr., Paulson, Joseph N., and Schiff, Steven J.

Published
2021
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18. Prediction of Benefit From Adjuvant Pertuzumab by 80-Gene Signature in the APHINITY (BIG 4-11) Trial

Author

Krop, Ian E., primary, Mittempergher, Lorenza, additional, Paulson, Joseph N., additional, Andre, Fabrice, additional, Bonnefoi, Herve, additional, Loi, Sherene, additional, Loibl, Sibylle, additional, Gelber, Richard D., additional, Caballero, Carmela, additional, Bhaskaran, Rajith, additional, Dreezen, Christa, additional, Menicucci, Andrea R., additional, Bernards, Rene, additional, van ’t Veer, Laura J., additional, and Piccart, Martine J., additional

Published
2024
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19. Vaginal microbiome topic modeling of laboring Ugandan women with and without fever

Author

Movassagh, Mercedeh, Bebell, Lisa M., Burgoine, Kathy, Hehnly, Christine, Zhang, Lijun, Moran, Kim, Sheldon, Kathryn, Sinnar, Shamim A., Mbabazi-Kabachelor, Edith, Kumbakumba, Elias, Bazira, Joel, Ochora, Moses, Mulondo, Ronnie, Nsubuga, Brian Kaaya, Weeks, Andrew D., Gladstone, Melissa, Olupot-Olupot, Peter, Ngonzi, Joseph, Roberts, Drucilla J., Meier, Frederick A., Irizarry, Rafael A., Broach, James R., Schiff, Steven J., and Paulson, Joseph N.

Published
2021
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20. A reference map of the human binary protein interactome

Author

Luck, Katja, Kim, Dae-Kyum, Lambourne, Luke, Spirohn, Kerstin, Begg, Bridget E., Bian, Wenting, Brignall, Ruth, Cafarelli, Tiziana, Campos-Laborie, Francisco J., Charloteaux, Benoit, Choi, Dongsic, Coté, Atina G., Daley, Meaghan, Deimling, Steven, Desbuleux, Alice, Dricot, Amélie, Gebbia, Marinella, Hardy, Madeleine F., Kishore, Nishka, Knapp, Jennifer J., Kovács, István A., Lemmens, Irma, Mee, Miles W., Mellor, Joseph C., Pollis, Carl, Pons, Carles, Richardson, Aaron D., Schlabach, Sadie, Teeking, Bridget, Yadav, Anupama, Babor, Mariana, Balcha, Dawit, Basha, Omer, Bowman-Colin, Christian, Chin, Suet-Feung, Choi, Soon Gang, Colabella, Claudia, Coppin, Georges, D’Amata, Cassandra, De Ridder, David, De Rouck, Steffi, Duran-Frigola, Miquel, Ennajdaoui, Hanane, Goebels, Florian, Goehring, Liana, Gopal, Anjali, Haddad, Ghazal, Hatchi, Elodie, Helmy, Mohamed, Jacob, Yves, Kassa, Yoseph, Landini, Serena, Li, Roujia, van Lieshout, Natascha, MacWilliams, Andrew, Markey, Dylan, Paulson, Joseph N., Rangarajan, Sudharshan, Rasla, John, Rayhan, Ashyad, Rolland, Thomas, San-Miguel, Adriana, Shen, Yun, Sheykhkarimli, Dayag, Sheynkman, Gloria M., Simonovsky, Eyal, Taşan, Murat, Tejeda, Alexander, Tropepe, Vincent, Twizere, Jean-Claude, Wang, Yang, Weatheritt, Robert J., Weile, Jochen, Xia, Yu, Yang, Xinping, Yeger-Lotem, Esti, Zhong, Quan, Aloy, Patrick, Bader, Gary D., De Las Rivas, Javier, Gaudet, Suzanne, Hao, Tong, Rak, Janusz, Tavernier, Jan, Hill, David E., Vidal, Marc, Roth, Frederick P., and Calderwood, Michael A.

Published
2020
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26. Neonatal Paenibacilliosis: Paenibacillus Infection as a Novel Cause of Sepsis in Term Neonates With High Risk of Sequelae in Uganda

Author

Ericson, Jessica E, primary, Burgoine, Kathy, additional, Kumbakumba, Elias, additional, Ochora, Moses, additional, Hehnly, Christine, additional, Bajunirwe, Francis, additional, Bazira, Joel, additional, Fronterre, Claudio, additional, Hagmann, Cornelia, additional, Kulkarni, Abhaya V, additional, Kumar, M Senthil, additional, Magombe, Joshua, additional, Mbabazi-Kabachelor, Edith, additional, Morton, Sarah U, additional, Movassagh, Mercedeh, additional, Mugamba, John, additional, Mulondo, Ronald, additional, Natukwatsa, Davis, additional, Kaaya, Brian Nsubuga, additional, Olupot-Olupot, Peter, additional, Onen, Justin, additional, Sheldon, Kathryn, additional, Smith, Jasmine, additional, Ssentongo, Paddy, additional, Ssenyonga, Peter, additional, Warf, Benjamin, additional, Wegoye, Emmanuel, additional, Zhang, Lijun, additional, Kiwanuka, Julius, additional, Paulson, Joseph N, additional, Broach, James R, additional, and Schiff, Steven J, additional

Published
2023
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27. Neonatal Paenibacilliosis: Paenibacillus infection as a Novel Cause of Sepsis in Term Neonates with High Risk of Sequelae in Uganda

Author

Ericson, Jessica E, Burgoine, Kathy, Kumbakumba, Elias, Ochora, Moses, Hehnly, Christine, Bajunirwe, Francis, Bazira, Joel, Fronterre, Claudio, Hagmann, Cornelia, Kulkarni, Abhaya V, Kumar, M Senthil, Magombe, Joshua, Mbabazi-Kabachelor, Edith, Morton, Sarah U, Movassagh, Mercedeh, Mugamba, John, Mulondo, Ronald, Natukwatsa, Davis, Nsubuga Kaaya, Brian, Olupot-Olupot, Peter, Onen, Justin, Sheldon, Kathryn, Smith, Jasmine, Ssentongo, Paddy, Ssenyonga, Peter, Warf, Benjamin, Wegoye, Emmanuel, Zhang, Lijun, Kiwanuka, Julius, Paulson, Joseph N, Broach, James R, Schiff, Steven J, Ericson, Jessica E, Burgoine, Kathy, Kumbakumba, Elias, Ochora, Moses, Hehnly, Christine, Bajunirwe, Francis, Bazira, Joel, Fronterre, Claudio, Hagmann, Cornelia, Kulkarni, Abhaya V, Kumar, M Senthil, Magombe, Joshua, Mbabazi-Kabachelor, Edith, Morton, Sarah U, Movassagh, Mercedeh, Mugamba, John, Mulondo, Ronald, Natukwatsa, Davis, Nsubuga Kaaya, Brian, Olupot-Olupot, Peter, Onen, Justin, Sheldon, Kathryn, Smith, Jasmine, Ssentongo, Paddy, Ssenyonga, Peter, Warf, Benjamin, Wegoye, Emmanuel, Zhang, Lijun, Kiwanuka, Julius, Paulson, Joseph N, Broach, James R, and Schiff, Steven J

Abstract

Paenibacillus thiaminolyticus may be an underdiagnosed cause of neonatal sepsis. We prospectively enrolled a cohort of 800 full-term neonates presenting with a clinical diagnosis of sepsis at two Ugandan hospitals. Quantitative polymerase chain reaction specific to P. thiaminolyticus and to the Paenibacillus genus were performed on the blood and cerebrospinal fluid (CSF) of 631 neonates who had both specimen types available. Neonates with Paenibacillus genus or species detected in either specimen type were considered to potentially have paenibacilliosis, (37/631, 6%). We described antenatal, perinatal, and neonatal characteristics, presenting signs, and 12-month developmental outcomes for neonates with paenibacillosis vs. clinical sepsis. Median age at presentation was 3 days (interquartile range 1, 7). Fever (92%), irritability (84%) and clinical signs of seizures (51%) were common. Eleven (30%) had an adverse outcome: 5 (14%) neonates died during the first year of life; 5 of 32 (16%) survivors developed postinfectious hydrocephalus (PIH) and one (3%) additional survivor had neurodevelopmental impairment without hydrocephalus. Paenibacillus species was identified in 6% of neonates with signs of sepsis who presented to two Ugandan referral hospitals; 70% were P. thiaminolyticus. Improved diagnostics for neonatal sepsis are urgently needed. Optimal antibiotic treatment for this infection is unknown but ampicillin and vancomycin will be ineffective in many cases. These results highlight the need to consider local pathogen prevalence and the possibility of unusual pathogens when determining antibiotic choice for neonatal sepsis. [Abstract copyright: © The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.]

Published
2023

28. Paenibacillus spp infection among infants with postinfectious hydrocephalus in Uganda:an observational case-control study

Author

Morton, Sarah U, Hehnly, Christine, Burgoine, Kathy, Ssentongo, Paddy, Ericson, Jessica E, Kumar, M Senthil, Hagmann, Cornelia, Fronterre, Claudio, Smith, Jasmine, Movassagh, Mercedeh, Streck, Nicholas, Bebell, Lisa M, Bazira, Joel, Kumbakumba, Elias, Bajunirwe, Francis, Mulondo, Ronald, Mbabazi-Kabachelor, Edith, Nsubuga, Brian K, Natukwatsa, Davis, Nalule, Esther, Magombe, Joshua, Erickson, Tim, Ngonzi, Joseph, Ochora, Moses, Olupot-Olupot, Peter, Onen, Justin, Ssenyonga, Peter, Mugamba, John, Warf, Benjamin C, Kulkarni, Abhaya V, Lane, Jessica, Whalen, Andrew J, Zhang, Lijun, Sheldon, Kathryn, Meier, Frederick A, Kiwanuka, Julius, Broach, James R, Paulson, Joseph N, Schiff, Steven J, Morton, Sarah U, Hehnly, Christine, Burgoine, Kathy, Ssentongo, Paddy, Ericson, Jessica E, Kumar, M Senthil, Hagmann, Cornelia, Fronterre, Claudio, Smith, Jasmine, Movassagh, Mercedeh, Streck, Nicholas, Bebell, Lisa M, Bazira, Joel, Kumbakumba, Elias, Bajunirwe, Francis, Mulondo, Ronald, Mbabazi-Kabachelor, Edith, Nsubuga, Brian K, Natukwatsa, Davis, Nalule, Esther, Magombe, Joshua, Erickson, Tim, Ngonzi, Joseph, Ochora, Moses, Olupot-Olupot, Peter, Onen, Justin, Ssenyonga, Peter, Mugamba, John, Warf, Benjamin C, Kulkarni, Abhaya V, Lane, Jessica, Whalen, Andrew J, Zhang, Lijun, Sheldon, Kathryn, Meier, Frederick A, Kiwanuka, Julius, Broach, James R, Paulson, Joseph N, and Schiff, Steven J

Abstract

Paenibacillus thiaminolyticus is a cause of postinfectious hydrocephalus among Ugandan infants. To determine whether Paenibacillus spp is a pathogen in neonatal sepsis, meningitis, and postinfectious hydrocephalus, we aimed to complete three separate studies of Ugandan infants. The first study was on peripartum prevalence of Paenibacillus in mother-newborn pairs. The second study assessed Paenibacillus in blood and cerebrospinal fluid (CSF) from neonates with sepsis. The third study assessed Paenibacillus in CSF from infants with hydrocephalus. In this observational study, we recruited mother-newborn pairs with and without maternal fever (mother-newborn cohort), neonates (aged ≤28 days) with sepsis (sepsis cohort), and infants (aged ≤90 days) with hydrocephalus with and without a history of neonatal sepsis and meningitis (hydrocephalus cohort) from three hospitals in Uganda between Jan 13, 2016 and Oct 2, 2019. We collected maternal blood, vaginal swabs, and placental samples and the cord from the mother-newborn pairs, and blood and CSF from neonates and infants. Bacterial content of infant CSF was characterised by 16S rDNA sequencing. We analysed all samples using quantitative PCR (qPCR) targeting either the Paenibacillus genus or Paenibacillus thiaminolyticus spp. We collected cranial ultrasound and computed tomography images in the subset of participants represented in more than one cohort. No Paenibacillus spp were detected in vaginal, maternal blood, placental, or cord blood specimens from the mother-newborn cohort by qPCR. Paenibacillus spp was detected in 6% (37 of 631 neonates) in the sepsis cohort and, of these, 14% (5 of 37 neonates) developed postinfectious hydrocephalus. Paenibacillus was the most enriched bacterial genera in postinfectious hydrocephalus CSF (91 [44%] of 209 patients) from the hydrocephalus cohort, with 16S showing 94% accuracy when validated by qPCR. Imaging showed progression from Paenibacillus spp-related meningitis to postinfectious

Published
2023

29. Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus

Author

Hehnly, Christine, primary, Shi, Aiqin, additional, Ssentongo, Paddy, additional, Zhang, Lijun, additional, Isaacs, Albert, additional, Morton, Sarah U., additional, Streck, Nicholas, additional, Erdmann-Gilmore, Petra, additional, Tolstoy, Igor, additional, Townsend, R. Reid, additional, Limbrick, David D., additional, Paulson, Joseph N., additional, Ericson, Jessica E., additional, Galperin, Michael Y., additional, Schiff, Steven J., additional, and Broach, James R., additional

Published
2022
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30. Neonatal Paenibacilliosis:Paenibacillus thiaminolyticusas a Novel Cause of Neonatal Sepsis with High Risk of Sequelae in Uganda

Author

Ericson, Jessica E., primary, Burgoine, Kathy, additional, Kumbakumba, Elias, additional, Ochora, Moses, additional, Hehnly, Christine, additional, Bajunirwe, Francis, additional, Bazira, Joel, additional, Fronterre, Claudio, additional, Hagmann, Cornelia, additional, Kulkarni, Abhaya V., additional, Kumar, M. Senthil, additional, Magombe, Joshua, additional, Mbabazi-Kabachelor, Edith, additional, Morton, Sarah U., additional, Movassagh, Mercedeh, additional, Mugamba, John, additional, Mulondo, Ronald, additional, Natukwatsa, Davis, additional, Kaaya, Brian Nsubuga, additional, Olupot-Olupot, Peter, additional, Onen, Justin, additional, Sheldon, Kathryn, additional, Smith, Jasmine, additional, Ssentongo, Paddy, additional, Ssenyonga, Peter, additional, Warf, Benjamin, additional, Wegoye, Emmanuel, additional, Zhang, Lijun, additional, Kiwanuka, Julius, additional, Paulson, Joseph N., additional, Broach, James R., additional, and Schiff, Steven J., additional

Published
2022
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31. Transcriptional immunogenomic analysis reveals distinct immunological clusters in pediatric nervous system tumours

Author

Nabbi, Arash, primary, Beck, Pengbo, additional, Delaidelli, Alberto, additional, Oldridge, Derek A., additional, Sudhaman, Sumedha, additional, Zhu, Kelsey, additional, Cindy Yang, S.Y., additional, Mulder, David T., additional, Bruce, Jeffrey P., additional, Paulson, Joseph N., additional, Raman, Pichai, additional, Zhu, Yuankun, additional, Resnick, Adam C., additional, Sorensen, Poul H., additional, Sill, Martin, additional, Brabetz, Sebastian, additional, Lambo, Sander, additional, Malkin, David, additional, Johann, Pascal D., additional, Kool, Marcel, additional, Jones, David T.W., additional, Pfister, Stefan M., additional, Jäger, Natalie, additional, and Pugh, Trevor J., additional

Published
2022
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33. Outcomes by BCL2 and MYC expression and rearrangements in untreated diffuse large B-cell lymphoma (DLBCL) from the POLARIX trial.

Author

Morschhauser, Franck, primary, Jiang, Yanwen, additional, Jardin, Fabrice, additional, Herrera, Alex Francisco, additional, Sehn, Laurie Helen, additional, Herbaux, Charles, additional, Flowers, Christopher, additional, Phillips, Tycel Jovelle, additional, López Guillermo, Armando, additional, Magid Diefenbach, Catherine S., additional, Gregory, Gareth, additional, Kim, Austin Injae, additional, Barbui, Anna Maria, additional, Balasubramanian, Sandhya, additional, Harris, Will, additional, Hirata, Jamie, additional, Paulson, Joseph N., additional, Lee, Calvin, additional, and Lenz, Georg, additional

Published
2022
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34. IMMU-04. Transcriptional analysis reveals distinct microenvironmental subgroups across pediatric nervous system tumors

Author

Nabbi, Arash, primary, Beck, Pengbo, additional, Delaidelli, Alberto, additional, Oldridge, Derek A, additional, Sudhaman, Sumedha, additional, Zhu, Kelsey, additional, Yang, S Y Cindy, additional, Mulder, David T, additional, Bruce, Jeffrey P, additional, Paulson, Joseph N, additional, Raman, Pichai, additional, Zhu, Yuankun, additional, Silll, Martin, additional, Brabetz, Sebastian, additional, Lambo, Sander, additional, Johann, Pascal D, additional, Resnick, Adam C, additional, Sorensen, Poul H, additional, Malkin, David, additional, Kool, Marcel, additional, Jones, David T W, additional, Pfister, Stefan M, additional, Jäger, Natalie, additional, and Pugh, Trevor J, additional

Published
2022
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35. The Network Zoo: a multilingual package for the inference and analysis of biological networks

Author

Guebila, Marouen Ben, primary, Wang, Tian, additional, Lopes-Ramos, Camila M., additional, Fanfani, Viola, additional, Weighill, Deborah, additional, Burkholz, Rebekka, additional, Schlauch, Daniel, additional, Paulson, Joseph N., additional, Altenbuchinger, Michael, additional, Sonawane, Abhijeet, additional, Lim, James, additional, Calderer, Genis, additional, van Ijzendoorn, David, additional, Morgan, Daniel, additional, Marin, Alessandro, additional, Chen, Cho-Yi, additional, Song, Alex, additional, Shutta, Kate, additional, DeMeo, Dawn, additional, Padi, Megha, additional, Platig, John, additional, Kuijjer, Marieke L., additional, Glass, Kimberly, additional, and Quackenbush, John, additional

Published
2022
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36. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, Oyserman, Ben O, Flores, Stalin Sarango, Griffioen, Thom, Pan, Xinya, van der Wijk, Elmar, Pronk, Lotte, Lokhorst, Wouter, Nurfikari, Azkia, Paulson, Joseph N, Movassagh, Mercedeh, Stopnisek, Nejc, Kupczok, Anne, Cordovez, Viviane, Carrión, Víctor J, Ligterink, Wilco, Snoek, Basten L, Medema, Marnix H, Raaijmakers, Jos M, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Oyserman, Ben O, Flores, Stalin Sarango, Griffioen, Thom, Pan, Xinya, van der Wijk, Elmar, Pronk, Lotte, Lokhorst, Wouter, Nurfikari, Azkia, Paulson, Joseph N, Movassagh, Mercedeh, Stopnisek, Nejc, Kupczok, Anne, Cordovez, Viviane, Carrión, Víctor J, Ligterink, Wilco, Snoek, Basten L, Medema, Marnix H, and Raaijmakers, Jos M

Published
2022

37. Cytomegalovirus Infections in Ugandan Infants:Newborn-Mother Pairs, Neonates with Sepsis, and Infants with Hydrocephalus

Author

Hehnly, Christine, Ssentongo, Paddy, Bebell, Lisa M., Burgoine, Kathy, Bazira, Joel, Fronterre, Claudio, Kumbakumba, Elias, Mulondo, Ronald, Mbabazi-Kabachelor, Edith, Morton, Sarah U., Ngonzi, Joseph, Ochora, Moses, Olupot-Olupot, Peter, Onen, Justin, Roberts, Drucilla J., Sheldon, Kathryn, Sinnar, Shamim A., Smith, Jasmine, Ssenyonga, Peter, Paulson, Joseph N., Meier, Frederick A., Ericson, Jessica E., Broach, James R., Schiff, Steven J., Hehnly, Christine, Ssentongo, Paddy, Bebell, Lisa M., Burgoine, Kathy, Bazira, Joel, Fronterre, Claudio, Kumbakumba, Elias, Mulondo, Ronald, Mbabazi-Kabachelor, Edith, Morton, Sarah U., Ngonzi, Joseph, Ochora, Moses, Olupot-Olupot, Peter, Onen, Justin, Roberts, Drucilla J., Sheldon, Kathryn, Sinnar, Shamim A., Smith, Jasmine, Ssenyonga, Peter, Paulson, Joseph N., Meier, Frederick A., Ericson, Jessica E., Broach, James R., and Schiff, Steven J.

Abstract

Objective To estimate the prevalence of cytomegalovirus (CMV) infections in newborn-mother pairs, neonates with sepsis, and infants with hydrocephalus in Uganda. Design and Methods Three populations: (1) newborn-mother pairs, (2) neonates with sepsis, and (3) infants (≤ 3 months) with non-postinfectious (NPIH) or postinfectious (PIH) hydrocephalus, were evaluated for CMV infection at three medical centers in Uganda. Quantitative PCR (qPCR) was used to characterize the prevalence of CMV. Results The overall CMV prevalence in 2498 samples in duplicate across all groups was 9%. In newborn-mother pairs, there was a 3% prevalence of cord blood CMV positivity and 33% prevalence of maternal vaginal shedding. In neonates with clinical sepsis there was a 2% CMV prevalence. Maternal HIV seropositivity (aOR, 25.20; 95% CI, 4.43-134.26; p= 0.0001), residence in Eastern Uganda (aOR, 11.06; 95% CI, 2.30-76.18; p=0.003), maternal age < 25 years (aOR, 4.54; 95% CI, 1.40-19.29; p=0.02), and increasing neonatal age (aOR, 1.08 for each day older; 95% CI, 1.00-1.16; p= 0.05), were associated risk factors for CMV in neonates with clinical sepsis. We found a two-fold higher maternal vaginal shedding in Eastern (45%) vs Western (22%) Uganda during parturition (n=22/49 vs. 11/50, Fisher's exact test, p=0.02). In infants with PIH, the prevalence in blood was 24% and in infants with NPIH it was 20%. CMV was present in the CSF of 13% of infants with PIH compared to 0.5% of infants with NPIH (n=26/205 vs. 1/194, p<0.0001). Conclusion Our findings highlight that congenital and postnatal CMV prevalence is substantial in this African setting and the long-term consequences are uncharacterized.

Published
2022

38. Microbiota that affect risk for shigellosis in children in low-income countries

Author

Lindsay, Brianna, Oundo, Joe, Hossain, M. Anowar, Antonio, Martin, Tamboura, Boubou, Walker, Alan W., Paulson, Joseph N., Parkhill, Julian, Omore, Richard, Faruque, Abu S.G., Das, Suman Kumar, Ikumapayi, Usman N., Adeyemi, Mitchell, Sanogo, Doh, Saha, Debasish, Sow, Samba, Farag, Tamer H., Nasrin, Dilruba, Li, Shan, Panchalingam, Sandra, Levine, Myron M., Kotloff, Karen, Magder, Laurence S., Hungerford, Laura, Sommerfelt, Halvor, Pop, Mihai, Nataro, James P., and Stine, O. Colin

Subjects
Microbiota (Symbiotic organisms) -- Health aspects, Diarrhea -- Health aspects, Gastrointestinal system -- Health aspects, RNA -- Health aspects, Escherichia coli -- Health aspects, Health
Abstract

Diarrheal disease contributes substantially to illness and death in children in low-income countries (1,2). Recent investigations of enteric illness have shown many cases with >1 pathogen identified (3-5). The paradigm [...]

Published
2015
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45. Additional file 4 of Differential richness inference for 16S rRNA marker gene surveys

Author

Kumar, M. Senthil, Slud, Eric V., Hehnly, Christine, Zhang, Lijun, Broach, James, Irizarry, Rafael A., Schiff, Steven J., and Paulson, Joseph N.

Abstract

Additional file 4. Presents a theoretic model for the generation of false species by misclassifying true species in a population survey. Characterizes the influence of false species accumulation on the observed and estimated unobserved richness components underlying standard richness estimators. Related figures and literature references are contained within the note.

Published
2022
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46. Additional file 1 of AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

Author

Skoufos, Giorgos, Almodaresi, Fatemeh, Zakeri, Mohsen, Paulson, Joseph N., Patro, Rob, Hatzigeorgiou, Artemis G., and Vlachos, Ioannis S.

Abstract

Additional file 1: Supplementary figures S1 ��� S11. Figures demonstrating benchmark results between the methods compared throughout the study. AGAMEMNON results using 16 publicly available RNA-Seq tissue samples from the ENCODE consortium.

Published
2022
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47. Additional file 1 of Prognostic mutational subtyping in de novo diffuse large B-cell lymphoma

Author

Kim, Eugene, Jiang, Yanwen, Xu, Tao, Bazeos, Alexandra, Knapp, Andrea, Bolen, Christopher R., Humphrey, Kathryn, Nielsen, Tina G., Penuel, Elicia, and Paulson, Joseph N.

Abstract

Additional file 1: Supplementary Methods and Results. Supplementary Table S1. Baseline disease characteristics of patients in the BEP and ITT study populations in GOYA and CAVALLI. Supplementary Table S2. Confusion matrix for Random Forest training model. Supplementary Table S3. A. CAVALLI ethics committees (EC) and/or institutional review boards (IRB) of participating centers. B. GOYA ethics committees (EC) and/or institutional review boards (IRB) of participating centers. Supplementary Figure S1. NMF-defined clusters in CAVALLI and their association with cell-of-origin. Supplementary Figure S2. Kaplan-Meier curves of PFS for NMF high- and low-risk prognostic groups in GOYA according to (A) treatment and (B) cell-of-origin (activated B-cell-like vs germinal center B-cell-like). Supplementary Figure S3. Kaplan-Meier curve of PFS for the BCL2/EZH2 versus MYD88/CD798 clusters in CAVALLI (de novo NMF clustering). Supplementary Figure S4. Training of a Random Forest model on NMF cluster labels in GOYA onto CAVALLI. (A) Clustering of gene features of predicted GOYA NMF groups onto CAVALLI. (B) Kaplan-Meier curves of PFS for predicted GOYA NMF groups in CAVALLI. Supplementary Figure S5. Kaplan-Meier curves of PFS for GOYA and CAVALLI. Supplementary Figure S6. Differential expression and pathway analysis of NMF highrisk vs low-risk patients in GOYA. (A) Volcano plot of all genes for patients with NMF risk categorization and RNA-Seq data. Limma was used to determine differential expression with no covariate adjustment. Labelled points outside of the red dotted lines indicate genes with a false discovery rate 1. (B) Pathways with false discovery rate

Published
2022
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50. Additional file 1 of Differential richness inference for 16S rRNA marker gene surveys

Author

Kumar, M. Senthil, Slud, Eric V., Hehnly, Christine, Zhang, Lijun, Broach, James, Irizarry, Rafael A., Schiff, Steven J., and Paulson, Joseph N.

Abstract

Additional file 1. Presents the theoretic models for substitution errors introduced during amplification and sequencing, incorporating back mutations. The influence of recovered abundance-dependent accumulation of false sequencing read classifications is characterized. Related figures and literature references are contained within the note.

Published
2022
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