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When General Grant Expelled the Jews. Schocken/Nextbook, 2012 
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Jewish Renaissance and Revival in America, Coedited with Eitan Fishbane. Brandeis University Press/UPNE, 2011.
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New Essays in American Jewish History [Commemorating 60th Anniversary of American Jewish Archives]. Coedited with Pamela S. Nadell and Lance J. Sussman. Ktav/AJA, 2010.
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Jews and the Civil War: A Reader. With Adam Mendelsohn. NYU Press, 2010. 
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A Time to Every Season: Letters to a Young Jew. Basic Books/Perseus, 2008. [Finalist, National Jewish Book Award in Jewish Family Literature, 2008]
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The History of the Jewish People: A Story of Tradition and Change, volume 1, with Jonathan B.Krasner, Behrman House, 2006; volume 2, with Jonathan B. Krasner, Behrman House, 2007 [Textbook for young people; Awarded Distinguished Achievement Award for Excellence in Educational Publishing, Social Studies Textbooks , Grades 6-8. Issued by the Association of Educational Publishers.]
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Three Hundred Fifty Years: An Album of Jewish Memory , co-editor, American Jewish Historical Society & American Jewish Archives, 2005
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Hayahadut BeAmerika, Merkaz Shazar, 2005 [Hebrew translation of American Judaism with new introduction] 
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American Judaism: A History Yale University Press, 2004 [winner, Everett Family Foundation “Jewish Book of the Year” Award, Jewish Book Council; Co-winner of the American Jewish Historical Society’s Saul Viener Prize for the Outstanding Book in American Jewish History, 2003-2004; Winner of the Weinberg Judaic Studies Institute 2005 Prize for Best Book in American Jewish Studies; Selected as a finalist for the 2005 Koret Jewish Book Awards in the History category; Selected by Publishers Weekly as a Best Book of 2004 in the Religion category; Selected by Choice Magazine as an Outstanding Academic Title for 2004.] Translated into Chinese, 2009. 
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America and Zion: Essays and Papers in Memory of Moshe Davis, edited with Eli Lederhendler, Wayne State University Press, 2002
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Jewish Polity and American Civil Society, co-edited with Alan Mittleman and Robert Licht, Rowman & Littlefield, 2002
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Jews and the American Public Square, co-edited with Alan Mittleman and Robert Licht, Rowman & Littlefield, 2002
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Women and American Judaism: Historical Perspectives, edited with Pamela S. Nadell, University Press of New England, 2001
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Religion and State in the American Jewish Experience, with David G. Dalin, University of Notre Dame Press, 1997 [Choice Magazine Outstanding Academic Book of 1998]
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Abba Hillel Silver and American Zionism, co-edited with Mark A. Raider and Ronald W. Zweig, Frank Cass, 1997
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Minority Faiths and the American Protestant Mainstream, edited, University of Illinois Press, 1997
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The Jews of Boston, with Ellen Smith, Combined Jewish Philanthropies/ Northeastern University Press, 1995; 2nd edition, Yale University Press, 2005. 
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Observing America's Jews by Marshall Sklare (edited, with foreword and headnotes) University Press of New England, 1993.
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Yehude Artsot Ha-Berit, edited with Lloyd Gartner, Merkaz Shazar, 1992.
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Ethnic Diversity and Civic Identity: Patterns of Conflict and Cohesion in Cincinnati Since 1820, edited with Henry D. Shapiro, University of Illinois Press, 1992.
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A Double Bond: The Constitutional Documents of American Jewry, edited with Daniel J. Elazar and Rela Geffen Monson, University Press of America, 1992.
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The Jews of Cincinnati, with Nancy H. Klein, Center for the Study of the American Jewish Experience, 1989.
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JPS: The Americanization of Jewish Culture (A history of the Jewish Publication Society 1888-1988) Jewish Publication Society, 1989.
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Yahadut Amerika: American Jewry: An Annotated Bibliography of Publications in Hebrew, with Janet Liss, Hebrew University, 1991.
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American Synagogue History: A Bibliography and State-of-the-Field Survey, with Alexandra S. Korros, Markus Wiener, 1988.
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The American Jewish Experience: A Reader, Holmes & Meier, 1986; 2nd revised edition, 1997. 
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Jews and the Founding of the Republic, (co-editor), Markus Wiener 1985.
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People Walk on Their Heads: Moses Weinberger's Jews and Judaism in New York (translated and edited), Holmes & Meier, 1982.
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Jacksonian Jew: The Two Worlds of Mordecai Noah, Holmes & Meier, 1981 (nominated for the National Jewish Book Award).
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Mordecai Manuel Noah: Jacksonian Politician and American Jewish Communal Leader -- A Biographical Study , Ph.D. Thesis, Yale University, 1979 (available from University Microfilms).
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Jews in New Haven (ed.) Jewish Historical Society of New Haven, 1978.